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@Article{Zarsky2022,
Title = {{Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split}},
Author = {J. {\v Z}{\'a}rsk{\'y} and V. {\v Z}{\'a}rsk{\'y} and M. Han{\'a}cek and V. {\v Z}{\'a}rsk{\'y}},
Journal = {Front. Plant Sci.},
Year = {2022},
Abstract = {Cryogenian origin of both Zygnematophyceae (Coleochaete-like ancestors) and zygomycetes might have sense. Somehow, it was also time of transition to sporic lifecycle of terrestrial plants from same Coleochaete-like ancestors},
Doi = {10.3389/fpls.2021.735020},
File = {zarsky2022_cryogenian_origin_embryophyta.pdf}
}
@Article{Sevcikova2015,
Title = {{Updating algal evolutionary relationships through plastid genome sequencing: Did alveolate plastids emerge through endosymbiosis of an ochrophyte?}},
Author = {T. {\v{S}}ev{\v{c}}{\'i}kov{\'a} and A. Hor{\'a}k and V. Klime{\v{s}} and V. Zbr{\'a}nkov{\'a} and E. Demir-Hilton and S. Sudek and J. Jenkins and J. Schmutz and P. Přibyl and J. Fousek and {\v{C}}. Vl{\v{c}}ek and B. F. Lang and M. Oborn{\'i}k and A. Z. Worden and M. Eli{\'a}{\v{s}}},
Journal = {Sci Rep},
Year = {2015},
Pages = {10134},
Volume = {5},
Abstract = {Probably yes},
Doi = {10.1038/srep10134},
File = {shevchikova2015_alveolate_plastids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26017773}
}
@Article{A2016,
Title = {{Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.}},
Author = {J. C. V. A and B. J. Crandall-Stotler and M. L. Hart and D. G. Long and L. L. Forrest},
Journal = {New Phytol.},
Year = {2016},
Number = {4},
Pages = {1734--1746},
Volume = {209},
Abstract = {As stated},
Doi = {10.1111/nph.13716},
File = {villareal2016_merchantiopsida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26505145}
}
@Article{A2015,
Title = {{Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.}},
Author = {J. C. V. A and B. J. Crandall-Stotler and M. L. Hart and D. G. Long and L. L. Forrest},
Journal = {New Phytol.},
Year = {2015},
Abstract = {As stated},
Doi = {10.1111/nph.13716},
File = {villareal2015_marchantiopsida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26505145}
}
@Article{Abbasi2008,
Title = {{Are we degenerate tetraploids? More genomes, new facts}},
Author = {A. A. Abbasi},
Journal = {Biol. Direct},
Year = {2008},
Number = {1},
Pages = {50},
Volume = {3},
Abstract = {Against 2R hypothesis},
Doi = {10.1186/1745-6150-3-50},
File = {ali_abbasi2008.pdf}
}
@Article{Abbott2011,
Title = {{Sequence homogeneity of internal transcribed spacer rDNA in Mikrocytos mackini and detection of Mikrocytos sp. in a new location}},
Author = {C. L. Abbott and S. R. Gilmore and G. Lowe and G. Meyer and S. Bower},
Journal = {Diseases of Aquatic Organisms},
Year = {2011},
Abstract = {Still unclear, BLAST (mine) returned some similarity with Minchinia},
File = {abbott2011_mikrocytos.pdf}
}
@Article{Abedin2008,
Title = {{The Premetazoan Ancestry of Cadherins}},
Author = {M. Abedin and N. King},
Journal = {Science},
Year = {2008},
Number = {5865},
Pages = {946--948},
Volume = {319},
Doi = {10.1126/science.1151084},
File = {abedin2008.pdf}
}
@Article{Abouheif1998,
Title = {{Limitations of Metazoan 18s r{RNA} sequence data: implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the cambrian explosion}},
Author = {E. Abouheif and R. Zardoya and A. Meyer},
Journal = {J. Mol. Evol.},
Year = {1998},
Pages = {394--405},
Volume = {47}
}
@Article{Abzhanov1999,
Title = {{Homeotic genes and the arthropod head: Expression patterns of the labial, proboscipedia, and deformed genes in crustaceans and insects}},
Author = {A. Abzhanov and T. C. Kaufman},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1999},
Number = {18},
Pages = {10224--10229},
Volume = {96}
}
@Article{Achatz2013,
Title = {{The Acoela: On their kind and kinships, especially with nemertodermatids and xenoturbellids (Bilateria incertae sedis).}},
Author = {J. G. Achatz and M. Chiodin and W. Salvenmoser and S. Tyler and P. Martinez},
Journal = {Org. Divers. Evol.},
Year = {2013},
Number = {2},
Pages = {267--286},
Volume = {13},
Abstract = {Basal but divergent},
Doi = {10.1007/s13127-012-0112-4},
File = {achatz2013_acoela.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24098090}
}
@Article{Achatz2012a,
Title = {{The Acoela: On their kind and kinships, especially with nemertodermatids and xenoturbellids (Bilateria incertae sedis)}},
Author = {J. G. Achatz and M. Chiodin and W. Salvenmoser and S. Tyler and P. Martinez},
Journal = {Org Divers Evol},
Year = {2012},
Abstract = {Basal but divergent},
Doi = {10.1007/s13127-012-0112-4},
File = {achatz2012_acoela.pdf},
Url = {http://turbellaria.umaine.}
}
@Article{Achatz2012b,
Title = {{The nervous system of Isodiametra pulchra (Acoela) with a discussion on the neuroanatomy of the Xenacoelomorpha and its evolutionary implications}},
Author = {J. G. Achatz and P. Martinez},
Journal = {Frontiers in Zoology},
Year = {2012},
Pages = {27},
Volume = {9},
Abstract = {Xenacoelomorpha separate},
File = {achatz2012_neural_system_acoela.pdf},
Url = {http://www.frontiersinzoology.com/content/9/1/27}
}
@Article{Acosta2012,
Title = {{Localized synthesis of the outer envelope from Thermus thermophilus.}},
Author = {F. Acosta and L. Alvarez and M. A. de Pedro and J. Berenguer},
Journal = {Extremophiles : life under extreme conditions},
Year = {2012},
Abstract = {Intermediate between G+ and Proteobacteria},
Doi = {10.1007/s00792-011-0427-7},
File = {acosta2012_thermus_cell_envelope.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22212658}
}
@Article{Adl2019,
Title = {{Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes}},
Author = {S. M. Adl and D. Bass and C. E. Lane and J. Lukes and C. L. Schoch and A. Smirnov and S. Agatha and C. Berney and M. W. Brown and F. Burki},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2019},
Abstract = {Notes made separatly, only few groups were somehow little known to me},
Doi = {10.1111/jeu.12691},
File = {adl2018_classif_eukaryotes.pdf}
}
@Article{Adl2007,
Title = {{Diversity, Nomenclature, and Taxonomy of Protists}},
Author = {S. M. Adl and B. S. Leander and A. G. B. Simpson and J. M. Archibald and O. R. Anderson and D. Bass and S. S. Bowser and G. Brugerolle and M. A. Farmer and S. Karpov and M. Kolisko and C. E. Lane and D. J. Lodge and D. G. Mann and R. Meisterfeld and L. Mendoza and J. Moestrup and S. E. Mozley-Standridge and A. V. Smirnov and F. Spiegel},
Journal = {Syst. Biol.},
Year = {2007},
Number = {4},
Pages = {37--41},
Volume = {56},
Abstract = {codes need to be changed},
File = {adl2007.pdf}
}
@Article{Adl2005,
Title = {{The new higher level classification of eukaryotes with emphasis on the taxonomy of protists}},
Author = {S. M. Adl and A. G. B. Simpson and M. A. Farmer and R. A. Andersen and O. R. Anderson and J. R. Barta and S. S. Bowser and G. Brugerolle and R. A. Fensome and S. Fredericq and T. Y. James and S. Karpov and P. Kugrens and J. Krug and C. E. Lane and L. A. Lewis and J. Lodge and D. H. Lynn and D. G. Mann and R. M. Mccourt and L. Mendoza and J. Moestrup and S. E. Mozley-Standridge and T. A. Nerad and C. A. Shearer and A. V. Smirnov and F. W. Spiegel and M. F. J. R. Taylor},
Journal = {J. Euk. Microbiol.},
Year = {2005},
Number = {5},
Pages = {399--451},
Volume = {52},
File = {adl2005.pdf},
Keywords = {pr1}
}
@Article{Adl2012,
Title = {{Erratum}},
Author = {S. M. Adl and A. G. B. Simpson and C. E. Lane and J. Lukes and D. Bass and S. S. Bowser and M. W. Brown and F. Burki and M. Dunthorn and V. Hampl and A. Heiss and M. Hoppenrath and E. Lara and L. le Gall and D. H. Lynn and H. McManus and E. A. D. Mitchell and S. E. MozleyStanridge and L. W. Parfrey and J. Pawlowski and S. Rueckert and L. Shadwick and C. L. Schoch and A. Smirnov and F. W. Spiegel},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2012},
Number = {8},
Pages = {432},
Volume = {4},
Abstract = {Some names and "bullets" ;) corrected},
Doi = {10.1111/j.1550-7408.2012.},
File = {adl2012_revised_classif_euk_erratum.pdf}
}
@Article{Adl2012a,
Title = {{The Revised Classification of Eukaryotes}},
Author = {S. M. Adl and A. G. B. Simpson and C. E. Lane and J. Lukes and D. Bass and S. S. Bowser and M. W. Brown and F. Burki and M. Dunthorn and V. Hampl and A. Heiss and M. Hoppenrath and E. Lara and L. le Gall and D. H. Lynn and H. McManus and E. A. D. Mitchell and S. E. Mozley-Stanridge and L. W. Parfrey and J. Pawlowski and S. Rueckert and L. Shadwick and C. L. Schoch and A. Smirnov and F. W. Spiegel},
Journal = {J. Eukaryot. Microbiol.},
Year = {2012},
Number = {5},
Pages = {429-493},
Volume = {59},
Abstract = {Many names, some interesting groups},
Doi = {10.1111/j.1550-7408.2012.00644.x},
File = {adl2012_revised_classif_euk.pdf}
}
@Article{Afanasjeva2008,
Title = {{Supraordinal Brachiopod Classification}},
Author = {G. A. Afanasjeva},
Journal = {Paleontological Journal},
Year = {2008},
Number = {8},
Pages = {792--802},
Volume = {42},
Abstract = {Review; Inarticulata, Articulata},
Doi = {10.1134/S0031030108080030},
File = {afanasjeva2008_brachiopod_classif.pdf}
}
@Article{Aguinaldo1997,
Title = {{Evidence for a clade of nematodes, athropods and other moulting animals}},
Author = {A. M. A. Aguinaldo and J. M. Turbeville and L. S. Linford and M. C. Rivera and J. R. Garey and R. A. Raff and J. A. Lake},
Journal = {Nature},
Year = {1997},
Pages = {489--493},
Volume = {387}
}
@Article{Ahmad2000,
Title = {{A protein-based phylogenetic tree for Gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene}},
Author = {S. Ahmad and A. Selvapandiyan and R. Bhatnagar},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2000},
Pages = {1387--1394},
Volume = {49}
}
@Article{Aho2003,
Title = {{Pitfalls in Detection of Novel Nanoorganisms}},
Author = {K. Aho and E. O. Kajander},
Journal = {J. Clin. Microbiol.},
Year = {2003},
Number = {7},
Pages = {3460--3461},
Volume = {41},
File = {aho2003.pdf}
}
@Article{Ahrendt2018,
Title = {{Leveraging single-cell genomics to expand the fungal tree of life.}},
Author = {S. R. Ahrendt and C. A. Quandt and D. Ciobanu and A. Clum and A. Salamov and B. Andreopoulos and J.-F. Cheng and T. Woyke and A. Pelin and B. Henrissat and N. K. Reynolds and G. L. Benny and M. E. Smith and T. Y. James and I. V. Grigoriev},
Journal = {Nat Microbiol},
Year = {2018},
Abstract = {Caulochytrium > Chytr.},
Doi = {10.1038/s41564-018-0261-0},
File = {ahrendt2018_single_cell_genomics_fungal_tol_calochytrium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30297742}
}
@Article{Aime2007,
Title = {{An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences}},
Author = {M. C. Aime and P. B. Matheny and D. A. Henk and E. M. Frieders and R. H. Nilsson and M. Piepenbring and D. J. McLaughlin and L. J. Szabo and D. Begerow and J. P. Sampaio and R. Bauer and M. Weiss and F. Oberwinkler and D. Hibbett},
Journal = {Mycologia},
Year = {2007},
Pages = {896--905},
Volume = {98},
Abstract = {Pucciniomycetes, Atractiellomycetes, Cystobasidiomycetes, Agaricostilbomycetes (incl. Mixia sed.m.), Microbotryomycetes (incl. Cryptomycocolacales, Classiculales)}
}
@Article{Akl2018,
Title = {{Genomes of Asgard archaea encode profilins that regulate actin.}},
Author = {C. Akıl and R. C. Robinson},
Journal = {Nature},
Year = {2018},
Number = {7727},
Pages = {439--443},
Volume = {562},
Doi = {10.1038/s41586-018-0548-6},
File = {akil2018_asgard_profilins_actin.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30283132}
}
@Article{Akam2004,
Title = {{The Hox gene complement of acoel flatworms, a basal bilaterian clade}},
Author = {M. Akam and E. Salo and C. E. Cook and E. Jime},
Journal = {Evol. Dev.},
Year = {2004},
Number = {3},
Pages = {154--163},
Volume = {6},
Abstract = {Hox of Cnidaria and Acoela are close},
File = {cook2004.pdf}
}
@Article{Aktipisa2010,
Title = {{A phylogeny of Vetigastropoda and other 'archaeogastropods'': Re-organizing old gastropod clades}},
Author = {S. W. Aktipisa and G. Giribet},
Journal = {Invertebrate Biology},
Year = {2010},
Pages = {1--21},
Abstract = {Vetigastropoda not monoph},
Doi = {10.1111/j.1744-7410.2010.00198.x},
File = {aktipis2010_gastropoda.pdf}
}
@Article{Alauzet2014,
Title = {{Multilocus analysis reveals diversity in the genus Tissierella: Description of Tissierella carlieri sp. Nov. In the new class Tissierellia classis nov.}},
Author = {C. Alauzet and H. Marchandin and P. Courtin and F. Mory and L. Lem{\'e}e and J.-L. Pons and M.-P. Chapot-Chartier and A. Lozniewski and E. Jumas-Bilak},
Journal = {Syst. Appl. Microbiol.},
Year = {2014},
Number = {1},
Pages = {23--34},
Volume = {37},
Abstract = {In Clostridia},
Doi = {10.1016/j.syapm.2013.09.007},
File = {alauzet2014_tissierellia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24268443}
}
@Article{Aleoshin2016,
Title = {{Heterokont Predator Develorapax marinus gen. Et sp. Nov. – A Model of the Ochrophyte Ancestor}},
Author = {V. V. Aleoshin and S. A. Karpov},
Journal = {Frontiers in Microbiology},
Year = {2016},
Doi = {10.3389/fmicb.2016.01194},
File = {aleoshin2016_developea.pdf},
Keywords = {Labyr (and MAST-4,6) || Opal (incl. MAST-3) || MAST-2 || Oo + Hyph || MAST-23 + MAST-1 || "Abyssal" + Developea || Pirsonia etc. || Ochrophyta},
Url = {www.frontiersin.org}
}
@Article{Aleshin2009,
Title = {{On the Phylogenetic Position of Insects in the Pancrustacea Clade}},
Author = {V. V. Aleshin and K. V. Mikhailov and A. V. Konstantinova and M. A. Nikitin and L. Yu. Rusin and D. A. Buinova and O. S. Kedrova and N. B. Petrov},
Journal = {Molecular Biology},
Year = {2009},
Number = {5},
Pages = {804--818},
Volume = {43},
Abstract = {Malac || Maxill || Brachiop || Hexap},
Doi = {10.1134/S0026893309050124},
File = {aleshin2009_pancrustacea.pdf}
}
@Article{Aleshin1998,
Title = {{Phylogeny of Nematoda and Cephalorhyncha derived from 18S rDNA}},
Author = {V. V. Aleshin and I. A. Milyutina and O. S. Kedrova and N. S. Vladychenskaya and N. B. Petrov},
Journal = {J. Mol. Evol.},
Year = {1998},
Pages = {597--605},
Volume = {47}
}
@Article{Alexander2008,
Title = {{Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin}},
Author = {E. Alexander and A. Stock and H. W. Breiner and A. Behnke and J. Bunge and M. M. Yakimov and T. Stoeck},
Journal = {Environ. Microbiol.},
Year = {2009},
Number = {2},
Pages = {360-381},
Volume = {11},
Abstract = {18S: Bicosoecida || Blastocystis + Proteromonas || MAST III; Haptophyta and Cryptophyta ~ Rhodo et al.},
Doi = {10.1111/j.1462-2920.2008.01777.x},
File = {alexander2008.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18826436}
}
@Article{Alie2010,
Title = {{The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans}},
Author = {A. Ali{\'e} and M. Manuel},
Journal = {BMC Evol. Biol.},
Year = {2010},
Pages = {34},
Volume = {10},
Abstract = {As stated},
Doi = {10.1186/1471-2148-10-34},
File = {alie2010_choanofl_postsynapt.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20128896}
}
@Article{Almeida2003,
Title = {{Polychaeta, Annelida, and Articulata are not monophyletic: articulating the Metameria (Metazoa, Coelomata)}},
Author = {W. de Almeida and M. L. Christoffersen and D. de Amorim and A. R. S. Garraffoni and G. S. Silva},
Journal = {Revista Brasileira de Zoologia},
Year = {2003},
Number = {1},
Pages = {23--57},
Volume = {20},
Abstract = {Deuter. and Ecsysozoa originate from Polychaeta},
File = {almeida2004.pdf}
}
@Article{Alonso2007,
Title = {{High local and global diversity of Flavobacteria in marine plankton}},
Author = {C. Alonso and F. Warnecke and R. Amann and J. Pernthaler},
Journal = {Environ. Microbiol.},
Year = {2007},
Number = {5},
Pages = {1253--1266},
Volume = {9},
File = {alonso2007.pdf}
}
@Article{Altenburger2013,
Title = {{Metamorphosis in Craniiformea revisited: Novocrania anomala shows delayed development of the ventral valve}},
Author = {A. Altenburger and A. Wanninger and L. E. Holmer},
Journal = {Zoomorphology},
Year = {2013},
Pages = {1--9},
Abstract = {Craniiformea ~ Rhynchonelliformea and maybe distand from Linguliformea},
Doi = {10.1007/s00435-013-0194-3},
File = {altenburger2013_craniiformea.pdf}
}
@Article{Alvarez2000,
Title = {{Evolution An ancestral MADS-box gene duplication occurred before the divergence of plants and animals}},
Author = {E. R. Alvarez-Buylla and S. Pelaz and S. J. Liljegren and S. E. Gold and C. Burgeff and G. S. Ditta and L. Ribas de Pouplana and L Martinez-Castilla and M. F. Yanofsky},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2000},
Number = {10},
Pages = {5328--5333},
Volume = {97}
}
@Book{Amlinskij1967,
Title = {Some problems of origin of multicellularity},
Author = {I. E. Amlinskij},
Publisher = {Nauka},
Year = {1967},
Address = {Moscow},
Note = {(In Russian)},
Abstract = {evoljucija, Metazoa}
}
@Article{An1998,
Title = {{The Origin and Evolution of Green Algal and Plant Actins}},
Author = {S. S. An and B. Mopps and K. Weber and D. Bhattacharya},
Journal = {Mol. Biol. Evol.},
Year = {1998},
Number = {2},
Pages = {275--285},
Volume = {16}
}
@Article{Anantharaman2016,
Title = {{Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum}},
Author = {K. Anantharaman and C. T. Brown and D. Burstein and C. J. Castelle and A. J. Probst and B. C. Thomas and K. H. Williams and J. F. Banfield},
Journal = {PeerJ},
Year = {2016},
Abstract = {Candidatus Peribacter riflensis, Genus Peribacter, Family
Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum
Peregrinibacteria},
Doi = {10.7717/peerj.1607},
File = {anantharaman2016_peribacteria_peregrinbacteria_cpr.pdf}
}
@InCollection{Andersen2007,
Title = {{Molecular systematics of the Chrysophyceae and Synurophyceae}},
Author = {R. A. Andersen},
Booktitle = {Unravelling the algae: the past, present and future of algae systematics. The Systematic Association special volume series 75},
Publisher = {CRC Press},
Year = {2007},
Address = {London},
Editor = {J. Brodie and J. Lewis},
Pages = {285--314},
Abstract = {Picophag || Eustig || Synur || Chromulin || others; Paraphysom somewhere}
}
@Article{Andersen2004,
Title = {{Biology and systematics of heterokont and haptophyte algae}},
Author = {R. A. Andersen},
Journal = {Amer. J. Bot.},
Year = {2004},
Number = {10},
Pages = {1508--1522},
Volume = {91},
Abstract = {Chryso incl. Synuro, Eust.; Diat incl. Bolido; Phaeo incl. Tetraspotopsis, Giraudyiopsis, Xan, Phaeoth, ?Schizocl ?~ ?Chrysomeridophyceae; Pelago incl. Dictyoch.},
File = {andersen2004.pdf}
}
@Article{Andersen1987,
Title = {{Synurophyceae Classis Nov., A New Class of Algae}},
Author = {R. A. Andersen},
Journal = {Amer. J. Bot.},
Year = {1987},
Pages = {337--353},
Volume = {74}
}
@Article{Andersen2011,
Title = {{The heterokont algal tree of life}},
Author = {R. A. Andersen and M. P. Ashworth and S. M. Boo and R. A. Cattolico and S. G. Draisma and M. L. Julius and H. Kawai and M. Jacobs and R. K. Jansen and T. Nakov and G. Rocap and E. Ruck and E. C. Theriot and E. C. Yang and H. S. Yoon and C. Zhengqiu},
Journal = {Journal of Phycology},
Year = {2011},
Pages = {1},
Volume = {47},
Abstract = {PX clade (Phaeophyceae/Xanthophyceae) includes the Schizocladiophyceae, Phaeothamniophyceae, Arearenophyceae, Chrysomerophyceae and Raphidophyceae. We also recover a large clade that includes the Chrysophyceae/Synurophyceae/Synchromophyceae/Eustigmatophyceae and perhaps the Pinguiophyceae. The relationships between the Bacillariophyceae/Bolidophyceae and Dictyochophyceae/Pelagophyceae are recovered, and there is weak evidence that these four classes form a larger clade},
File = {andersen_psa_abstracts_2011.pdf}
}
@Article{Andersen1999a,
Title = {{Phylogenetic Analysis of the SSU rRNA from Members of the Chrysophyceae}},
Author = {R. A. Andersen and Y. van de Peer and D. Potter and J. P. Sexton and M. Kawachi and T. Lajeunesse},
Journal = {Protist},
Year = {1999},
Number = {1},
Pages = {71--84},
Volume = {150}
}
@Article{Andersen1999,
Title = {{Characterization and phylogenetic position of the enigmatic golden alga \textit{Phaeothamnion confervicola}: ultrastructure, pigment composition and partial SSU rDNA sequence}},
Author = {R. A. Andersen and D. Potter and R. R. Bidigare and M. Latasa and K. Rowan and C. J. O'Kelly},
Journal = {J. Phycol.},
Year = {1999},
Number = {2},
Pages = {286--298},
Volume = {34}
}
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Title = {{Ultrastructure and 18S rRNA gene sequence for \textit{Pelagomonas calceolata} gen. et sp. nov. and the description of a new algal class, the Pelagophyceae classis nov.}},
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Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1993},
Number = {24},
Pages = {11558--11562},
Volume = {90}
}
@Article{Baldauf1996,
Title = {{The root of the universal tree and the origin of eukaryotes based on evolution factor phylogeny}},
Author = {S. L. Baldauf and J. D. Palmer and W. F. Doolittle},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1996},
Pages = {7749--7754},
Volume = {93}
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@Article{Baldauf2000,
Title = {{A kongdom-level phylogeny of Eukaryotes based on combined protein data}},
Author = {S. L. Baldauf and A. J. Roger and I. Wenk-Siefert and W. F. Doolittle},
Journal = {Science},
Year = {2000},
Pages = {972--977},
Volume = {290}
}
@Article{Ball2007,
Title = {{Implications of cnidarian gene expression patterns for the origins of bilaterality~---is the glass half full or half empty?}},
Author = {E. E. Ball and D. M. de Jong and B. Schierwater and C. Shinzato and D. C. Hayward and D. J. Miller},
Journal = {Integr. Comp. Biol.},
Year = {2007},
Number = {5},
Pages = {701--711},
Volume = {47},
Abstract = {cnidarians do not have ancestral bilateral symmetry},
Doi = {10.1093/icb/icm028},
File = {ball2007.pdf}
}
@Article{Ballesteros2019,
Title = {{A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error.}},
Author = {J. A. Ballesteros and P. P. Sharma},
Journal = {Syst. Biol.},
Year = {2019},
Abstract = {In Arachnida},
Doi = {10.1093/sysbio/syz011},
File = {ballesteros2019_xiphosura_in_chelicerata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30917194}
}
@Article{Balsamo2008,
Title = {{Global diversity of gastrotrichs (Gastrotricha) in fresh waters}},
Author = {M. Balsamo and J.-L. Hondt and J. Kisielewski and L. Pierboni},
Journal = {Hydrobiologia},
Year = {2008},
Pages = {85--91},
Volume = {595},
Doi = {10.1007/s10750-007-9006-4},
File = {balsamo2008.pdf}
}
@Article{Bamber2007,
Title = {{A holistic re-interpretation of the phylogeny of the Pycnogonida Latreille, 1810 (Arthropoda)}},
Author = {R. N. Bamber},
Journal = {Zootaxa},
Year = {2007},
Pages = {295--312},
Volume = {1668},
Abstract = {Typical system ("holistic" means "total evidence")},
File = {bamber2007.pdf}
}
@Article{Banfield2021,
Title = {{Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways}},
Author = {V. De Anda J. F. Banfield and L.-X. Chen and N. Dombrowski and Z.-S. H. W.-J. Li and B. J. Baker},
Journal = {Nature Communications},
Year = {2021},
Abstract = {Part of Cenarchaeota m.},
Doi = {10.1038/s41467-021-22736-6},
File = {de_anda_2021_brockarchaeota_cf_aigarchaeota.pdf},
ISSN = {2041-1723}
}
@Article{Bapteste2008b,
Title = {{Lateral gene transfer challenges principles of microbial systematics.}},
Author = {E. Bapteste and Y. Boucher},
Journal = {Trends Microbiol.},
Year = {2008},
Number = {5},
Pages = {200--207},
Volume = {16},
Abstract = {Replace taxa with composite evolutionary units; replace classification with interactive database of overlapping groups},
Doi = {10.1016/j.tim.2008.02.005},
File = {bapteste2008.pdf}
}
@Article{Bapteste2002,
Title = {{The analysis of 100 genes supports the grouping of three highly divergent amoebae: \textit{Dictyostelium}, \textit{Entamoeba}, and \textit{Mastigamoeba}}},
Author = {E. Bapteste and H. Brinkmann and D. V. Moore and C. W. Sensen and P. Gordon and L. Durufle and T. Gaasterland and P. Lopez. and M. Muller and H. Philippe},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2002},
Pages = {1414--1419},
Volume = {99}
}
@Article{Bapteste2009,
Title = {{Prokaryotic evolution and the tree of life are two different things}},
Author = {E. Bapteste and M. A. O'Malley and R. G. Beiko and M. Ereshefsky and J. P. Gogarten and L. Franklin-Hall and F.-J. Lapointe and J. Dupr{\'e} and T. Dagan and Y. Boucher and W. Martin},
Journal = {Biol. Direct},
Year = {2009},
Pages = {34},
Volume = {4},
Abstract = {As stated},
Doi = {10.1186/1745-6150-4-34},
File = {bapteste2009_tol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19788731}
}
@Article{Bapteste2008a,
Title = {{Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny}},
Author = {E. Bapteste and E. Susko and J. Leigh and I. Ruiz-Trillo and J. Bucknam and W. F. Doolittle},
Journal = {Mol. Biol. Evol.},
Year = {2008},
Number = {1},
Pages = {83--91},
Volume = {25},
Abstract = {As stated},
Doi = {10.1093/molbev/msm229},
File = {bapteste2008.pdf}
}
@Article{Barcyte2021,
Title = {{Olisthodiscus represents a new class of Ochrophyta}},
Author = {D. Barcyte and W. Eikrem and A. Engesmo and S. Seoane and J. Wohlmann and A. Hor{\'a}k and T. Yurchenko and M. Eli{\'a}{\v s}},
Journal = {Journal of Phycology},
Year = {2021},
Abstract = {Olisthodiscophyceae (Olisthodiscus luteus) || Pinguiophyceae; and together ~ Chrysophytina},
Doi = {10.1111/jp},
File = {barcyte2021_olisthodiscophyceae_pinguioph.djvu}
}
@Article{Bardunov2009,
Title = {{On the origin of bryophytes}},
Author = {L. V. Bardunov},
Journal = {Botanicheskij Zhurnal},
Year = {2009},
Number = {7},
Pages = {980--989},
Volume = {94},
Abstract = {Hybridization between green abd brown algae},
File = {bardunov2009_proish_mhov.djvu}
}
@Article{Barion2007,
Title = {{The first lines of divergence in the Bacteria domain were the hyperthermophilic organisms, the Thermotogales and the Aquificales, and not the mesophilic Planctomycetales}},
Author = {S. Barion and M. Franchi and E. Gallori and M. Di Giulio},
Journal = {Biosystems},
Year = {2007},
Number = {1},
Pages = {13--19},
Volume = {87},
Abstract = {As stated},
Doi = {10.1016/j.biosystems.2006.02.011},
File = {barion2007.pdf}
}
@Book{Barnes1988,
Title = {{The invertebrates: a new synthesis}},
Author = {R. S. K. Barnes and P. Calow and P. J. W. Olive},
Publisher = {Blackwell Scientific},
Year = {1988},
Address = {Oxford}
}
@Article{Barns2007,
Title = {{Acidobacteria phylum sequences in uranium contaminated subsurface sediments greatly expand the known diversity within the phylum}},
Author = {S. M. Barns and E. C. Cain and L. Sommerville and C. R. Kuske},
Journal = {Appl. Environ. Microbiol.},
Year = {2007},
Number = {9},
Pages = {3113--3116},
Volume = {73},
File = {barns2007.pdf}
}
@Article{Barr1992,
Title = {{Evolution and kingdoms of organisms from the perspective of a mycologist}},
Author = {D. J. S. Barr},
Journal = {Mycologia},
Year = {1992},
Number = {1},
Pages = {1--11},
Volume = {84}
}
@Article{Bart2006,
Title = {{What is \textit{Cryptosporidium}? Reappraising its biology and phylogenetic affinities}},
Author = {J. R. Barta and R. C. A. Thompson},
Journal = {Trends Parasitol.},
Year = {2006},
Number = {10},
Pages = {463--468},
Volume = {22},
Doi = {10.1016/j.pt.2006.08.001},
File = {barta2006.pdf}
}
@Article{Barthelemy2007,
Title = {{Translational machinery of the chaetognath \textit{Spadella cephaloptera}: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression.}},
Author = {R. M. Barthelemy and A. Chenuil and S. Blanquart and J. P. Casanova and E. Faure},
Journal = {BMC Evol. Biol.},
Year = {2007},
Number = {146},
Pages = {146},
Volume = {7},
Abstract = {...do not resolve the chaetognath phylogenetic position...}
}
@Article{BartosovaSojkova2014,
Title = {{Hidden diversity and evolutionary trends in malacosporean parasites (Cnidaria: Myxozoa) identified using molecular phylogenetics.}},
Author = {P. Barto{\v{s}}ov{\'a}-Sojkov{\'a} and M. Hrabcov{\'a} and H. Peckov{\'a} and S. Patra and A. Kod{\'a}dkov{\'a} and P. Jurajda and T. Tyml and A. S. Holzer},
Journal = {Int. J. Parasitol.},
Year = {2014},
Abstract = {One new lineage || Tetarcapsuloides},
Doi = {10.1016/j.ijpara.2014.04.005},
File = {bartosova-sojkova2014_malacosporea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24877770}
}
@InProceedings{Bartolomaeus2009b,
Title = {{The phylogeny of Protostomes}},
Author = {T. Bartolomaeus},
Booktitle = {{Systematics 2009. Leiden, August 11-14. Abstracts}},
Year = {2009},
Abstract = {Gnathifera, Gastr. in Ecdys., Ect + Moll || ([Brach] || Phor + Bryoz) || [Brach] + Anne; body cavities allow rapid growth -> escape from predators},
File = {bartolomaeus2009_protostomes.txt}
}
@Article{Bartolomaeus2005,
Title = {{Morphology, molecules, evolution and phylogeny in polychaeta and related taxa}},
Author = {T. Bartolomaeus and G. Purschke},
Journal = {Hydrobiologia},
Year = {2005},
Pages = {341--356},
Volume = {536},
Abstract = {Sibolginidae is a family inside Sabellida; Clitellata maybe sister},
File = {bartolomaeus2005.pdf}
}
@Article{Bartolomaeus2009,
Title = {{Nephridial development and body cavity formation in Artemia salina (Crustacea: Branchiopoda): No evidence for any transitory coelom}},
Author = {T. Bartolomaeus and B. Quast and M. Koch},
Journal = {Zoomorphology},
Year = {In press},
Abstract = {Our observations overall do not provide any support for the homology of coelomic cavities in annelids and arthropods},
Doi = {10.1007/s00435-008-0082-4},
File = {bartolomaeus2009_arthropod_coelom_ecdysozoa.pdf}
}
@Article{Barucca2006,
Title = {{All the three paraHox genes are present in \textit{Nuttallochiton mirandus} (Mollusca: Polyplacophora): evolutionary considerations}},
Author = {M. Barucca and M. A. Biscotti and E. Olmo and A. Canapa},
Journal = {J. Exp. Zool.},
Year = {2006},
Number = {2006},
Pages = {164--167},
Volume = {306B},
Abstract = {Sipunculida || Polyplacoph || Conchifera (Biv+Gastr+Ceph+Scaph)},
File = {barucca2006.pdf}
}
@Article{Bass2004,
Title = {{Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa)}},
Author = {D. Bass and T. Cavalier-Smith},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2004},
Pages = {63229--63220},
Volume = {54},
Abstract = {Metopion ~ root of Cercomonadida (incl. filose amoebae), Metromonas ~ Chlorarachn},
Doi = {10.1099/ijs.0.63229-0},
File = {bass2004.pdf}
}
@Article{Bass2009,
Title = {{Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised}},
Author = {D. Bass and E. E.-Y. Chao and S. Nikolaev and A. Yabuki and K.-i. Ishida and C. Berney and U. Pakzad and C. Wylezich and T. Cavalier-Smith},
Journal = {Protist},
Year = {2009},
Pages = {75--109},
Volume = {160},
Abstract = {Major revision. Proteomyxidea divided by filose Granofilosa (with desmoth. sequences, with "Gymnophrys cometa" -> Limnofila borokensis, w/o Leucodict./Reticuloam. sequences) and paraphyletic Proteomyxidea s.str. in Endomyxa (only Arachnula and new genera sequenced); Corallomyxa and Stereomyxa ~? Amoebozoa; "Arachnula" from Tekle et al. (2008) is a new species ~ Acramoeba; "Biomyxa" from Tekle et al. is also some leptomyxid Amoebozoa},
Doi = {10.1016/j.protis.2008.07.002},
File = {bass2008.pdf}
}
@Article{Bass2018a,
Title = {{Clarifying the Relationships between Microsporidia and Cryptomycota.}},
Author = {D. Bass and L. Czech and B. A. P. Williams and C. Berney and M. Dunthorn and F. Mah{\'e} and G. Torruella and G. D. Stentiford and T. A. Williams},
Journal = {J. Eukaryot. Microbiol.},
Year = {2018},
Abstract = {Expanded Microsporidia include Paramicrosporidium, Nucleophaga, Mitosporidium and multiple env samples; || Basal Marine Group || Rosellida || NCLC1 || Aphelidea},
Doi = {10.1111/jeu.12519},
File = {bass2018_microsporidia_cryptomycota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29603494}
}
@Article{Bass2009b,
Title = {{Phylogeny and Classification of Cercomonadida (Protozoa, Cercozoa): Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov.}},
Author = {D. Bass and A. T. Howe and A. P. Mylnikov and K. Vickerman and E. E. Chao and J. E. Smallbone and J. Snell and C. Cabral Jr and T. Cavalier-Smith},
Journal = {Protist},
Year = {In press},
Abstract = {As stated},
Doi = {10.1016/j.protis.2009.01.004},
File = {bass2009_cercomonadida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19589724}
}
@Article{Bass2005,
Title = {{Polyubiquitin Insertions and the Phylogeny of Cercozoa and Rhizaria}},
Author = {D. Bass and D. Moreira and P. Lopez-Garcia and S. Polet and E. E. Chao and S. von der Heyden and J. Pawlowski and T. Cavalier-Smith},
Journal = {Protist},
Year = {2005},
Pages = {149--161},
Volume = {156},
Abstract = {Imbricatea (Euglyphida, Spongomonadida, Thaumatomonadida); Thecofilosea (Cryomonadida, Phaeodarea); Sarcomonadea* (Metopion); Proteomyxidea (Desmothoracida, Dimorphida, Gymnophrys, Massisteria); Chlorarachmea (Metromonas, Sainouron sed.m.); Endomyxa: Phytomyxea, Ascetosporea, Grommidea, Foraminifera},
File = {bass2005.pdf}
}
@Article{Bass2018,
Title = {{Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. Gen.}},
Author = {D. Bass and D. V. Tikhonenkov and R. Foster and P. Dyal and J. Janouskovec and P. J. Keeling and M. Gardner and S. Neuhauser and H. Hartikainen and A. P. Mylnikov and C. Berney},
Journal = {J. Eukaryot. Microbiol.},
Year = {2018},
Abstract = {NC10 (incl. Aquavolon) + Tremulida || Proteomyxidea and other Endomyxa; Metromon inc. Metopion || Granofilosea || Cercomonadida || Panso + Glisso || (Ventrifilosea)},
Doi = {10.1111/jeu.12524},
File = {bass2018_rhizaria_aquavolon.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29658156}
}
@Article{Bass2012,
Title = {{Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases}},
Author = {D. Bass and A. Yabuki and S. Santini and S. Romac and C. Berney},
Journal = {PLOS One},
Year = {2012},
Number = {12},
Pages = {e49090},
Volume = {7},
Abstract = {As stated},
Doi = {10.1371/journal.pone.0049090},
File = {bass2012_reticulamoeba.pdf},
Url = {www.nerc.ac.uk)}
}
@Article{Bastin2019,
Title = {{Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity.}},
Author = {B. R. Bastin and S. Q. Schneider},
Journal = {BMC Evol. Biol.},
Year = {2019},
Number = {1},
Pages = {40},
Volume = {19},
Abstract = {Ctenophora / Porifera both basal},
Doi = {10.1186/s12862-019-1360-0},
File = {bastin2019_tektins_metazoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30704394}
}
@Article{Bateman1998,
Title = {{Early Evolution of Land Plants: Phylogeny, Physiology, and Ecology of the Primary Terrestrial Radiation}},
Author = {R. M. Bateman and P. R. Crane and W. A. Dimichele and P. R. Kenrick and N. P. Rowe and T. Speck and W. E. Stein},
Journal = {Annu. Rev. Ecol. Evol. Syst.},
Year = {1998},
Pages = {263--292},
Volume = {29}
}
@Article{Battistuzzi2004,
Title = {{A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis,phototrophy,and the colonization of land}},
Author = {F. U. Battistuzzi and A. Feijao and S. B. Hedges},
Journal = {BMC Evol. Biol.},
Year = {2004},
Number = {44},
Pages = {44},
Volume = {4}
}
@Article{Battistuzzi2008,
Title = {{A major clade of prokaryotes with ancient adaptations to life on land}},
Author = {F. U. Battistuzzi and S. B. Hedges},
Journal = {Mol. Biol. Evol.},
Year = {2009},
Number = {2},
Pages = {335--343},
Volume = {26},
Abstract = {Thermot || Aquif || Fusobacteria || Terrabacteria (Dein + Actino || Cyano + Chlolrofl || Clostr || Bacilli || Mollic) + Hydrobacteria (Spiro +? Plancto || Chlam + Bacteroid + Chlorob || e-prot || Solibacteres (> Acido: GenBank)+ d-prot || a-prot || g + b)},
Doi = {10.1093/molbev/msn247},
File = {battistuzzi2008.pdf}
}
@Article{Bauer2004,
Title = {{Archaea-Like Genes for C1-Transfer Enzymes in Planctomycetes: Phylogenetic Implications of Their Unexpected Presence in This Phylum}},
Author = {M. Bauer and T. Lombardot and H. Teeling and N. L. Ward and R. I. Amann and F. O. Gloeckner},
Journal = {J. Mol. Evol.},
Year = {2004},
Pages = {571--586},
Volume = {59},
File = {bauer2005.pdf}
}
@Article{Bauer2006,
Title = {{The simple-septate basidiomycetes: a synopsis}},
Author = {R. Bauer and D. Begerow and J. P. Sampaio and M. Weiss and F. Oberwinkler},
Journal = {Mycol Progress},
Year = {2006},
Pages = {41--66},
Volume = {5},
Abstract = {Mixia is unique},
File = {bauer2006.pdf}
}
@Article{Bauer2015,
Title = {{Entorrhizomycota: A New Fungal Phylum Reveals New Perspectives on the Evolution of Fungi.}},
Author = {R. Bauer and S. Garnica and F. Oberwinkler and K. Riess and M. Wei{\ss} and D. Begerow},
Journal = {PLoS ONE},
Year = {2015},
Number = {7},
Pages = {e0128183},
Volume = {10},
Abstract = {As stated.},
Doi = {10.1371/journal.pone.0128183},
File = {bauer2015_entorrhizomycota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10742046}
}
@Article{Baurain2010,
Title = {{Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes and stramenopiles}},
Author = {D. Baurain and H. Brinkmann and J.-r. Petersen and N. Rodr-guez-Ezpeleta and A. Stechmann and V. Demoulin and A. J. Roger and G. Burger and B. F. Lang and H. Philippe},
Journal = {Molecular Biology and Evolution},
Year = {2010},
Abstract = {As stated, > 100 proteins: Glauc || (Rhod || Crypt || Virid) + (Hapt || Stra || Alv)},
File = {baurian2010_chromalv.pdf}
}
@Article{Bazylinski2012,
Title = {{Magnetococcus marinus gen. Nov., Sp. Nov., A marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. Nov.; Magnetococcales ord. Nov.) At the base of the Alphaproteobacteria.}},
Author = {D. A. Bazylinski and T. J. Williams and C. T. Lef{\`e}vre and R. J. Berg and C. L. Zhang and S. S. Bowser and A. J. Dean and T. J. Beveridge},
Journal = {International journal of systematic and evolutionary microbiology},
Year = {2012},
Abstract = {zeta + (gamma + beta) || magnetococcus + other alpha},
Doi = {10.1099/ijs.0.038927-0},
File = {bazylinski2012_magnetococcales_alphaproteo.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22581902}
}
@Article{Beakes2011,
Title = {{The evolutionary phylogeny of the oomycete ???fungi???}},
Author = {G. W. Beakes and S. L. Glockling and S. Sekimoto},
Year = {2011},
Abstract = {Review},
Doi = {10.1007/s00709-011-0269-2},
File = {beakes2011_oomycetes.pdf}
}
@Article{Beam2015,
Title = {{Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.}},
Author = {J. P. Beam and Z. J. Jay and M. C. Schmid and D. B. Rusch and M. F. Romine and R. de M. Jennings and M. A. Kozubal and S. G. Tringe and M. Wagner and W. P. Inskeep},
Journal = {ISME J},
Year = {2015},
Abstract = {Calditenius: as stated},
Doi = {10.1038/ismej.2015.83},
File = {beam2015_aigarchaeota_ecol_calditenius.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26140529}
}
@Article{Becerra2007,
Title = {{The Very Early Stages of Biological Evolution and the Nature of the Last Common Ancestor of the Three Major Cell Domains}},
Author = {A. Becerra and L. Delaye and S. Islas and A. Lazcano},
Journal = {Annu. Rev. Ecol. Evol. Syst.},
Year = {2007},
Pages = {361--379},
Volume = {38},
Abstract = {RNA -> RNA+proteins -> DNA added -> Bact (Arch + Euk)},
File = {becerra2007.pdf}
}
@Article{Becker2000,
Title = {{MADS-Box Gene Diversity in Seed Plants 300 Million Years Ago}},
Author = {A. Becker and Kai-U. Winter and B. Meyer and H. Saedler and G. Theissen},
Journal = {Mol. Biol. Evol.},
Year = {2000},
Number = {10},
Pages = {1425--1434},
Volume = {17}
}
@Article{Becker2008,
Title = {{Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes}},
Author = {B. Becker and K. Hoef-Emden and M. Melkonian},
Journal = {BMC Evol. Biol.},
Year = {2008},
Number = {1},
Pages = {203},
Volume = {8},
Abstract = {Lots of LGT from chlamydial endosymbionts},
Doi = {10.1186/1471-2148-8-203},
File = {becker2008.pdf}
}
@Article{Becker2009,
Title = {{Streptophyte algae and the origin of embryophytes}},
Author = {B. Becker and B. Marin},
Journal = {Annals of Botany},
Year = {In press},
Abstract = {Review},
Doi = {10.1093/aob/mcp044,},
File = {becker2009_streptophytes.pdf},
Url = {www.aob.oxfordjournals.org}
}
@Article{Beckers2019,
Title = {{The central nervous system of Oweniidae (Annelida) and its implications for the structure of the ancestral annelid brain.}},
Author = {P. Beckers and C. Helm and G. Purschke and K. Worsaae and P. Hutchings and T. Bartolomaeus},
Journal = {Front. Zool.},
Year = {2019},
Pages = {6},
Volume = {16},
Abstract = {Basal brain, Sipunculida more advanced},
Doi = {10.1186/s12983-019-0305-1},
File = {beckers2019_oweniidae_nerv_syst.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30911320}
}
@Article{Beckers2013,
Title = {{The Nervous Systems of Basally Branching Nemertea (Palaeonemertea)}},
Author = {P. Beckers and R. Loesel and T. Bartolomaeus},
Journal = {PLOS One},
Year = {2013},
Number = {6},
Pages = {e66137},
Volume = {8},
Abstract = {~ basal mollusks and annelids},
Doi = {10.1371/journal.pone.0066137.g001},
File = {beckers2013_palaeonemertea_neural_system.djvu},
Url = {www.plosone.org}
}
@Article{Beckert1999,
Title = {{A molecular phylogeny of bryophytes based on nucleotide sequences of the mitochondrial nad5 gene}},
Author = {S. Beckert and S. Steinhauser and H. Muhle and V. Knoop},
Journal = {Pl. Syst. Evol.},
Year = {1999},
Pages = {179--192},
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Abstract = {Variosea || Archamoebae \& Myxogastrea; Variosea: Multicilia, Phalansterium and some amoebae || cavosteliids || protosteliids || A \& M},
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Title = {{The nop-1 gene of \textit{Neurospora crassa} encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins}},
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Title = {{Recent progress in reconstructing lophotrochozoan (spiralian) phylogeny}},
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Year = {2019},
Abstract = {(Gnathost || Cheatogn || Microgn + Rotifera), Dicyemida, (Cyclioph ?, Tetraneuralia: Entoprocta, Mollusca), ((Gastrotr ?| Brach || Bryoz + Phoron) | (Annel | Parenchymia: Nemert + Plathelm))},
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@Article{Bleidorn2007,
Title = {{Mitochondrial genome and nuclear sequence data support Myzostomida as part of the annelid radiation.}},
Author = {C. Bleidorn and I. Eeckhaut and L. Podsiadlowski and N. Schult and D. McHugh and K. M. Halanych and M. C. Milinkovitch and R. Tiedemann},
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Abstract = {|| Polycheata, sometimes inside Polychaeta, sometimes outside Annelida},
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Title = {{A PCR survey of Hox genes in the myzostomid Myzostoma cirriferum}},
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Year = {2009},
Number = {4},
Pages = {211--216},
Volume = {219},
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Title = {{On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?}},
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Year = {2020},
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Volume = {19}
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Volume = {32},
Abstract = {Homoscleromorpha sep. from Demospongiae s.str.},
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@Article{Borchiellini2001,
Title = {{Sponge paraphyly and the origin of the Metazoa}},
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Title = {{Myoanatomy of Barentsia discreta (Busk, 1886) (Kamptozoa: Coloniales)}},
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Year = {2012},
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@Article{Borner2014,
Title = {{A transcriptome approach to ecdysozoan phylogeny.}},
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Pages = {79--87},
Volume = {80},
Abstract = {clade of Tardigrada and Nematoda sister to Arhtr (inc. Onychophora)},
Doi = {10.1016/j.ympev.2014.08.001},
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@Article{Borowiec2015,
Title = {{Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa.}},
Author = {M. L. Borowiec and E. K. Lee and J. C. Chiu and D. C. Plachetzki},
Journal = {BMC Genomics},
Year = {2015},
Number = {1},
Pages = {987},
Volume = {16},
Abstract = {As stated; then sponges, Trichoplax, Cnidaria, Bilateria},
Doi = {10.1186/s12864-015-2146-4},
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Title = {{\textit{Thermobaculum terrenum} gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia.}},
Author = {L. M. Botero and K. B. Brown and S. Brumefield and M. Burr and R. W. Castenholz and M. Young and T. R. McDermott},
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Year = {2004},
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@Article{Botting2003,
Title = {{Cyathophycus and the origin of demosponges}},
Author = {J. P. Botting},
Journal = {Lethaia},
Year = {2003},
Pages = {335--344},
Volume = {36},
Abstract = {Morphology: Demospongea polyphyletic: Tetractinomorpha close to Homosclero or directly to Calcarea, part to Hexactinell},
Doi = {10.1080/00241160310006385},
File = {botting2007.pdf}
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@Article{Botting2004,
Title = {{Reconstructing early sponge relationships by using the Burgess Shale fossil Eiffelia globosa, Walcott}},
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Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2004},
Number = {5},
Pages = {1554--1559},
Volume = {102},
Abstract = {Hexa+Demo || Calc+Eumetaz},
File = {botting2005.pdf}
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Title = {{Revisiting the concept of lineage in prokaryotes: A phylogenetic perspective}},
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Year = {2009},
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@Article{Bourlat2006,
Title = {{Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida}},
Author = {S. J. Bourlat and T. Juliusdottir and C. J. Lowe and R. Freeman and J. Aronowicz and M. Kirschner and E. S. Lander and M. Thorndyke and H. Nakano and A. B. Kohn and A. Heyland and L. L. Moroz and R. R. Copley and M. J. Telford},
Journal = {Nature},
Year = {2006},
Pages = {1--4},
Volume = {444},
Abstract = {Xenoturbellida || Echi+Hemi; Uro and Cephalo do not resolve completely},
File = {bourlat2006.pdf}
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@Article{Bourlat2008,
Title = {{Testing the new animal phylogeny: A phylum level molecular analysis of the animal kingdom}},
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Journal = {Mol. Phyl. Evol.},
Year = {2008},
Pages = {23--31},
Volume = {49},
Abstract = {Concatenated data: Sipunc || Ech. + other Annel.; Nematoidea ||? Priap ||? Chelic || Myri || Crust || Hexap; Phoron in Ceph + Polypl group; Bryoz (?), Brach. + Nemert. (in Dunn et al., 2008 also!) in Bival + Gastr group; Anth || Hydr || Uroch || others; Xeno + Ambulacralia},
Doi = {10.1016/j.ympev.2008.07.008},
File = {bourlat2008.pdf}
}
@Article{Bourlat2003,
Title = {{\textit{Xenoturbella} is a deuterostome that eats molluscs}},
Author = {S. J. Bourlat and C. Nielsen and A. E. Lockyer and D. T. J. Littlewood and M. J. Telford},
Journal = {Nature},
Year = {2003},
Pages = {925--928},
Volume = {424},
Abstract = {Xenoturbella || Echin. + Hemich.},
File = {bourlat2003.pdf}
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@Article{Bourlat2009,
Title = {{The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes}},
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Journal = {BMC Evol Biol},
Year = {2009},
Number = {1},
Pages = {107},
Volume = {9},
Abstract = {Sometimes basal, sometimes not resolved},
Doi = {10.1186/1471-2148-9-107},
File = {bourlat2009_xenoturbella_mt.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19450249}
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@Article{BouryEsnault2002,
Title = {{Systematics and evolution of Demospongiae}},
Author = {N. Boury-Esnault},
Journal = {Can. J. Zool.},
Year = {2002},
Number = {2006},
Pages = {205--224},
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Abstract = {Homo + Calci + Demosp. s.str.},
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@Article{Boussau2008b,
Title = {{Parallel adaptations to high temperatures in the Archaean eon}},
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Journal = {Nature},
Year = {2008},
Number = {7224},
Pages = {942 - 945},
Volume = {456},
Abstract = {Aquifex || Thermotoga || Dein-Therm || others; Nanoar || others},
Doi = {10.1038/nature07393},
File = {boussau2008.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19037246}
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Doi = {10.1186/1471-2148-8-272},
File = {boussau2008.pdf}
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Title = {{Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes, and Chytridiomycetes}},
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Title = {{A comparative functional analysis of the major maxillopodan groups}},
Author = {G. A. Boxshall},
Booktitle = {{Crustacean phylogeny}},
Publisher = {A.A.Balkema},
Year = {1983},
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@Article{Boxshall2007,
Title = {{Crustacean classification: on-going controversies and unresolved problems}},
Author = {G. A. Boxshall},
Journal = {Zootaxa},
Year = {2007},
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File = {boxshall2007.pdf}
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@Article{Boxshall2010,
Title = {{A critique of biramous interpretations of the crustacean antennule}},
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Year = {2010},
Number = {2},
Pages = {153--167},
Volume = {83},
Abstract = {As stated},
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@Article{Brate2010,
Title = {{Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations}},
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Year = {2010},
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Volume = {10},
Abstract = {As stated},
Doi = {10.1186/1471-2180-10-168},
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Url = {http://www.ncbi.nlm.nih.gov/pubmed/20534135}
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Journal = {Molecular Phylogenetics and Evolution},
Year = {2010},
Abstract = {Onych || Arthr},
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@Article{Bradley1996,
Title = {{Diversity of free-living ``naked'' ameboid organisms}},
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@Article{Braukmann2009,
Title = {{Loss of all plastid ndh genes in Gnetales and conifers: Extent and evolutionary significance for the seed plant phylogeny}},
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@Article{Braun2018,
Title = {{Morphology and evolution of the central nervous system in adult tunicates}},
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@Article{Brawley2017,
Title = {{Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).}},
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Journal = {Proceedings of the National Academy of Sciences of the United States of America},
Year = {2017},
Number = {31},
Pages = {E6361 - E6370},
Volume = {114},
Abstract = {As stated},
Doi = {10.1073/pnas.1703088114},
File = {brawley2017_porphyra_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28360233}
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Title = {{Interesting, Provocative, and Enigmatic: Morphological Observations on Southeastern Quillworts (Isoetes Isoetaceae, Lycopodiophyta)}},
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Journal = {Castanea},
Year = {2018},
Number = {2},
Pages = {263--269},
Volume = {83},
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File = {bray2018_isoetes_morphology.pdf},
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Title = {{Ultrastructure and molecular phylogenetic position of a novel euglenozoan with extrusive episymbiotic bacteria: Bihospites bacati n. Gen. Et sp. (Symbiontida)}},
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Journal = {BMC microbiology},
Year = {2010},
Number = {1},
Pages = {145},
Volume = {10},
Abstract = {phagotrophic euglenids -> Symbiontida},
Doi = {10.1186/1471-2180-10-145},
File = {bregila2010_bihospites_symbiontida.djvu},
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Title = {{The Search Finds an End: Colpodidiids Belong to the Class Nassophorea (Ciliophora)}},
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Year = {2008},
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Pages = {100--102},
Volume = {55},
Abstract = {Karyorelictea, Heterotrichea || (Spirotrichea || Amorphea + Litostomatea) || (Phyllopharyngea || Nassophorea || Colpodea || Oligohymenophorea || Prostomatea || Plagiopylea)},
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Year = {2009},
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Abstract = {Closer to Pancrustacea},
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Title = {{Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?}},
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Title = {{Spotlight on the Thaumarchaeota}},
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Volume = {6},
Abstract = {"Aigarchaeota" are Thaum},
Doi = {10.1038/ismej.2011.145},
File = {brochier-armanet2012_aigarchaeota.pdf},
ISSN = {1751-7362},
Url = {www.nature.com/ismej}
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@Article{BrochierArmanet2011,
Title = {{Phylogeny and evolution of the Archaea: One hundred genomes later}},
Author = {C. Brochier-Armanet},
Journal = {Current Opinion in Microbiology},
Year = {2011},
Pages = {1--8},
Volume = {14},
Abstract = {Parva + Nano || Thermo; Kora || Eury; Algarchaeota (Caldiarchaeum subterraneum) + Thauma},
Doi = {10.1016/j.mib.2011.04.015},
File = {brochier-armanet2011_archaea.pdf},
ISSN = {1369-5274},
Url = {http://dx.doi.org/10.1016/j.mib.2011.04.015}
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@Article{BrochierArmanet2008,
Title = {{Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota}},
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Journal = {Nature Rev. Microbiol.},
Year = {2008},
Pages = {245--252},
Volume = {6},
Abstract = {As stated},
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File = {brochier-armanet2008.pdf}
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@Article{BrochierArmanet2006,
Title = {{Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers}},
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Pages = {1--9},
Volume = {2},
File = {brochier-armanet2006.pdf}
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Title = {{A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya}},
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Journal = {Biol. Direct},
Year = {2008},
Number = {1},
Pages = {54},
Volume = {3},
Abstract = {As stated},
Doi = {10.1186/1745-6150-3-54},
File = {brochier-armanet2008.pdf}
}
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Title = {{Testing the Cambrian explosion hypothesis by using a molecular dating technique}},
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Abstract = {Multiple groups in Microgenomates (OP11) and Parcubacteria (OD1)},
Doi = {10.1038/nature14486},
File = {brown2015_candidate_phyla_radiation.pdf},
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@Article{Brown2008b,
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@Article{Brown1999,
Title = {{Gene Descent, Duplication, and Horizontal Transfer in the Evolution of Glutamyl- and Glutaminyl-tRNA Synthetases}},
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@Article{Brown2012,
Title = {{Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria}},
Author = {M. W. Brown},
Journal = {Current Biology},
Year = {2012},
Pages = {1--5},
Volume = {22},
Abstract = {Guttulinopsis ~ Paracercomonas and Bigelowiella},
Doi = {10.1016/j.cub.2012.04.021},
File = {brown2012_rhizaria.pdf},
ISSN = {0960-9822},
Url = {http://dx.doi.org/10.1016/j.cub.2012.04.021}
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@Article{Brown2018,
Title = {{Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group.}},
Author = {M. W. Brown and A. A. Heiss and R. Kamikawa and Y. Inagaki and A. Yabuki and A. K. Tice and T. Shiratori and K.-I. Ishida and T. Hashimoto and A. G. B. Simpson and A. J. Roger},
Journal = {Genome Biol Evol},
Year = {2018},
Number = {2},
Pages = {427 - 433},
Volume = {10},
Abstract = {"CRUMS": Mantamonas + Rigifila + Collod; Malaw + Ancyrom},
Doi = {10.1093/gbe/evy014},
File = {brown2018_mantamonas_rigifila_collod_crums.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24789819}
}
@Article{Brown2014,
Title = {{Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads}},
Author = {M. W. Brown and S. C. Sharpe and J. D. Silberman and A. A. Heiss and B. F. Lang and A. G. B. Simpson and A. J. Roger},
Journal = {Proc R Soc B},
Year = {2014},
Number = {20131755},
Volume = {280},
Abstract = {Pygsuia biforma in Breviatea; ?Collod || Amoeb || Obazoa = (Brev || Apuso || Opistok); Malawi + Trimastix; Hapto + Telon; no Ancyromonads!},
Doi = {10.1098/rspb.2013.1755},
File = {brown2013_breviatea.pdf}
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@Article{Brown2011,
Title = {{A contemporary evaluation of the acrasids (Acrasidae, Heterolobosea, Excavata).}},
Author = {M. W. Brown and J. D. Silberman and F. W. Spiegel},
Journal = {European journal of protistology},
Year = {2011},
Abstract = {Only one genus Acrasis, Allovahlkampfia sister},
Doi = {10.1016/j.ejop.2011.10.001},
File = {brown2011_acrasids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22154141}
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@Article{Brown2010,
Title = {{???Slime Molds??? among the Tubulinea (Amoebozoa): Molecular Systematics and Taxonomy of Copromyxa}},
Author = {M. W. Brown and J. D. Silberman and F. W. Spiegel},
Journal = {Protist},
Year = {2010},
Number = {2},
Pages = {277--287},
Volume = {162},
Abstract = {Dermamoeba, Flabellinea, Protostelids etc., Phalanst + Acram vs. Acantha, Theca, Mayorella, Tubulinea (incl. Arcell., Hartm., Amoeb. and Copromyxa)},
Doi = {10.1016/j.protis.2010.09.003},
File = {brown2010_copromyxa.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2010.09.003}
}
@Conference{Brown2008,
Title = {{Evaluating Lindsay Olive's acrasids}},
Author = {M. W. Brown and J. D. Silberman and F. W. Spiegel},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Volume = {632},
Abstract = {Guttulinopsis vulgaris may not be a member of Heterolobosea},
File = {brown2008.txt}
}
@Article{Brown2009,
Title = {{Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta}},
Author = {M. W. Brown and F. W. Spiegel and J. D. Silberman},
Journal = {Mol. Biol. Evol.},
Year = {In press},
Abstract = {(Apusozoa || Breviata || Amoebozoa) || Holozoa: Corall || Icht || Caps || Minist || Choan || Metaz + Nucletmycea: (Fonticula + Nuclearia) || Blastocl || Chytr || others},
File = {brown2009_fonticula.pdf},
Keywords = {Fonticula alba, Opisthokonta, multicellularity, aggregation, Nucletmycea, protist}
}
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@Article{Brugerolle1990,
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@Article{Buaya2019,
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Journal = {Fungal Systematics and Evolution},
Year = {2019},
Pages = {35 - 40},
Volume = {3},
Abstract = {Miracula basal oomycete},
Doi = {10.3114/fuse.2019.03.04},
File = {buaya2019_miracula_basal_oomycete.pdf}
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@Article{Bucknam2006,
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Url = {http://www.ncbi.nlm.nih.gov/pubmed/26588818}
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@Article{Burger2013,
Title = {{Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists.}},
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Journal = {Genome Biol Evol},
Year = {2013},
Number = {2},
Pages = {418--438},
Volume = {5},
Abstract = {As stated},
Doi = {10.1093/gbe/evt008},
File = {burger2013_jacobida_mt_genomes.pdf},
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@Article{Burger2009,
Title = {{Group I-intron trans-splicing and mRNA editing in the mitochondria of placozoan animals}},
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Year = {2009},
Number = {9},
Pages = {381 - 386},
Volume = {25},
Abstract = {... atypical features qualify placozoan mitochondrial gene and genome organization as derived rather than primitive.},
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File = {burger2009_placozoa_mt.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19716620}
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Title = {{Deuterostome neuroanatomy and the body plan paradox}},
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Journal = {EVOLUTION \& DEVELOPMENT},
Year = {2011},
Pages = {110--115},
Volume = {1},
Abstract = {propose the hypothesis that in the ambulacraria the two parts are separated spatially and temporally over life history stages, whereas in chordates the two parts are united in a single central nervous systems},
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Title = {{Primordial neurosecretory apparatus identified in the choanoflagellate Monosiga brevicollis}},
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Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2011},
Number = {37},
Pages = {15264--15269},
Volume = {108},
Abstract = {As stated},
Doi = {10.1073/pnas.1106189108},
File = {burkhardt2011_monosiga_neural_snare.pdf}
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@Article{Burki2013,
Title = {{Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in rhizaria.}},
Author = {F. Burki and N. Corradi and R. Sierra and J. Pawlowski and G. R. Meyer and C. L. Abbott and P. J. Keeling},
Journal = {Curr. Biol.},
Year = {2013},
Number = {16},
Pages = {1541--1547},
Volume = {23},
Abstract = {|| Gromia + Corallomyxa},
Doi = {10.1016/j.cub.2013.06.033},
File = {burki2013_mikrocytos.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23968920}
}
@Article{Burki2009,
Title = {{Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates}},
Author = {F. Burki and Y. Inagaki and J. B. te and J. M. Archibald and P. J. Keeling and T. Cavalier-Smith and M. Sakaguchi and T. Hashimoto and A. Horak and S. Kumar and D. Klaveness and K. S. Jakobsen and J. Pawlowski and K. Shalchian-Tabrizi},
Journal = {Genome. Biol. Evol.},
Year = {2009},
Number = {1},
Pages = {231--238},
Volume = {1},
Abstract = {||| Plantae ||| CCTH: Hapto, Crypto, Telo, Centro ||| Rhiz ||| Chromalv; Malawimon still not placed well},
Doi = {10.1093/gbe/evp022},
File = {burki2009_centroh_telon.pdf}
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@Article{Burki2014,
Title = {{Rhizaria.}},
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Journal = {Curr. Biol.},
Year = {2014},
Number = {3},
Pages = {R103--7},
Volume = {24},
Abstract = {Review; nice scheme},
Doi = {10.1016/j.cub.2013.12.025},
File = {burki2014_rhizaria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24502779}
}
@Article{Burki2010,
Title = {{Evolution of Rhizaria: New insights from phylogenomic analysis of uncultivated protists}},
Author = {F. Burki and A. Kudryavtsev and M. V. Matz and G. V. Aglyamova and S. Bulman and M. Fiers and P. J. Keeling and J. Pawlowski},
Journal = {BMC Evolutionary Biology},
Year = {2010},
Pages = {377},
Volume = {10},
Abstract = {(Haplo) || Foram (incl. Reticulomyxa) + Acanth (~ Polycys) || Gromia + Phytomyxea || Cercoz},
Doi = {10.1186/1471-2148-10-377},
File = {burki2010_rhizaria.pdf},
Url = {http://www.biomedcentral.com/1471-2148/10/377}
}
@Article{Burki2006,
Title = {{Monophyly of Rhizaria and Multigene Phylogeny of Unicellular Bikonts}},
Author = {F. Burki and J. Pawlowski},
Journal = {Proteins},
Year = {2006},
Number = {10},
Pages = {1922--1930},
Volume = {23},
Abstract = {(Exca, Rhizar, Alv, Chr) || Plants || Opi+Ani},
File = {burki2006.pdf}
}
@Article{Burki2007,
Title = {{Phylogenomics Reshuffles the Eukaryotic Supergroups}},
Author = {F. Burki and K. Shalchian-Tabrizi and M. Minge and A. Skjaeveland and S. I. Nikolaev and K. S. Jakobsen and J. Pawlowski},
Journal = {PLoS One},
Year = {2007},
Number = {8},
Pages = {e790},
Volume = {2},
Abstract = {ESTs: `SAR' (Stramenopiles+Alveolates+Rhizaria), Hapto+Crypto, Plantae, Excavata (Malawimonas sister)},
File = {burki2007.pdf}
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@Article{Burki2008,
Title = {{Phylogenomics reveals a new ``megagroup'' including most photosynthetic eukaryotes}},
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Journal = {Biol. Lett.},
Year = {2008},
Number = {4},
Pages = {366--369},
Volume = {4},
Abstract = {Excav + Unik + ||| (Rhiz ||| Strame ||| Alveol) + (Crypt+Hapto ||| Glauco ||| Rhodo || Chloro)},
Doi = {10.1098/rsbl.2008.0224},
File = {burki2008.pdf}
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@Article{Burleigh2004,
Title = {{Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life}},
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Title = {{A review of recent information on the Haplosporidia, with special reference to \textit{Haplosporidium nelsoni} (MSX disease)}},
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Journal = {Aquat. Living Resour.},
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Number = {2004},
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Volume = {17},
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File = {bureson2004.pdf}
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Title = {{Insights from Diploblasts; the Evolution of Mesoderm and Muscle}},
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Volume = {310B},
Abstract = {For Radialia: striated muscles developed independetly in Cnid, Cten and Bilateria, entocodon is not a 3rd germ layer},
Doi = {10.1002/jez.b.21150},
File = {burton2008.pdf}
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Title = {{Comparative analysis of ribonuclease P RNA of the planctomycetes}},
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Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2004},
Pages = {1333--1344},
Volume = {54},
File = {butler2004.pdf}
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Title = {{Implication of Fossil Conifers for the Phylogenetic Relationships of Living}},
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Title = {{Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life}},
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Journal = {J. Mol. Evol.},
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Pages = {333--345},
Volume = {54}
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Title = {{Eccrinales (Trichomycetes) are not fungi, but a clade of protists at the early divergence of animals and fungi}},
Author = {M. J. Cafaro},
Journal = {Mol. Phyl. Evol.},
Year = {2005},
Pages = {21--34},
Volume = {35},
Abstract = {Eccrinales ~ Amoebidium},
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@Article{Cai2020,
Title = {{Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation}},
Author = {M. Cai and Y. Liu and X. Yin and Z. Zhou and M. W. Friedrich and T. Richter-Heitmann and R. Nimzyk and A. Kulkarni and X. Wang and W. Li and J. Pan and Y. Yang and J.-D. Gu and M. Li},
Journal = {SCIENCE CHINA Life Sciences},
Year = {2020},
Pages = {2020},
Volume = {12},
Abstract = {Heimdall: neigh. "Gerdarchaeota"},
Doi = {10.1007/s11427-020-1679-1},
File = {cai2020_gerdarchaeota.pdf}
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Title = {{Ancient Origin of Four-Domain Voltage-gated Na(+) Channels Predates the Divergence of Animals and Fungi.}},
Author = {X. Cai},
Journal = {The Journal of membrane biology},
Year = {2012},
Abstract = {Thecamonas},
Doi = {10.1007/s00232-012-9415-9},
File = {cai2012_na_channels_apusosoans.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22258316}
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Title = {{Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions.}},
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Journal = {J Oral Microbiol},
Year = {2014},
Volume = {6},
Abstract = {As stated},
Doi = {10.3402/jom.v6.25468},
File = {camanocha2014_lesser_known_bact_phyla_human_oral.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25317252}
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Title = {{Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla}},
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@Article{Cammarano1999,
Title = {{The Archaea Monophyly Issue: A Phylogeny of Translational Elongation Factor G(2) Sequences Inferred from an Optimized Selection of Alignment Positions}},
Author = {P. Cammarano and R. Creti and A. M. Sanangelantoni and P. Palm},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {524--537},
Volume = {49}
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@Article{Campbell1999,
Title = {{Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA}},
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Year = {1999},
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Title = {{A remarkable development of the sporophyte in Anthoceros fusiformis, Aust.}},
Author = {D. H. Campbell},
Journal = {Annals of Botany},
Year = {1924},
Pages = {473--483},
Abstract = {Large, capable for independent life in the experiment},
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Title = {{Koralionastetales, a new order of marine Ascomycota in the Sordariomycetes.}},
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Year = {2009},
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Pages = {373--380},
Volume = {113},
Abstract = {As stated},
Doi = {10.1016/j.mycres.2008.11.013},
File = {kampbell2008.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19084063}
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@InProceedings{Campbell2009,
Title = {{Sponges are not Eumetazoans: Complete mitochondrial genome support for a sister group relationship between Porifera and the other animals}},
Author = {L. I. Campbell and D. Pisani},
Booktitle = {{Systematics 2009. Leiden, August 11-14. Abstracts}},
Year = {2009},
Abstract = {Sponges most likely represent the (possibly paraphyletic) sister group(s) to all the other animals},
File = {campbell2009_sponges.txt}
}
@Article{Campbell2011,
Title = {{MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda}},
Author = {L. I. Campbell and O. Rota-Stabelli and G. D. Edgecombe and T. Marchioro and S. J. Longhorn and M. J. Telford and H. Philippe and L. Rebecchi and K. J. Peterson and D. Pisani},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2011},
Abstract = {Scalidophora || Nematom + Nemat || Tardigrada | Onychophora || Chel || Myriap || Pancrust},
Doi = {10.1073/pnas.1105499108},
File = {campbell2011_tardigrada_onych.pdf},
Url = {www.pnas.org/cgi/doi/10.1073/pnas.1105499108}
}
@Article{delCampo2011,
Title = {{Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys}},
Author = {J. del Campo and R. Massana},
Journal = {Protist},
Year = {2011},
Pages = {14},
Volume = {49},
Abstract = {Biosoec: Halocafeteria group || Cafeteria g || Boroka g || Bicosoeca g || Adriamonas g},
Doi = {10.1016/j.protis.2010.10.003},
File = {delcampo2011_env_chrysoph_bicosoec.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2010.10.003}
}
@Article{CampoPaysaa2008,
Title = {{Retinoic acid signaling in development: Tissue-specific functions and evolutionary origins}},
Author = {F. Campo-Paysaa and F. Marletaz and V. Laudet and M. Schubert},
Journal = {genesis},
Year = {2008},
Pages = {640--656},
Volume = {46},
Abstract = {standard hypothesis},
Doi = {10.1002/dvg.20444},
File = {campo-paysaa2008.pdf}
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@Article{CampoPaysaa2011,
Title = {{MicroRNA complements in deuterostomes: Origin and evolution of microRNAs}},
Author = {F. Campo-Paysaa and M. Se and M. Schubert},
Journal = {EVOLUTION \& DEVELOPMENT},
Year = {2011},
Pages = {15--27},
Volume = {1},
Abstract = {miRNAs can easily emerge within already transcribed regions of DNA},
Doi = {10.1111/j.1525-142X.2010.00452.x},
File = {campo-paysaa2011_microrna_origin.pdf}
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Title = {{Phylogenetic Relationships of Platyhelminthes Based on 18{S} Ribosomal Gene Sequences}},
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Journal = {Mol. Phyl. Evol.},
Year = {1998},
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Volume = {10}
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Title = {{A New Class and Order of Myxozoans to Accommodate Parasites of Bryozoans with Ultrastructural Observations on Tetracapsula bryosalmonae (PKX Organism)}},
Author = {E. U. Canning and A. Curry and S. W. Feist and M. Longshaw and B. Okamura},
Journal = {J. Euk. Microbiol.},
Year = {2000},
Number = {5},
Pages = {456--468},
Volume = {47}
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@Article{Canning2007,
Title = {{Ultrastructure of \textit{Buddenbrockia allmani} n. sp. (Myxozoa, Malacosporea), a Parasite of Lophopus crystallinus (Bryozoa, Phylactolaemata)}},
Author = {E. U. Canning and A. Curry and S. L. L. Hill and B. Okamura},
Journal = {J. Euk. Microbiol.},
Year = {2007},
Number = {3},
Pages = {247--262},
Volume = {54},
Abstract = {Tetracapsuloides and Buddenbrockia are separate; vermifom stage in not known for new species},
File = {canning2007.pdf}
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@Article{Canning2008,
Title = {{Early development of the myxozoan Buddenbrockia plumatellae in the bryozoans Hyalinella punctata and Plumatella fungosa, with comments on taxonomy and systematics of the Myxozoa}},
Author = {E. U. Canning and A. Curry and B. Okamura},
Journal = {Folia Parasitologica},
Year = {2008},
Pages = {241--255},
Volume = {255},
Abstract = {In view of the recent confirmation of the phylogenetic affinity of Buddenbrockia with the Cnidaria, we postulate how features observed in Buddenbrockia may be homologous with cnidarian structures},
File = {canning2008_buddenbrockia.txt}
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@Article{Cannon2014,
Title = {{Phylogenomic Resolution of the Hemichordate and Echinoderm Clade}},
Author = {J. T. Cannon},
Journal = {Current Biology},
Year = {2014},
Abstract = {Nothing new},
Doi = {10.1016/j.cub.2014.10.016},
File = {cannon2014_ambulacraria.pdf},
ISSN = {0960-9822},
Url = {http://dx.doi.org/10.1016/j.cub.2014.10.016}
}
@Article{Cannon2009,
Title = {{Molecular Phylogeny of Hemichordata, with Updated Status of Deep-Sea Enteropneusts}},
Author = {J. T. Cannon and A. L. Rychel and H. Eccleston and K. M. Halanych and B. J. Swalla},
Journal = {Mol. Phylogenet. Evol.},
Year = {In press},
Abstract = {Enteropn. paraphyletic},
Doi = {10.1016/j.ympev.2009.03.027},
File = {cannon2009_hemichordata.pdf}
}
@Article{Cannon2016,
Title = {{Xenacoelomorpha is the sister group to Nephrozoa.}},
Author = {J. T. Cannon and B. C. Vellutini and J. Smith III and F. Ronquist and U. Jondelius and A. Hejnol},
Journal = {Nature},
Year = {2016},
Number = {7588},
Pages = {89--93},
Volume = {530},
Abstract = {As stated, + Phoronida and Brach. || Annelida whereas Bryoz + Entoprocta || Platyzoa (various support)},
Doi = {10.1038/nature16520},
File = {cannon2016_xenacoelomorpha_nephrozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26842053}
}
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Journal = {Taxon},
Year = {2007},
Number = {2},
Pages = {822--846},
Volume = {2007},
Abstract = {PhyloCode names},
File = {cantino2007.pdf}
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Title = {{Eutherian phylogeny as inferred from mitochondrial DNA sequence data.}},
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@Article{CapellaGutierrez2012,
Title = {{Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi.}},
Author = {S. Capella-Guti{\'e}rrez and M. Marcet-Houben and T. Gabald{\'o}n},
Journal = {BMC Biol.},
Year = {2012},
Pages = {47},
Volume = {10},
Abstract = {Complete genomes: Micro || Chytr || Zygo || Bas + Asco},
Doi = {10.1186/1741-7007-10-47},
File = {capella-gutierrez2012_microsporidia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22651672}
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@Article{Carafa2005,
Title = {{Distribution of cell-wall xylans in bryophytes and tracheophytes: new insights into basal interrelationships of land plants}},
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Journal = {New Phytol.},
Year = {2005},
Pages = {231--240},
Volume = {168},
Abstract = {Anthoc || Pterid},
File = {carafa2005.pdf}
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@Article{Carapelli2007,
Title = {{Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea}},
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Journal = {BMC Evol. Biol.},
Year = {2007},
Number = {S8},
Pages = {1--13},
Volume = {7},
Abstract = {mt genomes: Coll || Diplu || (Decap + Cephaloc) + Insecta },
File = {carapelli2007.pdf}
}
@Article{Cardona2016,
Title = {{Origin of Bacteriochlorophyll a and the Early Diversification of Photosynthesis.}},
Author = {T. Cardona},
Journal = {PLoS ONE},
Year = {2016},
Number = {3},
Pages = {e0151250},
Volume = {11},
Abstract = {Some support for Terrabacteria},
Doi = {10.1371/journal.pone.0151250},
File = {cardona2016_terrabacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/14617179}
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@Article{Carnegie2003,
Title = {{Molecular detection of the oyster parasite Mikrocytos mackini, and a preliminary phylogenetic analysis}},
Author = {R. B. Carnegie and G. R. Meyer and J. Blackbourn and N. Cochennec-Laureau and F. C. J. Berthe and S. M. Bower},
Journal = {Diseases of Aquatic Organisms},
Year = {2003},
Pages = {219--227},
Volume = {54},
Abstract = {Mikrocytos mackini !~ any amitoch. protists},
File = {carnegie2003.pdf},
Url = {www.int-res.com}
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Title = {{Molecular phylogenetic analysis of the heterothophic chrysophyte genus \textit{Paraphysomonas} (Chrysophyceae), and the design of RNA-targeted oligonucteotide probes for two species}},
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Year = {1999},
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Volume = {35}
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Title = {{Cambrian suspension-feeding lobopodians and the early radiation of panarthropods.}},
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Journal = {BMC Evol. Biol.},
Year = {2017},
Number = {1},
Pages = {29},
Volume = {17},
Abstract = {Nematoda | Priapulida + Palaeoscolecida | Ovatiovermis | Hallucigenia | Tardigrada | Onychophora | ... Anomalocaris etc.},
Doi = {10.1186/s12862-016-0858-y},
File = {caron2017_lobopoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18447582}
}
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Title = {{Molecular phylogeny of choanoflagellates, the sister group to Metazoa}},
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Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {43},
Pages = {16641--16646},
Volume = {105},
Abstract = {Proterospongia is the stage of development of Salpingoeca; Choano || Calci + Cten || Cnid || Trich || Demosp},
Doi = {10.1073/pnas.0801667105},
File = {carr2008.pdf}
}
@Article{Carranza1997,
Title = {{Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences.}},
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Volume = {14}
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Year = {2007},
Number = {5},
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Title = {{Crystallin Sequences Support a Galliform-Anseriform Clade}},
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Journal = {Mol. Phyl. Evol.},
Year = {1997},
Number = {2},
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@Article{Cassens2000,
Title = {{Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages}},
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Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2000},
Number = {21},
Pages = {11343--11347},
Volume = {97}
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@Article{Castellani2011,
Title = {{New pentastomids from the late Cambrian of Sweden -- deeper insight of the ontogeny of fossil tongue worms}},
Author = {C. Castellani and A. Maas and D. Waloszek and J. T. Haug},
Journal = {Palaeontographica A},
Year = {2011},
Number = {4-6},
Pages = {95-145},
Volume = {293},
Abstract = {More baseal then thought?},
File = {castellani2011_cambrian_pentastomids.pdf}
}
@Article{Castelle2017,
Title = {{Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation.}},
Author = {C. J. Castelle and C. T. Brown and B. C. Thomas and K. H. Williams and J. F. Banfield},
Journal = {Sci Rep},
Year = {2017},
Pages = {40101},
Volume = {7},
Abstract = {OD1 superphylum includes OD1 (Parcu), Falkow, Jackson, Kuenen, Magasani, Uhr, Parcunitro, Moran},
Doi = {10.1038/srep40101},
File = {castelle2017_parcubacterium_od1.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/11081789}
}
@Article{Castelle2013,
Title = {{Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment.}},
Author = {C. J. Castelle and L. A. Hug and K. C. Wrighton and B. C. Thomas and K. H. Williams and D. Wu and S. G. Tringe and S. W. Singer and J. A. Eisen and J. F. Banfield},
Journal = {Nat Commun},
Year = {2013},
Pages = {2120},
Volume = {4},
Abstract = {Zixibacteria (RBG-1) ~ Bacteroidetes, Chlorobi},
Doi = {10.1038/ncomms3120},
File = {/home/alexey/coll/ref/os/1/bac/castelle2013_zixibacteria.pdf},
Keywords = {bacteria, catalytic domain, energy metabolism, genetic variation, genome, bacterial, geologic sediments, groundwater, iron-sulfur proteins, likelihood functions, molecular sequence data, oxidoreductases, phylogeny, ribosomal proteins},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21035426}
}
@Article{Castelle2015,
Title = {{Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.}},
Author = {C. J. Castelle and K. C. Wrighton and B. C. Thomas and L. A. Hug and C. T. Brown and M. J. Wilkins and K. R. Frischkorn and S. G. Tringe and A. Singh and L. M. Markillie and R. C. Taylor and K. H. Williams and J. F. Banfield},
Journal = {Curr. Biol.},
Year = {2015},
Number = {6},
Pages = {690--701},
Volume = {25},
Abstract = {DPANN: (Micrarchaeota (Micrarchaeum, ARMAN) + Diapherotrites (Iainarchaeum)) || Nanohaloarchaeota (Nanosalinarum) || Parvarchaeota (Parvarchaeum) + Nanoarchaeota || Pacearchaeota + Woesearchaeota; || Euryarchaeota incl. Thermococcales || TACK: Kora + Crena || (Geoarchaeota (NAG1) + Aigarchaeota || Thaum + Bathyarchaeota (MCG))},
Doi = {10.1016/j.cub.2015.01.014},
File = {castelle2015_archaea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25702576}
}
@Article{Castresana1999,
Title = {{Respiratory Chains in the Last Common Ancestor of Living Organisms}},
Author = {J. Castresana and D. Moreira},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {453--460},
Volume = {49}
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@Article{Cavaletti2006,
Title = {{New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil}},
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Journal = {Environ. Microbiol.},
Year = {2006},
Number = {6},
Pages = {4360--4369},
Volume = {72},
Abstract = {Ktedobacteria, ~ Chloroflexi},
File = {cavaletti2006.pdf}
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@InCollection{Cavalier-Smith2007,
Title = {{Evolution and relationships of algae: major branches of the tree of life}},
Author = {Th. Cavalier-Smith},
Booktitle = {Unravelling the algae: the past, present and future of algae systematics. The Systematic Association special volume series 75},
Publisher = {CRC Press},
Year = {2007},
Address = {London},
Editor = {J. Brodie and J. Lewis},
Pages = {21--56},
Abstract = {Cyano || Posi + Actino + "missing link"; Tetrophyceae for Tetraselmis; Chrysomeroph + Xantho + Phaeo s.l., incl. Phaeothamn.; "microheliozoan" in Centrohelea; Centrohrl. + Hapto; Postgaardea + Eugl. + Kineto + Diplo polytomy; support for Breviata || Ancyro (~ Micronuclearia) + Apuso, they are either || Loukozoa or branching on the Bikonta base}
}
@InCollection{Cavalier1993b,
Title = {{Classification of Percolozoa}},
Author = {T. Cavalier-Smith},
Booktitle = {Endocytobiol. V},
Publisher = {Tuebingen University Press},
Year = {1993},
Address = {Tuebingen},
Editor = {H. Ishikawa and M. Ishida and S. Sato},
Pages = {399--406},
Journal = {Endocytobiol.}
}
@Article{Cavalier1996/97,
Title = {{Amoeboflagellates and Mitochondrial Cristae in Eukaryote Evolution: Megasystematics of the New Protozoan Subkingdoms Eozoa and Neozoa}},
Author = {T. Cavalier-Smith},
Journal = {Arch. Protistenkd.},
Year = {1996/97},
Pages = {237--258},
Volume = {147}
}
@Article{CavalierSmith2021,
Title = {{Ciliary transition zone evolution and the root of the eukaryote tree: Implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi}},
Author = {T. Cavalier-Smith},
Journal = {Protoplasma},
Year = {2021},
Abstract = {changes in Protozoa (Percolozoa and around, p. 34-) and around Rhodophyta (p. 96-)},
Doi = {10.1007/s00709-021-01665-7},
File = {cavalier-smith2021_ciliary_transition_zone.pdf}
}
@Article{CavalierSmith2017,
Title = {{Origin of animal multicellularity: Precursors, causes, consequences-the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion.}},
Author = {T. Cavalier-Smith},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2017},
Number = {1713},
Volume = {372},
Abstract = {Presponge concept},
Doi = {10.1098/rstb.2015.0476},
File = {cavalier-smith2017_orig_animal_multicell.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28242741}
}
@Article{Cavalier-Smith2017,
Title = {{Euglenoid pellicle morphogenesis and evolution in light of comparative ultrastructure and trypanosomatid biology: Semi-conservative microtubule/strip duplication, strip shaping and transformation.}},
Author = {T. Cavalier-Smith},
Journal = {Eur. J. Protistol.},
Year = {2017},
Number = {Pt - A},
Pages = {137 - 179},
Volume = {61},
Abstract = {As stated},
Doi = {10.1016/j.ejop.2017.09.002},
File = {cavalier-smith2017_euglenoid_pellicle.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29073503}
}
@Article{Cavalier-Smith2017a,
Title = {{Kingdom Chromista and its eight phyla: A new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences.}},
Author = {T. Cavalier-Smith},
Journal = {Protoplasma},
Year = {2017},
Abstract = {classification table; no tree},
Doi = {10.1007/s00709-017-1147-3},
File = {cavalier-smith2017_chromista.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28875267}
}
@Article{CavalierSmith2016,
Title = {{Higher classification and phylogeny of Euglenozoa}},
Author = {T. Cavalier-Smith},
Journal = {European Journal of Protistology},
Year = {2016},
Pages = {250 - 276},
Volume = {56},
Abstract = {Subphyl. Euglenoida (classes Entosiphonea, Stavomonadea, Ploeotarea, Peranemea, Euglenophyceae), Postgaardea, Glycomonada (cl. Diplonemea, Kinetoplastea)},
Doi = {10.1016/j.ejop.2016.09.003},
File = {cavalier-smith2016_euglenozoa.pdf},
ISSN = {0932-4739},
Url = {http://dx.doi.org/10.1016/j.ejop.2016.09.003}
}
@Article{Cavalier-Smith2015,
Title = {{Mixed heterolobosean and novel gregarine lineage genes from culture ATCC 50646: Long-branch artefacts, not lateral gene transfer, distort $\alpha$-tubulin phylogeny.}},
Author = {T. Cavalier-Smith},
Journal = {Eur. J. Protistol.},
Year = {2015},
Number = {2},
Pages = {121--137},
Volume = {51},
Abstract = {Louk closer to all other euk than Eugl, Marine Anaerobic Mystery Clade ~ Rhodoph, Telonem ?},
Doi = {10.1016/j.ejop.2014.12.001},
File = {cavalier-smith2014_marine_anaer_mystery_clade.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25769111}
}
@Article{Cavalier-Smith2014,
Title = {{Gregarine site-heterogeneous 18S rDNA trees, revision of gregarine higher classification, and the evolutionary diversification of Sporozoa.}},
Author = {T. Cavalier-Smith},
Journal = {Eur. J. Protistol.},
Year = {2014},
Number = {5},
Pages = {472--495},
Volume = {50},
Abstract = {Apicomplexa: Gregarinomorphea (incl. Cryptosporidium), Paragregarea (Selenidium etc.), Coccidiomorphea. Perkinsozoa: Perkinsea, Squirmidea (Filipodium, Platyproteum)},
Doi = {10.1016/j.ejop.2014.07.002},
File = {cavalier-smith2014_sporozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25238406}
}
@Article{Cavalier-Smith2014a,
Title = {{The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life.}},
Author = {T. Cavalier-Smith},
Journal = {Cold Spring Harb Perspect Biol},
Year = {2014},
Number = {9},
Pages = {a016006},
Volume = {6},
Abstract = {Eozoa, podiates and corticates. Filarchaeota: Kora, Thauma, Crena},
Doi = {10.1101/cshperspect.a016006},
File = {cavalier-smith2014_neomuran_revolution.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25183828}
}
@Article{CavalierSmith2013,
Title = {{Symbiogenesis: Mechanisms, Evolutionary Consequences, and Systematic Implications}},
Author = {T. Cavalier-Smith},
Journal = {Annu. Rev. Ecol. Evol. Syst.},
Year = {2013},
Pages = {42},
Volume = {11},
Abstract = {CS-scheme; Podiates: Opistok; Corticates: Chromista (incl. Hacrobia) and Plantae; Chromista classification (almost nothing new)},
Doi = {10.1146/annurev-ecolsys-110411-160320},
File = {cavalier-smith2013_symbiogenesis.pdf}
}
@Article{CavalierSmith2012a,
Title = {{Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa}},
Author = {T. Cavalier-Smith},
Journal = {European Journal of Protistology},
Year = {2012},
Pages = {64},
Abstract = {Loukozoa: Tsukubea, Jacobea; Metamonada: Anaeromonadea, Trichomonadea, Carpomonadea (Carpedie, Chilomast, Dysnectes), Eopharyngea (Diplo, Retorto, Caviomonas); Malawimonadea. Protalveolata class: only Colponema. Sulcozoa: Thecomonadea, Breviatea (Breviata, Subulatomonas), Diphyllatea, Glissomonadea (Plano, Mantamonas, Discocelia (s)), Hilomonadea (Rigifila, Micronuclearia). Many new Variosea. Archamoebea incl. Rhizomastix. Choanozoa: Choanoflagellatea, Filasterea, Corallochytrea, Ichthyosporea, Cristidiscoidea, Rosellidea (incl. Aphelidida). Archemycota: Monoblepharidomy, Chytridiomy, Allomy, Zoomy, Glomomy, Mucoromy},
Doi = {10.1016/j.ejop.2012.06.001},
File = {cavalier-smith2012_loukozoa.pdf},
ISSN = {0932-4739},
Url = {http://dx.doi.org/10.1016/j.ejop.2012.06.001}
}
@Article{CavalierSmith2012b,
Title = {{Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea}},
Author = {T. Cavalier-Smith},
Journal = {European Journal of Protistology},
Year = {2012},
Abstract = {Opalozoa: Bikosea, Placididea, Nanomonadea (MAST-3), Opalomonadea (MAST-12), Opalinea, Blastocystea. MAST-1,2 ~ Pirsonia. MAST-6,4,11,7,8,9 ~ Labyr. Parmales (Triparma) ~ Bolidophyceae; Sulcophycidae (Olisthodiscus) ~ Pelago; Actinophtyida ~ Raphido.},
Doi = {10.1016/j.ejop.2012.09.002},
File = {cavalier-smith2012_placidozoa.pdf},
ISSN = {0932-4739},
Url = {http://dx.doi.org/10.1016/j.ejop.2012.09.002}
}
@Article{CavalierSmith2010,
Title = {{Deep phylogeny, ancestral groups and the four ages of life}},
Author = {T. Cavalier-Smith},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2010},
Number = {1537},
Pages = {111 - 132},
Volume = {365},
Abstract = {Eobacteria: Hado (Deino) and Chlorofl; Eozoa: Excav and Euglenozoa},
Doi = {10.1098/rstb.2009.0161},
File = {cavalier-smith2009_deep_phylogeny.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20008390}
}
@Article{CavalierSmith2010b,
Title = {{Origin of the cell nucleus, mitosis and sex: Roles of intracellular coevolution}},
Author = {T. Cavalier-Smith},
Journal = {Biology direct},
Year = {2010},
Number = {1},
Pages = {7},
Volume = {5},
Abstract = {Big tale...},
Doi = {10.1186/1745-6150-5-7},
File = {cavalier-smith2010_orig_of_cell.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20132544}
}
@Article{CavalierSmith2009,
Title = {{Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree}},
Author = {T. Cavalier-Smith},
Journal = {Biology letters},
Year = {2009},
Abstract = {Eozoa: Eugl and Excavata (incl. ?Diphyllatea); Chromista -- Harosa for SAR and Hacrobia. Euglenozoa vs. all euk.},
Doi = {10.1098/rsbl.2009.0948},
File = {cavalier-smith2009_protozoa_chromista.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20031978}
}
@Article{CavalierSmith2009a,
Title = {{Predation and eukaryote cell origins: A coevolutionary perspective.}},
Author = {T. Cavalier-Smith},
Journal = {Int. J. Biochem. Cell Biol.},
Year = {2009},
Pages = {307--322},
Volume = {41},
Abstract = {Same scheme with Negibacteria etc.},
Doi = {10.1016/j.biocel.2008.10.002},
File = {cavalier-smith2009.pdf}
}
@Article{CavalierSmith2009b,
Title = {{Megaphylogeny, Cell Body Plans, Adaptive Zones: Causes and Timing of Eukaryote Basal Radiations}},
Author = {Th. Cavalier-Smith},
Journal = {J. Euk. Micriobiol.},
Year = {2009},
Pages = {26--33},
Volume = {56},
Abstract = {Unikonta || Apus (or near Amoeboz.) || Excav || corticates; Choanozoa: Cristidiscoidia (Nuclear., Fonticul.); Choanofila: Choanoflagellatea, Filasterea (Capsasp, Ministeria), Ichthyosporea; Loukozoa: Vanomonada (Jacobea, Malawimonadea) and Diphyllatia},
Doi = {10.1111/j.1550-7408.2008.00373.x},
File = {cavalier-smith2008e.pdf}
}
@Article{CavalierSmith2006a,
Title = {{Rooting the tree of life by transition analyses}},
Author = {T. Cavalier-Smith},
Journal = {Biology Direct},
Year = {2006},
Number = {19},
Pages = {1--83},
Volume = {1},
Abstract = {new bacterial classification},
File = {cavalier-smith2006.pdf}
}
@Article{CavalierSmith2006c,
Title = {{Cell evolution and Earth history: stasis and revolution}},
Author = {T. Cavalier-Smith},
Journal = {Phil. Trans. R. Soc. B},
Year = {2006},
Pages = {969--1006},
Volume = {361(1470)},
File = {cavalier-smith2006c.pdf}
}
@Article{CavalierSmith2004,
Title = {{Only six kingdoms of life}},
Author = {T. Cavalier-Smith},
Journal = {Proc. R. Soc. B},
Year = {2004},
Pages = {1251--1262},
Volume = {271},
File = {cavalier-smith2004a.pdf},
Keywords = {pr1}
}
@Article{CavalierSmith2003a,
Title = {{The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa}},
Author = {T. Cavalier-Smith},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2003},
Pages = {1741--1758},
Volume = {53},
File = {cavalier-smith2003c.pdf}
}
@Article{CavalierSmith2003c,
Title = {{Protist phylogeny and the high-level classification of Protozoa}},
Author = {T. Cavalier-Smith},
Journal = {Eur. J. Protistol.},
Year = {2003},
Pages = {338--348},
Volume = {39},
Abstract = {Proteomyxidea: Pseudospora, Leucodictyon, Reticuloamoeba, Massisteria, Dimorpha, Gymnophrys, Borkovia; Thecofilosea ~ Cerco: Cryptodifflugia, Cryothecomonas; Spongo ~ Cerco; Bonamia, Claustrosporidium, Microcytos > Ascetosp; Xeno + Schizocladus > Foram; Postgaardea (incl. Calkinsia) ~ Kinetoplastea; Colponemea \& Perkinsea > Protalveolata; },
File = {cavalier-smith2003e.pdf}
}
@Article{Cavalier-Smith2002,
Title = {{The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa}},
Author = {T. Cavalier-Smith},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2002},
Pages = {297--354},
Volume = {52}
}
@Article{Cavalier-Smith2002b,
Title = {{The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification}},
Author = {T. Cavalier-Smith},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2002},
Pages = {7--76},
Volume = {52}
}
@InCollection{Cavalier-Smith2000,
Title = {{Flagellate megaevolution: the basis for eukaryote diversification}},
Author = {T. Cavalier-Smith},
Booktitle = {The Flagellates: Unity, Diversity and Evolution},
Publisher = {Chapman and Hall},
Year = {2000},
Address = {London},
Pages = {361--390}
}
@Article{Cavalier1999,
Title = {{Principles of Protein and Lipid Targeting in Secondary Symbiogenesis: Euglenoid, Dinoflagellate, and Sporozoan Plastid Origins and the Eukaryote Family Tree}},
Author = {T. Cavalier-Smith},
Journal = {J. Euk. Microbiol.},
Year = {1999},
Number = {4},
Pages = {347--366},
Volume = {46}
}
@Article{Cavalier1998,
Title = {{A revised six-kingdom system of life}},
Author = {T. Cavalier-Smith},
Journal = {Biol. Rev.},
Year = {1998},
Number = {2},
Pages = {203--266},
Volume = {73},
Keywords = {pr1}
}
@Article{Cavalier1996,
Title = {{Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny}},
Author = {T. Cavalier-Smith},
Journal = {Eur. J. Phycol.},
Year = {1996},
Number = {4},
Pages = {315--328},
Volume = {31}
}
@Article{Cavalier1995,
Title = {{Zooflagellate phylogeny and classification}},
Author = {T. Cavalier-Smith},
Journal = {Tsitologiya},
Year = {1995},
Number = {11},
Pages = {1010--1029},
Volume = {37}
}
@Article{Cavalier1993,
Title = {{The protozoan phylum Opalozoa}},
Author = {T. Cavalier-Smith},
Journal = {J. Euk. Microbiol.},
Year = {1993},
Number = {5},
Pages = {609--615},
Volume = {40}
}
@Article{Cavalier1993a,
Title = {{Kingdom Protozoa and its 18 phyla}},
Author = {T. Cavalier-Smith},
Journal = {Microbiol. Mol. Biol. Rev.},
Year = {1993},
Pages = {953--994},
Volume = {57}
}
@Article{Cavalier1987,
Title = {{ Eukaryotes with no mitochondria}},
Author = {T. Cavalier-Smith},
Journal = {Nature},
Year = {1987},
Number = {6111},
Pages = {332--333},
Volume = {326}
}
@Article{Cavalier1996b,
Title = {{Sponge phylogeny, animal monophyly, and the origin of the nervous system: 18S RNA evidence}},
Author = {T. Cavalier-Smith and M.T.E.P. Allsop and E.E. Chao and N. Boury-Esnault and J. Vacelet},
Journal = {Can. J. Zool.},
Year = {1996},
Pages = {2031--2045},
Volume = {74}
}
@Article{Cavalier1994,
Title = {{Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic?}},
Author = {T. Cavalier-Smith and M. T. Allsopp and E. E. Chao},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1994},
Number = {24},
Pages = {11368--11372},
Volume = {91}
}
@Article{Cavalier1996c,
Title = {{Corallochytrium, an Enigmatic Non-flagellate Protozoan Related to Choanoflagellates}},
Author = {T. Cavalier-Smith and M. T. P. Allsopp},
Journal = {Eur. J. Protistol.},
Year = {1996},
Pages = {306--310},
Volume = {32}
}
@Article{Cavalier1996/97a,
Title = {{Sarcomonad Ribosomal RNA Sequences, Rhizopod Phylogeny, and the Origin of Euglyphid Amoebae}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {Arch. Protistenkd.},
Year = {1996/97},
Pages = {227--236},
Volume = {147}
}
@Article{CavalierSmith2012d,
Title = {{Oxnerella micra sp. N . (Oxnerellidae fam. N.), A Tiny Naked Centrohelid, and the Diversity and Evolution of Heliozoa}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {Protist},
Year = {2012},
Pages = {28},
Abstract = {Heliozoa: Centrohelea + Microhelida (Microheliella, Didymoeca); Cryptista: Palpitea, Cryprom, Leucocr, Telon; "Harosa" = SAR; Ventrifilosia includes Luffisphaera, Paraluffisphaera, Rotosphaerida, Clathrella, Acanthocystis p.p.},
Doi = {10.1016/j.protis.2011.12},
File = {cavalier-smith2012_heliozoa.djvu},
Url = {http://www.elsevier.de/protis}
}
@Article{CavalierSmith2010c,
Title = {{Phylogeny and Evolution of Apusomonadida (Protozoa: Apusozoa): New Genera and Species}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {Protist},
Year = {2010},
Abstract = {4 new genera; ~ Opisthokonts; Micronuclearia -- incertae},
Doi = {10.1016/j.protis.2010.04.002},
File = {cavalier-smith2010_apusomonadida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20537943}
}
@Article{CavalierSmith2004c,
Title = {{Protalveolate phylogeny and systematics and the origins of Sporozoa and dinoflagellates (phylum Myzozoa nom. nov.)}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {Eur. J. Protistol.},
Year = {2004},
Pages = {185--212},
Volume = {40},
Abstract = {Perkinsus || Colpodella || Voromonas || Apicomplexa; Protalveolata: Colponemea -- Colponema, Algovora; Myzomonadea -- Voromonas, Aplphamonas, Chilovora; Perkinsea -- Perkinsus, Rastrimonas, Parvilucifera, Phagodinium; Ellobiopsea; Apicomonadea -- Colpodella, Acrocoelus},
File = {cavalier-smith2004c.pdf}
}
@Article{Cavalier1998a,
Title = {{\textit{Hyperamoeba} rRNA Phylogeny and the Classification of the Phylum Amoebozoa}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {J. Euk. Microbiol.},
Year = {1998},
Pages = {1--8},
Volume = {45}
}
@Article{Cavalier1996a,
Title = {{Molecular phylogeny of the free-living archezoan \textit{Trepomonas agilis} and the nature of the first eukaryote}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {J. Mol. Evol.},
Year = {1996},
Number = {6},
Pages = {551--562},
Volume = {43}
}
@Article{Cavalier1995a,
Title = {{The opalozoan \textit{Apuzomonas} is related to the common ancestor of animals, fungi and choanoflagellates}},
Author = {T. Cavalier-Smith and E. E. Chao},
Journal = {Proc. R. Soc. B},
Year = {1995},
Pages = {1--6},
Volume = {261}
}
@Article{CavalierSmith2018,
Title = {{Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: Contrasting cell organisation of sister phyla Cercozoa and Retaria.}},
Author = {T. Cavalier-Smith and E. E. Chao and R. Lewis},
Journal = {Protoplasma},
Year = {2018},
Abstract = {Harcobia::Alveidia: Ancoracysta; Chlorar incl. Minorisa; other finding support works with Malawimonas an CRUM and/or current OS},
Doi = {10.1007/s00709-018-1241-1},
File = {cavalier-smith2018_rhizaria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29666938}
}
@Article{Cavalier-Smith2016,
Title = {{187-Gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution.}},
Author = {T. Cavalier-Smith and E. E. Chao and R. Lewis},
Journal = {Mol. Phylogenet. Evol.},
Year = {2016},
Pages = {275--296},
Volume = {99},
Abstract = {Cutosea (incl. Squamamoeba, Saprocribum) || Tubil + Discosea },
Doi = {10.1016/j.ympev.2016.03.023},
File = {cavalier-smith2016_cutosea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27001604}
}
@Article{CavalierSmith2015,
Title = {{Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista.}},
Author = {T. Cavalier-Smith and E. E. Chao and R. Lewis},
Journal = {Mol. Phylogenet. Evol.},
Year = {2015},
Pages = {331--362},
Volume = {93},
Abstract = {Centrohel + Hapto incl. Rappephyceae; Cryptista: Rollominadia (Crypto etc.), Palpitia, Corbihelia (Endohelia -- Microheliella, Heliomorpha; Corbistoma -- Picomonas, Telonema, Lateronema)},
Doi = {10.1016/j.ympev.2015.07.004},
File = {cavalier-smith2015_heliozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26234272}
}
@Article{CavalierSmith2014,
Title = {{Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa.}},
Author = {T. Cavalier-Smith and E. E. Chao and E. A. Snell and C. Berney and A. M. Fiore-Donno and R. Lewis},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Pages = {71--85},
Volume = {81C},
Abstract = {Eozoa || Corticates || Malawimonas || Sulcozoa (grade) || other Podiates -- all unstable},
Doi = {10.1016/j.ympev.2014.08.012},
File = {cavalier-smith2014_sulcozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25152275}
}
@Article{CavalierSmith2008b,
Title = {{Planomonadida ord. nov. (Apusozoa): Ultrastructural Affinity with Micronuclearia podoventralis and Deep Divergences within Planomonas gen. nov.}},
Author = {T. Cavalier-Smith and E. E. Chao and A. Stechmann and B. Oates and S. Nikolaev},
Journal = {Protist},
Year = {2008},
Number = {4},
Pages = {535--562},
Volume = {159},
Abstract = {RAxML on 18S: Breviatea + (strong!) Apuso || Planomonadida || Hapto + Centroh; Diphylleia + Micronuclearia || Excavata; Hilomonadea (Plano + Micron) only on the actin tree and weak, but morophology is generally similar; Hemimastigophora probably belong to Thecofilosea; Diphyleia ~ Excavates},
Doi = {doi:10.1016/j.protis.2008.06.002},
File = {cavalier-smith2008b.djvu},
Keywords = {pr1}
}
@Article{CavalierSmith2020,
Title = {{Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).}},
Author = {T. Cavalier-Smith and E. E.-Y. Chao},
Journal = {Protoplasma},
Year = {2020},
Abstract = {Archebacteria: Euryarchaeota and Filarchaeota (Lokiarchaea, Crenarchaeota: Sulfolobia, Nitrososphaeria (Thauma), Korarchaeota); 14 bacterial phyla; do not trust candidatus phyla and environmental groups},
Doi = {10.1007/s00709-019-01442-7},
File = {cavalier-smith2020_bacteria.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31900730}
}
@Article{CavalierSmith2006,
Title = {{Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista)}},
Author = {T. Cavalier-Smith and E. E.-Y. Chao},
Journal = {J. Mol. Evol.},
Year = {2006},
Pages = {388--420},
Volume = {62},
Abstract = {Bigyra: Lab; Bico (Placidiales incl. Wobbia, Borokales, Anoecales incl. Cafeteria, Caecitellus, Bicoecales, Pseudodendromonadales); Opalo (Blasto, Opalino+Protero, Nucleohelea (Actinophryida));; Hypho, Pirsonia, Develop > Oo;; Diato+Bolido; Eust+Picophagea (Picophagus, Chlamydomyxa)+Chromulin(incl. Oiko)+Paraphys+Hibber+Ochro; Raphi; Actino+Pelago; Pingui; Chrysomeridopohyceae+Xantho+Phaeot+Schiz+Phaeophy},
File = {cavalier-smith2006.pdf}
}
@Article{CavalierSmith2003,
Title = {{Molecular Phylogeny of Centrohelid Heliozoa, a Novel Lineage of Bikont Eukaryotes That Arose by Ciliary Loss}},
Author = {T. Cavalier-Smith and E. E.-Y. Chao},
Journal = {J. Mol. Evol.},
Year = {2003},
Pages = {387--396},
Volume = {56},
Abstract = {Centroh || Hapto},
Doi = {10.1007/s00239-002-2409-y},
File = {cavalier-smith2003a.pdf}
}
@Article{CavalierSmith2003b,
Title = {{Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution}},
Author = {T. Cavalier-Smith and E. E.-Y. Chao},
Journal = {J. Mol. Evol.},
Year = {2003},
Pages = {540--563},
Volume = {56},
Abstract = {Ministeria || Choano, Demosp+Hexac ! Calcisp, Paramyx -> Ascetosp, Radiol + Foram = Retaria},
Doi = {10.1007/s00239-002-2424-z},
File = {cavalier-smith2003b.pdf}
}
@Article{CavalierSmith2003d,
Title = {{Phylogeny and Classification of Phylum Cercozoa (Protozoa)}},
Author = {T. Cavalier-Smith and E. E.-Y. Chao},
Journal = {Protist},
Year = {2003},
Pages = {341--358},
Volume = {154},
Abstract = {Metopion || Chlorarachn. (incl. in Cerco); Thecofilosea: Testofilosida \& Cryomonadida; 5.8 Filosa \& Endomyxa; Commation \& Vampyrellida -- Protista i.s.},
File = {cavalier-smith2003d.pdf}
}
@Article{CavalierSmith2004a,
Title = {{Molecular phylogeny of Amoebozoa and the evolutionary signifcance of the unikont Phalansterium}},
Author = {T. Cavalier-Smith and E. E.-Y. Chao and B. Oates},
Journal = {Eur. J. Protistol.},
Year = {2004},
Pages = {21--48},
Volume = {40}
}
@Article{Cavalier-Smith2015a,
Title = {{Multigene phylogeny resolves deep branching of Amoebozoa.}},
Author = {T. Cavalier-Smith and A. M. Fiore-Donno and E. Chao and A. Kudryavtsev and C. Berney and E. A. Snell and R. Lewis},
Journal = {Mol. Phylogenet. Evol.},
Year = {2015},
Pages = {293--304},
Volume = {83},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2014.08.011},
File = {cavalier-smith2015_amoebozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25150787}
}
@Article{Cavalier-Smith2014b,
Title = {{Multigene phylogeny resolves deep branching of Amoebozoa}},
Author = {T. Cavalier-Smith and A. M. Fiore-Donno and E. Chao and A. Kudryavtsev and C. Berney and E. A. Snell and R. Lewis},
Journal = {Molecular Phylogenetics and Evolution},
Year = {2014},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2014.08.011},
File = {cavalier-smith2014_amoebozoa.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2014.08.011}
}
@Article{CavalierSmith2007,
Title = {{Molecular phylogeny, scale evolution and taxonomy of centrohelid Heliozoa}},
Author = {T. Cavalier-Smith and S. von der Heyden},
Journal = {Mol. Phyl. Evol.},
Year = {2007},
Number = {3},
Pages = {1186--1203},
Volume = {44},
Abstract = {support for Centro + Hapto; Luffi ~ Centro?},
File = {cavalier-smith2007.pdf}
}
@Article{CavalierSmith2011,
Title = {{Paracercomonas Kinetid Ultrastructure, Origins of the Body Plan of Cercomonadida, and Cytoskeleton Evolution in Cercozoa}},
Author = {T. Cavalier-Smith and S. A. Karpov},
Journal = {Protist},
Year = {2011},
Abstract = {"Tremulida" -> Skiomonadea, "Thecofilosea" -> Ventrifilosea; some analogies with chromists and plants},
Doi = {10.1016/j.protis.2011.06},
File = {cavalier-smith2011_paracercomonas.djvu}
}
@Article{CavalierSmith2009c,
Title = {{Helkesimastix marina n. Sp. (Cercozoa: Sainouroidea superfam. N.) A gliding zooflagellate of novel ultrastructure and unusual ciliary behaviour}},
Author = {T. Cavalier-Smith and R. Lewis and E. E. Chao and B. Oates and D. Bass},
Journal = {Protist},
Year = {2009},
Number = {3},
Pages = {452--479},
Volume = {160},
Abstract = {Metro || Chlorar || Granofil (Nanofila, Massist, Desmo) || Sarcomonadea (Metop., Cerco, Panso, Glisso) || Theco + Spongo + Thaumat + Eugly. High diversity of Cerc -> Hemimast. are there?},
Doi = {10.1016/j.protis.2009.03.003},
File = {cavalier-smith2009_helkesimastix.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19523874}
}
@Article{CavalierSmith2008a,
Title = {{Morphology and Phylogeny of Sainouron acronematica sp. n. and the Ultrastructural Unity of Cercozoa}},
Author = {T. Cavalier-Smith and R. Lewis and E. E. Chao and B. Oates and D. Bass},
Journal = {Protist},
Year = {2008},
Number = {4},
Pages = {591--620},
Volume = {159},
Abstract = {Metromonas || Chlorar + Proteomyx || Metopion || Cercomonadidae || other Cerc. (inc. Sainouridae) || Thecofilosea || Imbricatea},
Doi = {10.1016/j.protis.2008.04.002},
File = {cavalier-smith2008.pdf}
}
@Article{CavalierSmith2008c,
Title = {{The Zooflagellates Stephanopogon and Percolomonas are a Clade (Class Percolatea: Phylum Percolozoa)}},
Author = {T. Cavalier-Smith and S. Nikolaev},
Journal = {Int. J. Euk. Microbiol.},
Year = {2008},
Number = {6},
Pages = {501--509},
Volume = {55},
Abstract = {Percolozoa: Tetramitia incl. Lyro, Percolo (incl. Stephanopogon), Heterolo; Pharyngomonada incl. Pharyngomonas (Trichomastix) and 'Macropharyngomonas'. Gamma- and covarion-corrected trees show some supp. for Andaluc + Malaw + Jacob; Breviat ~ Excav; Apusom ~ Amoebozoa},
Doi = {10.1111/j.1550-7408.2008.00356.x},
File = {cavalier-smith2008b.pdf}
}
@Article{CavalierSmith2012c,
Title = {{Ultrastructure of Allapsa vibrans and the Body Plan of Glissomonadida (Cercozoa).}},
Author = {T. Cavalier-Smith and B. Oates},
Journal = {Protist},
Year = {2012},
Number = {2},
Pages = {165--187},
Volume = {163},
Abstract = {Metromonadea: Metopion, Micrimetopion, and Metromonas, Kitoksia; Sarcomonadea: Cercomonadida, Glissomonadida, Pansomonadida},
Doi = {10.1016/j.protis.2011.10.006},
File = {cavalier-smith2012_allapsa_glissomonadida.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22209009}
}
@Article{Cenci2018,
Title = {{Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids.}},
Author = {U. Cenci and S. J. Sibbald and B. A. Curtis and R. Kamikawa and L. Eme and D. Moog and B. Henrissat and E. Mar{\'e}chal and M. Chabi and C. Djemiel and A. J. Roger and E. Kim and J. M. Archibald},
Journal = {BMC Biol.},
Year = {2018},
Number = {1},
Pages = {137},
Volume = {16},
Abstract = {(Rhodophyta || Cryptista! || Glauco + Chloro) || Haptista || SAR => Chromobionta | Hacrobia | Chlorob},
Doi = {10.1186/s12915-018-0593-5},
File = {cenci2018_goniomonas_genome_close_archaeplastida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30482182}
}
@Article{Cepicka2010a,
Title = {{Rhizomastix biflagellata sp. nov., A new amoeboflagellate of uncertain phylogenetic position isolated from frogs}},
Author = {I. Cepicka},
Journal = {European Journal of Protistology},
Year = {2010},
Abstract = {~ Archamoebae (?, no electron micriscopy or molecular data)},
Doi = {10.1016/j.ejop.2010.08.004},
File = {cepicka2010_rhizomastix.pdf},
ISSN = {0932-4739},
Url = {http://dx.doi.org/10.1016/j.ejop.2010.08.004}
}
@Article{Cepicka2010b,
Title = {{Critical Taxonomic Revision of Parabasalids with Description of one new Genus and three new Species.}},
Author = {I. Cepicka and V. Hampl and J. Kulda},
Journal = {Protist},
Year = {2010},
Abstract = {Hypotrichomonadea, Trichomonadea, Tritrichomonadea, Cristamonadea, Trichonymphea, and Spirotrichonymphea},
Doi = {10.1016/j.protis.2009.11.005},
File = {cepicka2010_parabasalida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20093080}
}
@Article{Cepicka2008,
Title = {{Non-monophyly of Retortamonadida and high genetic diversity of the genus Chilomastix suggested by analysis of SSU rDNA}},
Author = {I. Cepicka and M. Kostka and M. Uzlikova and J. Kulda and J. Flegr},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {2},
Pages = {770--775},
Volume = {48},
Abstract = {Fornicata: Carpediemonas || Dysnectes || Chilomonas || Retotamonas || Giardia || others},
Doi = {doi:10.1016/j.ympev.2008.04.036},
File = {cepicka2008.pdf}
}
@Article{Chambouvet2019,
Title = {{Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi.}},
Author = {A. Chambouvet and A. Monier and F. Maguire and S. Ito{\"i}z and J. Del Campo and P. Elies and B. Edvardsen and W. Eikreim and T. A. Richards},
Journal = {Current biology : CB},
Year = {2019},
Number = {23},
Pages = {4093 - 4101 - e4},
Volume = {29},
Abstract = {NCLC1 sister to Rozella},
Doi = {10.1016/j.cub.2019.09.074},
File = {chambouvet2019_nclc1_rozell.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31735677}
}
@Article{Chan2011,
Title = {{Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes}},
Author = {C. X. Chan},
Journal = {Current Biology},
Year = {2011},
Pages = {1--6},
Volume = {21},
Abstract = {Support for red + green},
Doi = {10.1016/j.cub.2011.01.037},
File = {chan2011_red_green_algae.pdf},
ISSN = {0960-9822},
Url = {http://dx.doi.org/10.1016/j.cub.2011.01.037}
}
@InProceedings{Chan2005,
Title = {{A more accurate and efficient whole genome phylogeny}},
Author = {P. Y. Chan and T. W. Lam and S. M. Yiu and C. M. Liu},
Booktitle = {Proceedings of the 4th Asia-Pacific Bioinformatics Conference},
Year = {2005},
Pages = {1--15},
File = {chan2005.pdf}
}
@Article{Chang2020,
Title = {{Plastome structure and phylogeny of Gnetum luofuense C.Y. Cheng (Gnetaceae, Gnetales)}},
Author = {A. C. G. Chang and M. A. C. Bautista and Y. Zheng and T. Wan and T. Chen},
Journal = {Mitochondrial DNA Part B},
Year = {2020},
Number = {3},
Pages = {3387 - 3388},
Volume = {5},
Doi = {10.1080/23802359.2020.1821818},
File = {chang2020_gnetum_luofuense_plastome_gnetifer.pdf},
Keywords = {gnetifer}
}
@Article{Chang2015,
Title = {{Genomic insights into the evolutionary origin of Myxozoa within Cnidaria}},
Author = {E. S. Chang and M. Neuhof and N. D. Rubinstein and A. Diamant and H. Philippe and D. Huchon},
Journal = {PNAS},
Year = {2015},
Abstract = {(Octocorallia, Hexacorallia) | ([Myxozoa: Polypodium | Tetr. + Budd. | rest] (Hydrozoa (Cubozoa, Scyphozoa)))},
Doi = {10.1073/pnas.1511468112},
File = {chang2015_myxozoa.pdf},
Url = {http://dx.doi.org/10.1073/pnas.1511468112}
}
@Article{Chang2017,
Title = {{Taxonomic revision of Dictyochales (Dictyochophyceae) based on morphological, ultrastructural, biochemical and molecular data}},
Author = {F. H. Chang and J. Sutherland and J. Bradford-Grieve},
Journal = {Phycological Research},
Year = {2017},
Pages = {235 - 247},
Volume = {65},
Abstract = {Review woth photo},
Doi = {10.1111/pre.12181},
File = {ekanayaka2017_discomycetes.pdf}
}
@Article{Chang2013,
Title = {{Patterns of clade support across the major lineages of moss phylogeny}},
Author = {Y. Chang and S. W. Graham},
Journal = {Cladistics},
Year = {2013},
Pages = {1--17},
Abstract = {Takak | Sphagn | Andr || Oedip | Polytr , Tetraphid || Bryopsida},
Doi = {10.1111/cla.12066},
File = {chang2014_clade_support_mosses.pdf}
}
@Article{Chang2011,
Title = {{Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set}},
Author = {Y. Chang and S. W. Graham},
Journal = {American Journal of Botany},
Year = {2011},
Number = {5},
Pages = {839--849},
Volume = {98},
Doi = {10.3732/ajb.0900384},
File = {chang2011_mosses.pdf},
Keywords = {Hep || (Tak || Sph || Andr || Oed || Atri || Bux || others) || Ant || Lycop || Pter || Sperm},
Url = {http://www.amjbot.org/}
}
@InProceedings{Chang2009,
Title = {{Inference of higher-order relationships in Bryophyta from multiple plastid genes}},
Author = {Y. Chang and S. W. Graham},
Booktitle = {{Botany and Mycology 2009. Snowbird, Utah, July 25-29. Abstracts}},
Year = {2009},
Abstract = {Takakia (Takakiopsida) as sister group of all other mosses. The remaining successive sister-group splits are respectively represented by: (i) Sphagnopsida, (ii) a clade comprising Andreaea and Andreaeobryum (Andreaeopsida and Andreaeobryopsida), and (iii) Oedipodum (Oedipodiopsida). The relative positions of Polytrichopsida, Tetraphidopsida and Bryopsida remain less well supported},
File = {chang2009_bryophyta.txt}
}
@Article{Chang2021,
Title = {{Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi}},
Author = {Y. Chang and D. Rochon and S. Sekimoto and Y. Wang and M. Chovatia and L. Sandor and A. Salamov and I. V. Grigoriev and J. E. Stajich and J. W. Spatafora},
Journal = {Scientific Reports},
Year = {2021},
Volume = {6},
Abstract = {Olpidium || Kicx},
Doi = {10.1038/s41598-021-82607-4},
File = {chang2021_oplidium_sister_to_non_zoosp_fungi.pdf},
ISSN = {2045-2322}
}
@Article{Chang2015a,
Title = {{Phylogenomic analyses indicate that early fungi evolved digesting cell walls of algal ancestors of land plants.}},
Author = {Y. Chang and S. Wang and S. Sekimoto and A. Aerts and C. Choi and A. Clum and K. LaButti and E. Lindquist and C. Y. Ngan and R. A. Ohm and A. Salamov and I. V. Grigoriev and J. W. Spatafora and M. Berbee},
Journal = {Genome Biol Evol},
Year = {2015},
Abstract = {Zygomycota I: Coemansia, Conidiobolus and II: others incl. Glomerulomycota},
Doi = {10.1093/gbe/evv090},
File = {chang2015_fungi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25977457}
}
@Article{Changa2013,
Title = {{Patterns of clade support across the major lineages of moss phylogeny}},
Author = {Y. Changa and S. W. Grahama},
Journal = {Cladistics},
Year = {2013},
Pages = {1--17},
Abstract = {Takak || Sph || Andr. all || Oedip || Polytr || ?Tetraph || Bryopsida: Buxba || Diphys || others},
Doi = {10.1111/cla.12066},
File = {chang2013_mosses.pdf}
}
@Article{Chantangsi2008,
Title = {{Morphology and molecular phylogeny of a marine interstitial tetraflagellate with putative endosymbionts: Auranticordis quadriverberis n. gen. et sp. (Cercozoa).}},
Author = {C. Chantangsi and H. J. Esson and B. S. Leander},
Journal = {BMC Microbiol.},
Year = {2008},
Number = {1},
Pages = {123},
Volume = {8},
Abstract = {Proteomyx || Cryomon, Ebrii || Auranticordis + Pseudopirsonia || Thaumato || Cerco + Euglyph},
Doi = {10.1186/1471-2180-8-123},
File = {chantangsi2008.djvu}
}
@Article{Chantangsi2010,
Title = {{Evolutionary Relationships among Marine Cercozoans as Inferred from Combined SSU and LSU rDNA Sequences and Polyubiquitin Insertions}},
Author = {C. Chantangsi and M. Hoppenrath and B. S. Leander},
Journal = {Molecular phylogenetics and evolution},
Year = {2010},
Abstract = {(Plasm + Phago) + (Gromii + Asceto) || Filosea: Chlorar || Metro || Metopi || Granofilosea (Desmo, Massis, Limnoph, Mesoph) || Cerco (Glisso, Panso, Helkesi, Claut, Aurant, Discomonas, Sain)|| Eugly || Thaum || Ventrifissuridae || Verrucomonanidae || Botuliformidae, Ebri + Cryo},
Doi = {10.1016/j.ympev.2010.07.007},
File = {chantangsi2010_cercozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20654723}
}
@Article{Chantangsi2009,
Title = {{An SSU rDNA Barcoding Approach to the Diversity of Marine Interstitial Cercozoans, including Descriptions of Four Novel Genera and Nine Novel Species}},
Author = {C. Chantangsi and B. S. Leander},
Journal = {IJSEM},
Year = {In press},
Volume = {11},
Abstract = {Cryomonadida, Botuliforma, Ebria + Spongom, Metopion, Discimonadidae, Verrucomonadidae, Ventrifissuridae},
Doi = {10.1099/ijs.0.013888-0},
File = {chantangsi2009_cercozoa.pdf}
}
@Article{Chantangsi2009b,
Title = {{Ultrastructure, Life Cycle and Molecular Phylogenetic Position of a Novel Marine Sand-Dwelling Cercozoan: Clautriavia biflagellata n. Sp.}},
Author = {C. Chantangsi and B. S. Leander},
Journal = {Protist},
Year = {In press},
Volume = {16},
Abstract = {((Ventrifissuridae || Thauma || Eugly || Clautiriavia || Pseudopirs + Aurant) + (Verrucomonadidae + Glissomnadidae)) || Pseudodiff || Ebria + Botuliforma || Cryomonadida},
Doi = {10.1016/j.protis.2009.09.001},
File = {chantangsi2009_clautriavia.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2009.09.001}
}
@Book{Chapman1973,
Title = {{The Algae}},
Author = {D. J. Chapman and V. J. Chapman},
Publisher = {McMillan Co. Ltd.},
Year = {1973},
Address = {Glasgow}
}
@Article{Chaw1993,
Title = {{The phylogenetic position of Taxaceae based on 18S rRNA sequences.}},
Author = {S. M. Chaw and H. Long and B. S. Wang and A. Zharkikh and W. H. Li},
Journal = {J. Mol. Evol.},
Year = {1993},
Number = {6},
Pages = {624--630},
Volume = {37}
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@Article{Chaw1995,
Title = {{The phylogenetic positions of the conifer genera \textit{Amentotaxus}, \textit{Phyllocladus}, and \textit{Nageia} inferred from 18S rRNA sequences}},
Author = {S. M. Chaw and H. M. Sung and H. Long and A. Zharkikh and W. H. Li},
Journal = {J. Mol. Evol.},
Year = {1995},
Number = {2},
Pages = {224--230},
Volume = {41}
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@Article{Chaw1997,
Title = {{Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences.}},
Author = {S. M. Chaw and A. Zharkikh and H. M. Sung and T. C. Lau and W. H. Li},
Journal = {Mol. Biol. Evol.},
Year = {1997},
Number = {1},
Pages = {56--68},
Volume = {14}
}
@Article{Chaw2000,
Title = {{Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers}},
Author = {Shu-M. Chaw and C. L. Parkinson and Y. Cheng and T. M. Vincent and J. D. Palmer},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2000},
Number = {8},
Pages = {4086--4091},
Volume = {97}
}
@Article{Chen2004,
Title = {{A new `great-appendage' arthropod from the Lower Cambrian of China and homology of chelicerate chelicerae and raptorial antero-ventral appendages}},
Author = {J. Chen and D. Waloszek and A. Maas},
Journal = {Lethaia},
Year = {2004},
Pages = {3--20},
Volume = {37},
Abstract = {Anomalocarida || Chelicerata},
Doi = {10.1080/00241160410004764},
File = {chen2004.pdf}
}
@Article{Chen2010,
Title = {{A Red-Shifted Chlorophyll}},
Author = {M. Chen and M. Schliep and R. D. Willows and Z.-L. Cai and B. A. Neilan and H. Scheer},
Journal = {Science},
Year = {2010},
Number = {5997},
Pages = {1318--1319},
Volume = {329},
Abstract = {Chlorophyll f in Shark Bay stromatolites cyanobacteria},
Doi = {10.1126/science.1191127},
Eprint = {http://www.sciencemag.org/cgi/reprint/329/5997/1318.pdf},
File = {chen2010_chlorophyll_f.pdf},
Url = {http://www.sciencemag.org/cgi/content/abstract/329/5997/1318}
}
@Article{Cheng2019,
Title = {{Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution}},
Author = {S. Cheng and W. Xian and Y. Fu and B. Marin and J. Keller and T. Wu and W. Sun and X. Li and Y. Xu and Y. Zhang and S. Wittek and T. Reder and G. G{\"u}nther and A. Gontcharov and S. Wang and L. Li and X. Liu and J. Wang and H. Yang and X. Xu and P.-M. Delaux and B. Melkonian and G. K.-S. Wong and M. Melkonian},
Journal = {Cell},
Year = {2019},
Number = {5},
Pages = {1057--1067},
Volume = {179},
Abstract = {Zygnematophyceae incl. Spirogloea },
Doi = {10.1016/j.cell.2019.10.019},
File = {cheng2019_spirogloea_zygn_land_plants_sister.pdf},
ISSN = {0092-8674}
}
@Article{Cheng1999,
Title = {{Phylogeny Of Taxaceae And Cephalotaxaceae Genera Inferred From Chloroplast Mat K Gene And Nuclear Rdna Its Region}},
Author = {Y. Cheng and R. G. Nicolson and K. Tripp and Shu-M. Chaw},
Journal = {Mol. Phyl. Evol.},
Year = {1999},
Pages = {353--365},
Volume = {14}
}
@Article{Chernikova2011,
Title = {{A late origin of the extant eukaryotic diversity: Divergence time estimates using rare genomic changes}},
Author = {D. Chernikova and S. Motamedi and M. Csuros and E. V. Koonin and I. B. Rogozin},
Journal = {Biology Direct},
Year = {2011},
Pages = {26},
Volume = {6},
Abstract = {Two branches: red algae and opis},
Doi = {10.1186/1745-6150-6},
File = {chernikova2011_leca_estimation.djvu},
Url = {http://www.biology-direct.com/content/6/1/26}
}
@PhdThesis{Chernyshev2008,
Title = {{Comparative morphology, taxonomy and phylogeny of nemertines}},
Author = {A. Chernyshev},
School = {Institute of Marine Biology, Vladivostok},
Year = {2008},
Note = {(In Russian)},
Abstract = {Archynchocoela Chernyshev 1995 (Archynchonemertes)},
File = {chernyshev2008.pdf},
Pages = {1--44}
}
@Article{Chernyshev1995,
Title = {About higher taxta of nemertines with the review of subclass Anopla},
Author = {A. V. Chernyshev},
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Title = {{Origin of mitochondria in relation to evolutionary history of eucaryotic alanyl-tRNA synthetase}},
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Year = {2013},
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Pages = {e55499},
Volume = {8},
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File = {chiodin2013_acoelomorpha_mesoderm_unique.pdf},
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@Article{Chipman2014,
Title = {{The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima.}},
Author = {A. D. Chipman and D. E. K. Ferrier and C. Brena and J. Qu and D. S. T. Hughes and R. Schr{\"o}der and M. Torres-Oliva and N. Znassi and H. Jiang and F. C. Almeida and C. R. Alonso and Z. Apostolou and P. Aqrawi and W. Arthur and J. C. J. Barna and K. P. Blankenburg and D. Brites and S. Capella-Guti{\'e}rrez and M. Coyle and P. K. Dearden and L. Du Pasquier and E. J. Duncan and D. Ebert and C. Eibner and G. Erikson and P. D. Evans and C. G. Extavour and L. Francisco and T. Gabald{\'o}n and W. J. Gillis and E. A. Goodwin-Horn and J. E. Green and S. Griffiths-Jones and C. J. P. Grimmelikhuijzen and S. Gubbala and R. Guig{\'o} and Y. Han and F. Hauser and P. Havlak and L. Hayden and S. Helbing and M. Holder and J. H. L. Hui and J. P. Hunn and V. S. Hunnekuhl and L. Jackson and M. Javaid and S. N. Jhangiani and F. M. Jiggins and T. E. Jones and T. S. Kaiser and D. Kalra and N. J. Kenny and V. Korchina and C. L. Kovar and F. B. Kraus and F. Lapraz and S. L. Lee and J. Lv and C. Mandapat and G. Manning and M. Mariotti and R. Mata and T. Mathew and T. Neumann and I. Newsham and D. N. Ngo and M. Ninova and G. Okwuonu and F. Ongeri and W. J. Palmer and S. Patil and P. Patraquim and C. Pham and L.-L. Pu and N. H. Putman and C. Rabouille and O. M. Ramos and A. C. Rhodes and H. E. Robertson and H. M. Robertson and M. Ronshaugen and J. Rozas and N. Saada and A. S{\'a}nchez-Gracia and S. E. Scherer and A. M. Schurko and K. W. Siggens and D. Simmons and A. Stief and E. Stolle and M. J. Telford and K. Tessmar-Raible and R. Thornton and M. van der Zee and A. von Haeseler and J. M. Williams and J. H. Willis and Y. Wu and X. Zou and D. Lawson and D. M. Muzny and K. C. Worley and R. A. Gibbs and M. Akam and S. Richards},
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Year = {2014},
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Pages = {e1002005},
Volume = {12},
Abstract = {Far from Pancrustacea},
Doi = {10.1371/journal.pbio.1002005},
File = {chipman2014_strigamia_myriapod_genome.pdf},
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@Article{Chiu1999,
Title = {{Molecular Evolution of Glutamate Receptors: {A} Primitive Signaling Mechanism that Existed Before Plants and Animals Diverged}},
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Year = {1999},
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Pages = {826--838},
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@Article{Cho2004,
Title = {{\textit{Lentisphaera araneosa} gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae}},
Author = {J.-C. Cho and K. L. Vergin and R. M. Morris and S. J. Giovannoni},
Journal = {Environ. Microbiol.},
Year = {2004},
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Pages = {611--621},
Volume = {6},
Abstract = {Lentisphaerae, ~ Verrumicrobiae},
File = {cho2004.pdf}
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@Article{Choi2017,
Title = {{A genome Tree of Life for the Fungi kingdom.}},
Author = {J. Choi and S.-H. Kim},
Journal = {Proceedings of the National Academy of Sciences of the United States of America},
Year = {2017},
Number = {35},
Pages = {9391 - 9396},
Volume = {114},
Abstract = {Nothing original},
Doi = {10.1073/pnas.1711939114},
File = {choi2017_genome_tol_fungi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17051209}
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@Article{Chong2014,
Title = {{Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species.}},
Author = {J. Chong and C. Jackson and J. I. Kim and H. S. Yoon and A. Reyes-Prieto},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Pages = {181--188},
Volume = {76},
Abstract = {As stated; ~ 7 new species},
Doi = {10.1016/j.ympev.2014.03.019},
File = {chong2014_glaukophyta.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24680917}
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@Article{Choo2007,
Title = {{\textit{Puniceicoccus vermicola} gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ``Verrucomicrobia''}},
Author = {Y.-J. Choo and K. Lee and J. Song and J.-C. Cho},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2007},
Pages = {532--537},
Volume = {57},
Abstract = {Opitutae > Verrumicrobia},
File = {choo2007.pdf}
}
@Article{Chouari2005,
Title = {{Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester}},
Author = {R. Chouari and D. L. Paslier and P. Daegelen and P. Ginestet and J. Weissenbach and A. Sghir},
Journal = {Environ. Microbiol.},
Year = {2005},
Number = {8},
Pages = {1104--1115},
Volume = {7},
Abstract = {Synergistes/OP9/OP8},
File = {chouari2005.pdf}
}
@Article{Christenhusz2018,
Title = {{PPG recognises too many fern genera}},
Author = {M. J. M. Christenhusz and M. W. Chase},
Journal = {TAXON},
Year = {2018},
Doi = {10.12705/673.2},
File = {christenhusz2018_too_many_fern_genera.pdf},
Url = {https://doi.org/10.12705/673.2}
}
@Article{Christenhusz2014,
Title = {{Trends and concepts in fern classification.}},
Author = {M. J. M. Christenhusz and M. W. Chase},
Journal = {Ann. Bot.},
Year = {2014},
Number = {4},
Pages = {571--594},
Volume = {113},
Abstract = {enlarged families},
Doi = {10.1093/aob/mct299},
File = {christenhusz2014_fern_classif.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24532607}
}
@Article{Christenhusz2011,
Title = {{Linear sequence, classification, synonymy, and bibliography of vascular plants: Lycophytes, ferns, gymnosperms and angiosperms}},
Author = {M. J. M. Christenhusz and M. W. Chase and M. F. Fay},
Journal = {Phytotaxa},
Year = {2011},
Pages = {4--134},
Volume = {19},
Abstract = {Cladistic approach},
File = {linear_seq_plant_classif_2011.pdf},
Url = {www.mapress.com/}
}
@Article{Christenhusz2011a,
Title = {{A new classification and linear sequence of extant gymnosperms}},
Author = {M. J. M. Christenhusz and J. L. Reveal and A. Farjon and M. F. Gardner and R. R. Mill and M. W. Chase},
Journal = {Phytotaxa},
Year = {2011},
Pages = {55--70},
Volume = {19},
Abstract = {As stated},
File = {christenhulz2011_linear_seq_gymnosperms.pdf},
Url = {www.mapress.com/}
}
@Article{Christenhusz2011b,
Title = {{A linear sequence of extant families and genera of lycophytes and ferns}},
Author = {M. J. M. Christenhusz and X.-C. Zhang and H. Schneider},
Journal = {Phytotaxa},
Year = {2011},
Pages = {7--54},
Volume = {19},
Abstract = {As stated},
File = {christenhulz2011_linear_seq_ferns.pdf},
Url = {www.mapress.com/}
}
@Article{Christer2020,
Title = {{Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids}},
Author = {E. Christer and W. W. Bronwyn and M. H. Kevin and M. H. Kenneth and R. S. Scott and W. J. Samuel and C. d. C. Michel and E. A. Frank},
Journal = {Zoologica Scripta},
Year = {2020},
Pages = {614--640},
Volume = {49},
Abstract = {Ae_o_losoma and Hrabeiella probably just outside, not yet clear},
Doi = {10.1111/zsc.12426},
File = {erseus2020_clitellata.pdf}
}
@Article{Christoffersen2013,
Title = {{A systematic monograph of the Recent Pentastomida, with a compilation of their hosts}},
Author = {M. L. Christoffersen and J. E. De Assis},
Journal = {Zool. Med. Leiden},
Year = {2013},
Number = {1},
Pages = {1--206},
Volume = {87},
Abstract = {Monograph},
File = {christoffersen2013_zoologische_mededelingen_systematic_monograph_recent_pentastomida.pdf}
}
@Article{Chystyakova2012,
Title = {{Morphology of Mastigamoeba aspera Schulze, 1875 (Archamoebae, Pelobiontida)}},
Author = {L. V. Chystyakova and O. A. Miteva and A. O. Frolov},
Journal = {Cell and Tissue Biology},
Year = {2012},
Number = {2},
Pages = {189--196},
Volume = {6},
Abstract = {As stated},
Doi = {10.1134/S1990519X12020058},
File = {chistyakova2012_mastigamoeba.pdf}
}
@Article{Ciccarelli2006,
Title = {{Toward Automatic Reconstruction of a Highly Resolved Tree of Life}},
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Journal = {Science},
Year = {2006},
Number = {2006},
Pages = {1283--1287},
Volume = {311},
Abstract = {Firmi: Clostr+others, Spiro+Plancto, Acido+Delta. Tree is on itol.org},
Doi = {10.1126/science.1123061},
File = {ciccarelli2006.pdf},
Url = {www.sciencemag.org}
}
@Article{Clark1995,
Title = {{Direct evidence for secondary loss of mitochondria in \textit{Entamoeba histolytica}}},
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@Article{Clay1999,
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Pages = {43--59},
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@Article{Clay1999a,
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@Article{Coats2010,
Title = {{Tintinnophagus acutus n. G., N. Sp. (Phylum Dinoflagellata}},
Author = {D. W. Coats and S. Kim and T. R. Bachvaroff and S. M. Handy and C. F. Delwiche},
Journal = {The Journal of Eukaryotic Microbiology},
Year = {2010},
Abstract = {Just curious ;)},
Doi = {10.1111/j.1550-7408.2010.00504.x},
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@Article{Cocquyt2010a,
Title = {{Complex phylogenetic distribution of a non-canonical genetic code in green algae.}},
Author = {E. Cocquyt and G. H. Gile and F. Leliaert and H. Verbruggen and P. J. Keeling and O. De Clerck},
Journal = {BMC evolutionary biology},
Year = {2010},
Number = {1},
Pages = {327},
Volume = {10},
Abstract = {Smooth transition},
Doi = {10.1186/1471-2148-10-327},
File = {cocquyt2010_nc-gc_green_algae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20977766}
}
@Article{Cocquyt2010b,
Title = {{Evolution and Cytological Diversification of the Green Seaweeds (Ulvophyceae)}},
Author = {E. Cocquyt and H. Verbruggen and F. Leliaert and O. De Clerck},
Journal = {Mol. Biol. Evol.},
Year = {2010},
Number = {9},
Pages = {2052--2061},
Volume = {27},
Abstract = {Bryopsidales, Dasycladales and Chladophorales may evolve independetly from "normal" cell ancestors (Chara also have multinucleate cells)},
Doi = {10.1093/molbev/msq091},
File = {cocquyt2010_ulvophyceae.pdf}
}
@Article{Cocquyt2009b,
Title = {{Phylogeny and diversification of the green algae inferred from nuclear and chloroplast genes}},
Author = {E. Cocquyt and H. Verbruggen and F. Leliaert and O. De Clerck},
Journal = {Phycologia},
Year = {2009},
Number = {4},
Pages = {1--153},
Volume = {48},
Abstract = {monophyly of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC-classes) and reveal a sister relationship between Chlorophyceae and Ulvophyceae},
File = {cockquyt2009_chlorophyta.txt}
}
@Article{Cocquyt2009,
Title = {{Gain and loss of elongation factor genes in green algae}},
Author = {E. Cocquyt and H. Verbruggen and F. Leliaert and F. W. Zechman and K. Sabbe and O. De Clerck},
Journal = {BMC Evolutionary Biology},
Year = {2009},
Pages = {39},
Volume = {9},
Abstract = {Contradictory; Strept + Ulvophyceae (EF-1a); EFL: three prasino (Prasinoc., Nephr., Tetr.), Mesost ~ Nephr., Centroh ~ Prasinoc. and Hapto},
Doi = {10.1186/1471-2148-9-39},
File = {cocquyt2009_ef_genes_green_algae.pdf},
Url = {http://www.biomedcentral.com/1471-2148/9/39}
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@Article{Cohen2012,
Title = {{Rerooting the rDNA gene tree reveals phoronids to be brachiopods without shells; dangers of wide taxon samples in metazoan phylogenetics (Phoronida; Brachiopoda}},
Author = {B. L. Cohen},
Journal = {Zoological Journal of the Linnean Society},
Year = {2012},
Abstract = {As stated},
Doi = {10.1111/j.1096-3642.2012.00869.x},
File = {cohen2012_phoronida_brachiopoda.pdf}
}
@Article{Cohen2000,
Title = {{Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.)}},
Author = {Bernard L. Cohen},
Journal = {Proc. R. Soc. B},
Year = {2000},
Pages = {225--231},
Volume = {267}
}
@Article{Cohen2005,
Title = {{Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian)}},
Author = {B. L. Cohen and A. Weydmann},
Journal = {Org. Divers. Evol.},
Year = {2005},
Pages = {253--273},
Volume = {5},
Abstract = {Brachiopoda: subph. Linguliformea (cl. Craniata, Phoronata, Lingulata) and Rhynchonelliformea (cl. Rhynchonellata); Rh || Ph || Cr || Li},
File = {cohen2005.pdf}
}
@Article{Cole2009,
Title = {{PARVAMOEBA MONOURA, N. SP.: A Description of a New 'Amoebozoan' Isolated from the American Lobster, Homarus americanus}},
Author = {J. Cole and O. R. Anderson and Y. I. Tekle and J. Grant and L. A. Katz and T. Nerad},
Journal = {J. Euk. Microbiol.},
Year = {In press},
Abstract = {Flabellinea || Mayorella, Phalanst, Stenamoeb, Thecamoeb, Balamuth + Acanthop || Parvamoeb + other Tubulinea || Multic, Acram, Filam, Cochliopodium || Archamoebae || Mycetozoa},
Doi = {10.1111/j.1550-7408.2009.00445.x},
File = {cole2009_amoebozoan.pdf}
}
@Article{Coleman2021,
Title = {{A rooted phylogeny resolves early bacterial evolution}},
Author = {G. A. Coleman and A. A. Dav{\'i}n and T. A. Mahendrarajah and L. L. Sz{\'a}nth{\'o} and A. Spang and P. Hugenholtz and G. J. Sz{\"o}llősi and T. A. Williams},
Journal = {Science},
Year = {2021},
Pages = {588},
Volume = {372},
Abstract = {Fuso, DST, Terra: Cyano+Margiulis, Armati+Eremio, Chlorof+Dormi, CPR, Actino, Firmicutes; Gracilicutes: Spiro, Elusi, PVC, FCB, Dependitae, Aquif+Campylo+Deferri, Acido, Nitro, Proteo s.l.},
Doi = {10.1126/science.abe0511},
File = {coleman2021_bacteria_rooted_phylogeny.pdf}
}
@Article{Coleman2020,
Title = {{A rooted phylogeny resolves early bacterial evolution}},
Author = {G. A. Coleman and A. A. Dav{\'i}n and T. Mahendrarajah and A. Spang and P. Hugenholtz and G. J. Sz{\"o}llősi and T. A. Williams},
Journal = {bioRxiv},
Year = {2020},
Abstract = {Fuso, DST (Deino + Synerg + Therm) , Terrabacteria: Cyano + Margulis || Armatimonadota +
Eremiobacterota (WPS-2) || Chloroflexota +
Dormibacterota || CPR || Firmicutes},
Doi = {10.1101/2020.07.15.205187.},
File = {coleman2020_bacteria.pdf}
}
@Article{Colgan2008,
Title = {{Multi-Gene Analyses of the Phylogenetic Relationships among the Mollusca, Annelida, and Arthropoda}},
Author = {D. J. Colgan and P. A. Hutchings and E. Beacham},
Journal = {Zoological Studies},
Year = {2008},
Number = {3},
Pages = {338--351},
Volume = {47},
Abstract = {Support for Chaeto + Ecdysozoa, Brachiopoda > Annelida, Tardigrada > Arthropoda},
File = {colgan2008.pdf},
Url = {http://zoolstud.sinica.edu.tw/Journals/47.3/338.pdf}
}
@Article{Colgan2006,
Title = {{A multigene framework for polychaete phylogenetic studies}},
Author = {D. J. Colgan and P. A. Hutchings and M. Braunea},
Journal = {Org. Divers. Evol.},
Year = {2006},
Number = {2006},
Pages = {220--235},
Volume = {6},
Abstract = {Clitellata, Echiura, Myzo, Sipunc and Phoronis (!) nested within Polych},
File = {colgan2006.pdf}
}
@Article{Collins2002,
Title = {{Phylogeny of Medusozoa and the evolution of cnidarian life cycles}},
Author = {A.G. Collins},
Journal = {J. Evol. Biol.},
Year = {2002},
Pages = {418--432},
Volume = {15}
}
@Article{Collins1998,
Title = {{Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence}},
Author = {A. G. Collins},
Journal = {Proc. Natl. Acad. Sci. USA},
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Pages = {15458--15463},
Volume = {95}
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@Article{Collins2006,
Title = {{Solution to the phylogenetic enigma of Tetraplatia, a worm-shaped cnidarian}},
Author = {A. G. Collins and B. Bentlage and G. I. Matsumoto and S. H. D. Haddock and K. J. Osborn and B. Schierwater},
Journal = {Biol. Lett.},
Year = {2006},
Pages = {120--124},
Volume = {2},
Abstract = {Anthozoa || Staurozoa || Medusozoa},
File = {collins2006b.pdf}
}
@Article{Collins2006b,
Title = {{Medusozoan Phylogeny and Character Evolution Clarified by New Large and Small Subunit rDNA Data and an Assessment of the Utility of Phylogenetic Mixture Models}},
Author = {A. G. Collins and P. S. Chuchert and A. C. M. Arques and T. H. J. Ankowski and M. O. M. Edina and B. E. S. Chierwater},
Journal = {Syst. Biol.},
Year = {2006},
Number = {1},
Pages = {97--115},
Volume = {55},
Abstract = {Antho || Stauromedusae || Cubo+Scypho || Hydro},
File = {collins2006a.pdf}
}
@Article{Colson2011,
Title = {{The Giant Cafeteria roenbergensis Virus That Infects a Widespread Marine Phagocytic Protist Is a New Member of the Fourth Domain of Life}},
Author = {P. Colson and G. Gimenez and M. Boyer and G. Fournous and D. Raoult},
Journal = {Proteins},
Year = {2011},
Number = {4},
Pages = {2011},
Volume = {29},
Abstract = {Fourth domain of Life composed of nucleocytoplasmic large DNA viruses (NCLDVs); crap, viruses are frags of every Big Bang event (A. Mushegjan, pers. comm.)},
Doi = {10.1371/journal.pone.0018935},
File = {colson2011_ncldv.pdf},
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@Article{Comandi2009,
Title = {{The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects}},
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Journal = {Gene},
Year = {2009},
Number = {1 - 2},
Pages = {25--34},
Volume = {439},
Abstract = {Micro || Zygen || Pteryg},
Doi = {10.1016/j.gene.2009.02.020},
File = {comandi2009_zygentoma.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19285124}
}
@Article{ConwayMorris2004,
Title = {{Halwaxiids and the Early Evolution of the Lophotrochozoans}},
Author = {S. Conway-Morris and J.-B. Caron},
Journal = {Science},
Year = {2004},
Pages = {1255--1258},
Volume = {62},
Abstract = {Moll || Anne || Brachio},
File = {conway-morris2007.pdf}
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@Article{Conway1982,
Title = {{The origins and evolution of Acanthocephala}},
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@Conference{Copeland2008,
Title = {{Investigating non-canonical introns of Gregarina niphandrodes}},
Author = {A. Copeland and C. Omoto},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
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@Article{LeCorguill2009,
Title = {{Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: Further insights on the evolution of red-algal derived plastids}},
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Journal = {BMC Evolutionary Biology},
Year = {2009},
Pages = {253},
Volume = {9},
Abstract = {Hapto + Crypto vs. Heterok. plastids},
Doi = {10.1186/1471-2148-9-253},
File = {corguille2009_brown_plastids.pdf},
Url = {http://www.biomedcentral.com/1471-2148/9/253}
}
@Article{Corliss1994,
Title = {{An iterim utilitation [``user-friendly''] hierarchial classification and characterization of protists}},
Author = {J. O. Corliss},
Journal = {Acta Protozool.},
Year = {1994},
Number = {1},
Pages = {1--51},
Volume = {33},
Keywords = {pr1}
}
@Article{Corliss1989,
Title = {{Protistan diversity and origin of multicellular/multitissued organisms}},
Author = {J. O. Corliss},
Journal = {Boll. Zool.},
Year = {1989},
Pages = {227--234},
Volume = {56},
Keywords = {pr1}
}
@Article{Corliss1984,
Title = {{The kingdom Protista and its 45 phyla}},
Author = {J. O. Corliss},
Journal = {BioSystems},
Year = {1984},
Number = {2},
Pages = {87--126},
Volume = {17},
Keywords = {pr1}
}
@Article{Cornell2007,
Title = {{Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi}},
Author = {M. J. Cornell and I. Alam and D. M. Soanes and H. M. Wong and C. Hedeler and N. W. Paton and M. Rattray and S. J. Hubbard and N. J. Talbot and S. G. Oliver},
Journal = {Genome Res.},
Year = {2007},
Pages = {1809--1822},
Volume = {17},
Abstract = {Microsporidia basal, Rhizopus (Mucorales) next},
File = {cornell2007.pdf}
}
@Conference{Corradi2008,
Title = {{High gene order conservation between the mating type locus of Phycomyces blakesleeanus (Zygomycota) and three microsporidian parasites may reveal a fungal like sexual reproduction in the microsporidia and a close evolutionary link with zygomycetes}},
Author = {N. Corradi and D. Akiyoshi and H. Morrison and S. C. Lee and J. Heitman and P. J. Keeling},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {As stated, ~ Phycomyces (Mucorales)},
File = {corradi2008.txt}
}
@Article{Corrad2009,
Title = {{Microsporidia: A journey through radical taxonomical revisions}},
Author = {N. Corradi and P. J. Keeling},
Journal = {Fungal biology},
Year = {In press},
Pages = {1--8},
Abstract = {Review},
Doi = {10.1016/j.fbr.2009.05.001},
File = {corradi2009_microsporidia.pdf},
ISSN = {1749-4613}
}
@InBook{Corsaro2022,
Title = {{Insights into Microsporidia Evolution from Early Diverging Microsporidia}},
Author = {D. Corsaro},
Pages = {71-90},
Year = {2022},
Abstract = {Rozellomycota (Rozellaceae, Paramicrosporidiaceae, Morellosporaceae, Mitosporidiaceae, Nucleophagaceae); Microsporidia (classes Chytridiopsidea, Rudimicrosporea, Eumicrosporea)},
Booktitle = {{Microsporidia}},
File = {corsaro2022_early_div_microsporidia.pdf}
}
@Article{Corsaro2016,
Title = {{Molecular identification of Nucleophaga terricolae sp. Nov. (Rozellomycota), and new insights on the origin of the Microsporidia.}},
Author = {D. Corsaro and R. Michel and J. Walochnik and D. Venditti and K.-D. M{\"u}ller and B. Haur{\"o}der and C. Wylezich},
Journal = {Parasitol. Res.},
Year = {2016},
Abstract = {Aphelidea || (Rosella || Mitosporidium || Nucleophaga || Paramicrosp || micr) + other fungi; Metchnikoviellea (Rudimicrosporea) and Chytridiopsida could be other basal microsp branches},
Doi = {10.1007/s00436-016-5055-9},
File = {corsaro2016_nucleophaga.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27075306}
}
@Article{Corsaro2020,
Title = {{Solving an old enigma: Morellospora saccamoebae gen. Nov., Sp. Nov. (Rozellomycota), a Sphaerita-like parasite of free-living amoebae}},
Author = {D. Corsaro and J. Walochnik and D. Venditti and B. Haur{\"o}der and R. Michel},
Journal = {Parasitology Research},
Year = {2020},
Abstract = {As stated},
Doi = {10.1007/s00436-020-06623-5},
File = {corsaro2020_morellospora_rozell.pdf}
}
@Article{Corsaro2014a,
Title = {{Rediscovery of Nucleophaga amoebae, a novel member of the Rozellomycota.}},
Author = {D. Corsaro and J. Walochnik and D. Venditti and K.-D. M{\"u}ller and B. Haur{\"o}der and R. Michel},
Journal = {Parasitol. Res.},
Year = {2014},
Number = {12},
Pages = {4491--4498},
Volume = {113},
Abstract = {Nuclearidae || Aphelidea || Rozellomycota incl. Rozella, Nucleophaga, Paramicrosporidium || Neocall + Chytr || Blastocl || Olp + Basidiob || other Zygo (grade) || Glome || Dikarya},
Doi = {10.1007/s00436-014-4138-8},
File = {corsaro2014_nucleophaga_rozellomycota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25258042}
}
@Article{Corsaro2014,
Title = {{Microsporidia-like parasites of amoebae belong to the early fungal lineage Rozellomycota.}},
Author = {D. Corsaro and J. Walochnik and D. Venditti and J. Steinmann and K.-D. M{\"u}ller and R. Michel},
Journal = {Parasitol. Res.},
Year = {2014},
Number = {5},
Pages = {1909--1918},
Volume = {113},
Abstract = {Paramicrosporidium; Nuclearia || Aphelidea || Rozellomycota: Rosella + Paramicr + Micr || Blastocl || Neocall + Chytr || others},
Doi = {10.1007/s00436-014-3838-4},
File = {corsaro2014_microsporidia_rozellomycota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24652444}
}
@Article{Corsaro2018,
Title = {{Filling gaps in the microsporidian tree: RDNA phylogeny of Chytridiopsis typographi (Microsporidia: Chytridiopsida).}},
Author = {D. Corsaro and C. Wylezich and D. Venditti and R. Michel and J. Walochnik and R. Wegensteiner},
Journal = {Parasitol. Res.},
Year = {2018},
Abstract = {Rozella || Paramicro || Mitosp || Nucleoph || Chytridiopsis || Metchn || core Microsp},
Doi = {10.1007/s00436-018-6130-1},
File = {corsaro2018_chytridiopsis_microsp.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30421347}
}
@Article{DelCortona2020,
Title = {{Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.}},
Author = {A. Del Cortona and C. J. Jackson and F. Bucchini and M. Van Bel and S. D'hondt and P. {\v S}kaloud and C. F. Delwiche and A. H. Knoll and J. A. Raven and H. Verbruggen and K. Vandepoele and O. De Clerck and F. Leliaert},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2020},
Abstract = {Pedino || Chlorodendro || Chlorellophyceae in monoph. Trebouxiophyceae},
Doi = {10.1073/pnas.1910060117},
File = {del_cortona_2020_green_algae_timetree.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31911467}
}
@Article{Costello2006,
Title = {{Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment}},
Author = {E. K. Costello and S. K. Schmidt},
Journal = {Environ. Microbiol.},
Year = {2006},
Number = {8},
Pages = {1471--1486},
Volume = {8},
Abstract = {A07, C05 > Chloroflexi},
File = {costello2006.pdf}
}
@Article{Cotton2010,
Title = {{Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function}},
Author = {J. A. Cotton and J. O. McInerney},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2010},
Number = {40},
Pages = {17252--17255},
Volume = {107},
Abstract = {As stated},
Doi = {10.1073/pnas.1000265107/-/DCSupplemental},
File = {cotton2010_euk_genes_of_diff_origin.pdf},
Url = {www.pnas.org/lookup/suppl/}
}
@Article{Coudert2012,
Title = {{ASL/LBD phylogeny suggests that genetic mechanisms of root initiation downstream of auxin are distinct in lycophytes and euphyllophytes}},
Author = {Y. Coudert and A. Dievart and G. Droc and P. Gantet},
Journal = {Mol. Biol. Evol.},
Year = {2012},
Abstract = {As stated},
File = {coudert2012_auxin_lycophytes_euphyllophytes.djvu}
}
@Article{Cox2019,
Title = {{Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies}},
Author = {C. J. Cox},
Journal = {Critical Reviews in Plant Sciences},
Year = {2019},
Abstract = {As stated},
Doi = {10.1080/07352689.2018.1482443},
File = {cox2018_land_plant_mol_phyl_hypotheses.pdf},
Url = {https://www.tandfonline.com/loi/bpts20}
}
@Article{Cox2008,
Title = {{The archaebacterial origin of eukaryotes}},
Author = {C. J. Cox and P. G. Foster and R. P. Hirt and S. R. Harris and T. M. Embley},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {51},
Pages = {20356--20361},
Volume = {105},
Abstract = {Archaea paraphyletic (sic!), support for eocyte hypothesis},
Doi = {10647105/DCSupplemental.},
File = {cox2008.pdf},
Keywords = {pr1},
Url = {www.pnas.org/cgi/content/full/}
}
@Article{Cox2004,
Title = {{Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments}},
Author = {C. J. Cox and B. Goffinet and A. J. Shaw and S. B. Boles},
Journal = {Syst. Bot.},
Year = {2004},
Number = {2},
Pages = {234--250},
Volume = {29}
}
@Article{Cox2010,
Title = {{Phytotaxa, Moss diversity: A molecular phylogenetic analysis of genera}},
Author = {C. J. Cox and B. Goffinet and N. J. Wickett and S. B. Boles and A. J. Shaw},
Journal = {Phytotaxa},
Year = {2010},
Pages = {175--195},
Volume = {9},
Abstract = {Takakia | Sphagnum || Andreaea || Tetraphis, Oedipodium, Polytrichaceae | others},
File = {cox2010_moss_genera.pdf},
Url = {www.mapress.com}
}
@Article{Cox2014,
Title = {{Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions}},
Author = {C. J. Cox and B. Li and P. G. Foster and T. M. Embley and P. Civ{\'a}ň},
Journal = {Systematic Biology},
Year = {2014},
Abstract = {Bryophyta monophyletic},
File = {cox2014_land_plants.pdf}
}
@Article{Crandall1986,
Title = {{Morphogenesis, developmental anatomy and bryophyte phylogenetics: contradictions of monophyly}},
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Journal = {J. Bryol.},
Year = {1986},
Pages = {1--23},
Volume = {14}
}
@InCollection{Crandall-Stotler2008,
Title = {{Morphology and classification of the Marchantiophyta}},
Author = {B. Crandall-Stotler and R. E. Stotler and D. G. Long},
Booktitle = {Bryophyte Biology},
Publisher = {Oxford University Press},
Year = {2008},
Address = {Cambridge},
Editor = {B. Goffinet and A. J. Shaw},
Pages = {1--54},
Abstract = {Haplomitriops. incl. Treubia, Marchantiops. incl. Blasia, Jungermanniops. incl. Pellia}
}
@Article{CrandallStotler2009,
Title = {{Phylogeny and classification of the Marchantiophyta}},
Author = {B. Crandall-Stotler and R. E. Stotler and D. G. Long},
Journal = {Edinb. J. Bot.},
Year = {2009},
Number = {1},
Pages = {155--198},
Volume = {66},
Abstract = {Haplom. (incl. Treub.), March. (incl. Blas.), Jungerm. (incl. the rest)},
Doi = {10.1017/S0960428609005393},
File = {crandall-stotler2009_marchantiophyta.pdf},
Keywords = {Classification scheme, family diagnoses, liverworts}
}
@Article{Crane1996,
Title = {{The fossil history of the Gnetales}},
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Year = {1996},
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Pages = {50--57},
Volume = {157}
}
@Article{Crane1997,
Title = {{Diverted development of reproductive organs: a source of morphological innovation in land plants}},
Author = {P. R. Crane and P. Kenrick},
Journal = {Pl. Syst. Evol.},
Year = {1997},
Pages = {161--174},
Volume = {206}
}
@Article{Crane1997a,
Title = {{Problems in cladistic classification: higher-level relationships in land plants}},
Author = {P. R. Crane and P. Kenrick},
Journal = {Aliso},
Year = {1997},
Number = {2},
Pages = {87--104},
Volume = {15}
}
@Article{Criscuolo2011,
Title = {{Large-scale phylogenomic analyses indicate a deep origin of primary plastids within Cyanobacteria}},
Author = {A. Criscuolo and S. Gribaldo},
Journal = {Mol. Biol. Evol.},
Year = {2011},
Abstract = {As stated},
File = {criscuolo2011_origin_plastids_cyanob.pdf}
}
@Article{Takhtajan1966,
Title = {On the Higher Taxa of Embryobionta},
Author = {Cronquist, Arthur and Takhtajan, Armen and Zimmermann, Walter},
Journal = {Taxon},
Year = {1966},
Number = {4},
Pages = {129--134},
Volume = {15},
ISSN = {00400262},
Url = {http://www.jstor.org/stable/1217531}
}
@Article{Csuros2011,
Title = {{A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes}},
Author = {M. Csuros and I. B. Rogozin and E. V. Koonin},
Journal = {PLoS Computational Biology},
Year = {2011},
Number = {9},
Pages = {e1002150},
Volume = {7},
Abstract = {Plants and Chromista separate, Unikonta},
Doi = {10.1371/journal.pcbi.1002150},
File = {csuros2011_introns_euk_phyl.pdf}
}
@Article{Cui2020,
Title = {{A novel bacterial phylum that participates in carbon and osmolyte cycling in the Challenger Deep sediments}},
Author = {G. Cui and Y. Zhou and W. Li and Z. Gao and J. Huang and Y. Wang},
Journal = {Environ. Microbiol.},
Year = {2020},
Abstract = {Tianyabacteria ~ Marinimicrobia},
Doi = {10.1111/1462-2920.15363},
File = {cui2020_tianyabacteria_fcb.pdf}
}
@Article{Cunha2019,
Title = {{A congruent topology for deep gastropod relationships.}},
Author = {T. J. Cunha and G. Giribet},
Journal = {Proc. Biol. Sci.},
Year = {2019},
Number = {1898},
Pages = {20182776},
Volume = {286},
Abstract = {Ceph || Bivalv || Scaph || Gastr},
Doi = {10.1098/rspb.2018.2776},
File = {cunha2019_deep_gastropod_relationships.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30862305}
}
@Article{daCunha2022,
Title = {{The expanding Asgard archaea and their elusive relationships with Eukarya}},
Author = {V. da Cunha and M. Ga{\"i}a and P. Forterre},
Journal = {mLife},
Year = {2022},
Abstract = {Lokiarcheia (~ 10 groups) and Heimdallarcheia (~ 6 groups)},
Doi = {10.1002/mlf2.12012},
File = {da_cunha_2022_the_expanding_asgard_archaea.pdf}
}
@Article{Cunha2017,
Title = {{Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes.}},
Author = {V. D. Cunha and M. Gaia and D. Gadelle and A. Nasir and P. Forterre},
Journal = {PLoS Genet.},
Year = {2017},
Number = {6},
Pages = {e1006810},
Volume = {13},
Abstract = {Asgard superphulym sister to Euryarchaeota},
Doi = {10.1371/journal.pgen.1006810},
File = {dacunha2017_lokiarchaea_are_euryarchaeota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18274537}
}
@Article{Cunha2018,
Title = {{Asgard archaea do not close the debate about the universal tree of life topology.}},
Author = {V. D. Cunha and M. Gaia and A. Nasir and P. Forterre},
Journal = {PLoS Genet.},
Year = {2018},
Number = {3},
Pages = {e1007215},
Volume = {14},
Abstract = {Contradictory signals; Asgard sister to Euryarchaeota},
Doi = {10.1371/journal.pgen.1007215},
File = {dacunha2018_asgard_archaea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25977477}
}
@Article{Cuvelier2008,
Title = {{Widespread distribution of a unique marine protistan lineage}},
Author = {M. L. Cuvelier and A. Ortiz and E. Kim and H. Moehlig and D. E. Richardson and J. F. Heidelberg and J. M. Archibald and A. Z. Worden},
Journal = {Environ. Microbiol.},
Year = {2008},
Number = {6},
Pages = {1621--1634},
Volume = {10},
Abstract = {Glauco || "Biliphytes" (incl. "Picobiliphytes") ||| Katableph ||| Crypto},
Doi = {10.1111/j.1462-2920.2008.01580.x},
File = {cuvelier2008.pdf}
}
@Article{Czaker2011,
Title = {{Dicyemid's dilemma: Structure versus genes. The unorthodox structure of dicyemid reproductio}},
Author = {R. Czaker},
Journal = {Cell Tissue Res},
Year = {2011},
Volume = {17},
Abstract = {In favor to chimaera hypothesis},
Doi = {10.1007/s00441-010-1124-z},
File = {czaker2011_dicyemid_fertilization.pdf}
}
@Article{Czuros2008,
Title = {{Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum likelihood approach}},
Author = {M. Czuros and I. B. Rogozin and E. V. Koonin},
Journal = {Mol. Biol. Evol.},
Year = {2008},
Number = {5},
Pages = {903--911},
Volume = {25},
Abstract = {As stated},
Doi = {doi:10.1093/molbev/msn039},
File = {czuros2008.pdf}
}
@Article{Dacks2002,
Title = {{Analyses of RNA Polymerase II Genes from Free-Living Protists: Phylogeny, Long Branch Attraction, and the Eukaryotic Big Bang}},
Author = {Joel B. Dacks and Alexandra Marinets and W. Ford Doolittle and Thomas Cavalier-Smith and John M. Logsdon, Jr},
Journal = {Mol. Biol. Evol.},
Year = {2002},
Pages = {830--840},
Volume = {19}
}
@Article{Dacks2007,
Title = {{Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution}},
Author = {J. B. Dacks and P. P. Poon and M. C. Field},
Journal = {Proc. Natl. Acad. Sci. USAs},
Year = {2007},
Number = {2},
Pages = {588--593},
Volume = {105},
Abstract = {Some endocytic features developed after eukaryote origin},
File = {dacks2008.pdf}
}
@Article{Dagan2010,
Title = {{Genome networks root the tree of life between prokaryotic domains}},
Author = {T. Dagan and M. Roettger and D. Bryant and W. Martin},
Journal = {Genome Biology and Evolution},
Year = {2010},
Abstract = {As stated; Cyano and Actino close to root, epsilon are most distant from other Proteo},
Doi = {10.1093/gbe/evq025},
File = {dagan2010_prok_root.pdf}
}
@Article{Dallai2010,
Title = {{Sperm accessory microtubules suggest the placement of Diplura as the sister-group of Insecta s.s.}},
Author = {R. Dallai and D. Mercati and A. Carapelli and F. Nardi and R. Machida and K. Sekiya and F. Frati},
Journal = {Arthropod Structure \& Development},
Year = {2010},
Abstract = {As stated},
File = {dallai2010_diplura.djvu}
}
@Article{Daly2007,
Title = {{The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus}},
Author = {M. Daly and M. R. Brugler and P. Cartwright and A. G. Collins and M. N. Dawson and D. G. Fautin and S. C. France and C. S. Mcfadden and D. M. Opresko and E. Rodriguez and S. L. Romano and J. L. Stake},
Journal = {Zootaxa},
Year = {2007},
Pages = {127--182},
Volume = {1668},
Abstract = {Antho || ((Cubo, Hydro, Scypho) || Stauro); Polypodium not listed},
File = {daly2007.pdf}
}
@Article{vanDam2009,
Title = {{Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi}},
Author = {T. J. P. van Dam and H. Rehmann and J. L. Bos and B. Snel},
Journal = {Cell. Signal.},
Year = {2009},
Number = {11},
Pages = {1579--1585},
Volume = {21},
Abstract = {Support for Unikonta},
Doi = {10.1016/j.cellsig.2009.06.004},
File = {vandam2009_cdc25_opisthokonta.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19567266}
}
@Article{Damste2007,
Title = {{Structural characterization of diabolic acid-based tetraester, tetraether and mixed ether/ester, membrane-spanning lipids of bacteria from the order Thermotogales}},
Author = {J. S. S. Damste and W. I. C. Rijpstra and E. C. Hopmans and S. Schouten and M. Balk and A. J. M. Stams},
Journal = {Arch. Microbiol.},
Year = {2007},
Number = {6},
Pages = {629--641},
Volume = {188},
Abstract = {Very basal and unusual},
Doi = {10.1007/s00203-007-0284-z},
File = {damste2008.pdf}
}
@Article{Danczak2017,
Title = {{Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities.}},
Author = {R. E. Danczak and M. D. Johnston and C. Kenah and M. Slattery and K. C. Wrighton and M. J. Wilkins},
Journal = {Microbiome},
Year = {2017},
Number = {1},
Pages = {112},
Volume = {5},
Abstract = {Fig. 3 is a candidate phyla radiation tree},
Doi = {10.1186/s40168-017-0331-1},
File = {danczak2017_candidate_phyla_radiation_ohio.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27572647}
}
@Article{Daniels2009,
Title = {{Identification of a crenarchaeal orthologue of Elf1: Implications for chromatin and transcription in Archaea}},
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Journal = {Biol. Direct},
Year = {2009},
Number = {1},
Pages = {24},
Volume = {4},
Abstract = {As stated},
Doi = {10.1186/1745-6150-4-24},
File = {daniels2009_archaea_ef1.pdf}
}
@Article{Daugbjerg1997,
Title = {{Phylogenetic analyses of the rbcL sequences from haptophytes and heterokont algae suggest their chloroplasts are unrelated.}},
Author = {N. Daugbjerg and R. A. Andersen},
Journal = {Mol. Biol. Evol.},
Year = {1997},
Number = {12},
Pages = {1242--1251},
Volume = {14}
}
@Article{David2011,
Title = {{Rapid evolutionary innovation during an Archaean genetic expansion}},
Author = {L. A. David and E. J. Alm},
Journal = {Nature},
Year = {2011},
Number = {7328},
Pages = {93--96},
Volume = {469},
Abstract = {As stated},
Doi = {10.1038/nature09649},
File = {david2010_archaean_gene_expansion.pdf},
ISSN = {0028-0836}
}
@Article{Davis2013,
Title = {{The Genomes of the Erysipelotrichia Clarify the Firmicute Origin of the Mollicutes.}},
Author = {J. J. Davis and F. Xia and R. A. Overbeek and G. J. Olsen},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2013},
Abstract = {To Firmicutes},
Doi = {10.1099/ijs.0.048983-0},
File = {davis2013_mollucites_firmicutes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23606477}
}
@Article{Davis2010,
Title = {{Many hexapod groups originated earlier and withstood extinction events better than previously realized: Inferences from supertrees.}},
Author = {R. B. Davis and S. L. Baldauf and P. J. Mayhew},
Journal = {Proceedings. Biological sciences / The Royal Society},
Year = {2010},
Abstract = {Collembola in},
Doi = {10.1098/rspb.2009.2299},
File = {davis2010_hexapods.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20129983}
}
@Article{Deasey1982,
Title = {{Spore Formation by the Cellular Slime Mold Fonticula alba}},
Author = {M. C. Deasey},
Journal = {Mycologia},
Year = {1982},
Number = {4},
Pages = {607--613},
Volume = {74},
Abstract = {discoid cristae},
File = {deasey1982_fonticula_spores.pdf},
Url = {http://www.jstor.org/stable/3792748}
}
@Article{Decelle2011,
Title = {{Molecular Phylogeny and Morphological Evolution of the Acantharia (Radiolaria).}},
Author = {J. Decelle and N. Suzuki and F. Mah{\'e} and C. de Vargas and F. Not},
Journal = {Protist},
Year = {2011},
Abstract = {New tree},
Doi = {10.1016/j.protis.2011.10.002},
File = {decelle2011_acantharia.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22154393}
}
@Article{Dedysh2018,
Title = {{Refining the taxonomic structure of the phylum Acidobacteria}},
Author = {S. N. Dedysh and P. Yilmaz},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2018},
Abstract = {Classes: Acidobacteriia , Blastocatellia, Holophagae now + Vicinamibacteria and Thermoanaerobaculia (Solibacteres was not in a paper)},
Doi = {10.1099/ijsem.0.003062},
File = {dedysh2018_acidobacteria.txt},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30325293}
}
@Article{Dee2015,
Title = {{Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi.}},
Author = {J. Dee and M. R. N. Mollicone and J. E. Longcore and R. W. Roberson and M. Berbee},
Journal = {Mycologia},
Year = {2015},
Abstract = {As stated},
Doi = {10.3852/14-275},
File = {dee2015_monoblepharidiomycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25911696}
}
@Article{Deeds2005,
Title = {{Prokaryotic phylogenies inferred from protein structural domains}},
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Journal = {Genome Res.},
Year = {2005},
Pages = {393--402},
Volume = {15}
}
@Article{Delarbre1990,
Title = {{The Complete Nucleotide Sequence of the Mitochondrial DNA of the Agnathan \textit{Lampetra fluviatilis}: Bearings on the Phylogeny of Cyclostomes}},
Author = {C. Delarbre and H. Escriva and C. Gallut and V. Barriel and P. Kourilsky and P. Janvier and V. Laudet and G. Gachelin},
Journal = {Mol. Biol. Evol.},
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Pages = {519--529},
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@Article{Torre2006,
Title = {{ESTimating plant phylogeny: lessons from partitioning}},
Author = {J. E. Delatorre and M. G. Egan and M. S. Katari and E. D. Brenner and D. W. Stevenson and G. M. Coruzzi and R. DeSalle},
Journal = {BMC Evol. Biol.},
Year = {2006},
Number = {48},
Pages = {1--15},
Volume = {6},
Abstract = {Gnepine},
File = {delatorre2006.pdf}
}
@InCollection{Delflandre1952,
Title = {{Classe des Ebriedines}},
Author = {G. Delflandre},
Booktitle = {Traite de Zoologie},
Publisher = {Masson et Co.},
Year = {1952},
Address = {Paris},
Pages = {407--424}
}
@Article{Delgado2000,
Title = {{Molecular Phylogeny of Parabasalids Based on Small Subunit rRNA Sequences, with Emphasis on the Trichomonadinae Subfamily}},
Author = {P. Delgado-Viscogliosi and E. Viscogliosi and D. Gerbod and M. L. Sogin and V. P. Edgcomb and J. Kulda},
Journal = {J. Euk. Microbiol.},
Year = {2000},
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Pages = {70--75},
Volume = {47}
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@Article{Deline2018,
Title = {{Evolution of metazoan morphological disparity.}},
Author = {B. Deline and J. M. Greenwood and J. W. Clark and M. N. Puttick and K. J. Peterson and P. C. J. Donoghue},
Journal = {Proceedings of the National Academy of Sciences of the United States of America},
Year = {2018},
Number = {38},
Pages = {E8909--E8918},
Volume = {115},
Doi = {10.1073/pnas.1810575115},
File = {deline2018_metazoa_morph_dispar.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19106296}
}
@Article{DellAmpio2008,
Title = {{Testing for misleading effects in the phylogenetic reconstruction of ancient lineages of hexapods: influence of character dependence and character choice in analyses of 28S rRNA sequences}},
Author = {E. Dell'Ampio and N. U. Szucsich and A. Carapelli and F. Frati and G. Steiner and A. Steinacher and G. N. Pass},
Journal = {Zoologica Scripta},
Year = {2008},
Number = {2},
Pages = {155--170},
Volume = {38},
Abstract = {28S: sometimes Diplura and Protura (Nonoculata) separated from other Hexa, if select only core -- monophyl. Hexa: Branchiopoda || Insecta || Entognatha (Nonoculata + Collembola)},
Doi = {10.1111/j.1463-6409.2008.00368.x},
File = {dellampio2008.pdf}
}
@Article{Dellaporta2006,
Title = {{Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum}},
Author = {S. L. Dellaporta and A. Xu and S. Sagasser and W. Jakob and M. A. Moreno and L. W. Buss and B. Schierwater},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2006},
Number = {23},
Pages = {8751--8756},
Volume = {103},
Abstract = {Trich || Demosp || Cnidaria},
File = {dellaporta2006.pdf}
}
@Article{Dellinger2014,
Title = {{Haplomyxa saranae gen. Nov. Et sp. Nov., A New Naked Freshwater Foraminifer.}},
Author = {M. Dellinger and A. Labat and L. Perrouault and P. Grellier},
Journal = {Protist},
Year = {2014},
Number = {3},
Pages = {317--329},
Volume = {165},
Abstract = {Sister to Reticulomyxa filosa},
Doi = {10.1016/j.protis.2014.03.007},
File = {ddellinger2014_haplomyxan.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24810177}
}
@Article{Delsuc2018,
Title = {{A phylogenomic framework and timescale for comparative studies of tunicates.}},
Author = {F. Delsuc and H. Philippe and G. Tsagkogeorga and P. Simion and M.-K. Tilak and X. Turon and S. L{\'o}pez-Legentil and J. Piette and P. Lemaire and E. J. P. Douzery},
Journal = {BMC Biol.},
Year = {2018},
Number = {1},
Pages = {39},
Volume = {16},
Abstract = {Appendicularia (very separate branch) || all others},
Doi = {10.1186/s12915-018-0499-2},
File = {delsuc2018_tunicates.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23709623}
}
@Article{Delsuc2008,
Title = {{Additional molecular support for the new chordate phylogeny}},
Author = {F. Delsuc and G. Tsagkogeorga and N. Lartillot and H. Philippe},
Journal = {genesis},
Year = {2008},
Pages = {592--604},
Volume = {46},
Abstract = {phylogenomics: Xeno || Hemi || Echin + Cepha || Tunic || Cyclost || Vertebr},
Doi = {10.1002/dvg.20450},
File = {delsuc2008.pdf}
}
@Article{Demoulin1985,
Title = {{The red algal-higher fungi phylogenetic link: The last ten years}},
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Volume = {18}
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@Article{Demoulin1974,
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@Article{Derelle2011,
Title = {{Rooting the eukaryotic tree with mitochondrial and bacterial proteins}},
Author = {R. Derelle and B. F. Lang},
Journal = {Molecular Biology and Evolution},
Year = {2011},
Abstract = {Between bikonts and unikots; Malawimonas went to Unikonts},
File = {derelle2011_rooting_euk_tree.djvu}
}
@Article{Derelle2016,
Title = {{A phylogenomic framework to study the diversity and evolution of stramenopiles (=heterokonts)}},
Author = {R. Derelle and others},
Journal = {Mol. Biol. Evol.},
Year = {2016},
Abstract = {I do no see anything new},
File = {derelle2016_stramenopiles.pdf}
}
@Article{Derelle2015,
Title = {{Bacterial proteins pinpoint a single eukaryotic root.}},
Author = {R. Derelle and G. Torruella and V. Klime{\v{s}} and H. Brinkmann and E. Kim and {\v{C}}. Vl{\v{c}}ek and B. F. Lang and M. Eli{\'a}{\v{s}}},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2015},
Number = {7},
Pages = {E693--9},
Volume = {112},
Abstract = {Opimoda: Malawi + Collo + Amoeb || Theca + Opist; Diphoda: Discoba || Archaepl + Crypt || SAR},
Doi = {10.1073/pnas.1420657112},
File = {derelle2015_euk_root_malawim_collod.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21527387}
}
@Article{Desalle2010,
Title = {{Evolution of cysteine patterns in the large extracellular loop of tetraspanins from animals, fungi, plants and single-celled eukaryotes}},
Author = {R. Desalle and R. Mares and A. Garcia-Espana},
Journal = {Molecular phylogenetics and evolution},
Year = {2010},
Abstract = {Nothing significant},
Doi = {10.1016/j.ympev.2010.02.015},
File = {desalle2010_cysteine.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20171294}
}
@Article{Desalle2008,
Title = {{An even "newer" animal phylogeny}},
Author = {R. Desalle and B. Schierwater},
Journal = {Bioessays},
Year = {2008},
Number = {11-12},
Pages = {1043 - 1047},
Volume = {30},
Abstract = {Critics of Dunn et al.},
Doi = {10.1002/bies.20842},
File = {desalle2008b.pdf}
}
@Article{DeSalle2007,
Title = {{Key transitions in animal evolution}},
Author = {R. DeSalle and B. Schierwater},
Journal = {Integrative and Comparative Biology},
Year = {2007},
Number = {5},
Pages = {667--669},
Volume = {47},
Doi = {10.1093/icb/icm042},
File = {desalle2007_key_trans_animal_evol.pdf}
}
@Article{Deschamps2010,
Title = {{Phylogenomic analysis of kinetoplastids supports that trypanosomatids arose from within bodonids}},
Author = {P. Deschamps and E. Lara and W. Marande and P. L{\'o}pezGarc{\'i}a and F. Ekelund and D. Moreira},
Journal = {Molecular Biology and Evolution},
Year = {2010},
Volume = {28},
Abstract = {As stated},
File = {deschamps2010_trymanosomatids.pdf}
}
@Article{Deschamps2009,
Title = {{Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes}},
Author = {P. Deschamps and D. Moreira},
Journal = {Mol. Biol.Evol.},
Year = {In press},
Abstract = {Glaucophyta may be first; or Biliphyta (Gla + Rhod)},
File = {deschamps2009_biliphyta.pdf}
}
@Article{Desmond2009,
Title = {{Phylogenomics of sterol synthesis: Insights into the origin, evolution and diversity of a key eukaryotic feature}},
Author = {E. Desmond and S. Gribaldo},
Journal = {Genome Biology and Evolution},
Year = {In press},
Abstract = {Support for Opist, Amoeb, Exca, Plants + SAR},
Doi = {10.1093/gbe/evp036},
File = {desmond2009_sterol_phylogenomics.pdf}
}
@Article{Desnickij1990,
Title = {{Chromosomes of Dinophyta}},
Author = {A. G. Desnickij},
Journal = {Bot. Zhurn.},
Year = {1990},
Note = {(In Russian)},
Number = {11},
Pages = {1489--1496},
Volume = {75},
Abstract = {citologija, evoljucija, Dinozoa},
Annote = {Blizki k Infusoria, no otlichajutsja kolichestvom gistonov u Noctiluca, zamescheniem 4--19% timina 5-gidroksimetiluracilom}
}
@Article{Desnickij1980,
Title = {The origin of energy-producing cell organelles in relation with the new data about organisation of nuclear, chloroplast and mitochondrial genomes},
Author = {A. G. Desnickij and A. V. Pinevich},
Journal = {Vestnik LGU},
Year = {1980},
Note = {(In Russian)},
Number = {4},
Pages = {80--85},
Volume = {21},
Abstract = {evoljucija, citologija, Protista}
}
@Article{Deutsch2008,
Title = {{Do acoels climb up the ``Scale of Beings''?}},
Author = {J. S. Deutsch},
Journal = {Evol. Devel.},
Year = {2008},
Number = {2008},
Pages = {135--140},
Volume = {10},
Abstract = {Acoelomorpha || Deuterostomia},
File = {deutsch2008.pdf},
Keywords = {pr1}
}
@Article{Dewel2000,
Title = {{Colonial Origin for Eumetazoa: Major Morphological Transitions and the Origin of Bilaterian Complexity}},
Author = {R. A. Dewel},
Journal = {J. Morphol.},
Year = {2000},
Pages = {35--74},
Volume = {243},
Abstract = {Porifera+Ctenophora || Cnidaria + Bilateria},
File = {dewel2000.pdf}
}
@Article{Dewel2003,
Title = {{Bridging Morphological Transitions to the Metazoa}},
Author = {R. A. Dewel and M. U. Connell and W. C. Dewel},
Journal = {Integr. Comp. Biol.},
Year = {2003},
Pages = {28--46},
Volume = {43},
File = {dewel2003.pdf}
}
@Article{Dickinson2009,
Title = {{Bridging the generation gap: Flowering plant gametophytes and animal germlines reveal unexpected similarities}},
Author = {H. G. Dickinson and R. Grant-Downton},
Journal = {Biological reviews of the Cambridge Philosophical Society},
Year = {In press},
Abstract = {As stated},
Doi = {10.1111/j.1469-185X.2009.00088.x},
File = {dickinson2009_plant_animal_germlines_similarity.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19725820}
}
@Article{Diruggiero1999,
Title = {{DNA Repair Systems in Archaea: Mementos from the Last Universal Common Ancestor?}},
Author = {J. Diruggiero and J. R. Brown and A. P. Bogert and F. T. Robb},
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Year = {1999},
Pages = {474--484},
Volume = {49}
}
@Article{Dixelius2016,
Title = {{Evolutionary origins of rhizarian parasites}},
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Journal = {Mol. Biol. Evol.},
Year = {2016},
Abstract = {Four major groups of Rhizaria: Filosa || Phytorhiza (Vampyrellida, Phytomyxea) || Ascetosporea (incl. Mikrocytos) + Apofilosa (Gromia, Floreta) || and Retaria: Acantharea || Polycystinea || Reticulomyxa + Foraminifera},
File = {sierra2015_phytorhiza_microcytos.pdf}
}
@Article{Dodsworth2013,
Title = {{Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.}},
Author = {J. A. Dodsworth and P. C. Blainey and S. K. Murugapiran and W. D. Swingley and C. A. Ross and S. G. Tringe and P. S. G. Chain and M. B. Scholz and C.-C. Lo and J. Raymond and S. R. Quake and B. P. Hedlund},
Journal = {Nat Commun},
Year = {2013},
Pages = {1854},
Volume = {4},
Abstract = {Atribacteria (Caldatribacterium); OP9 ~ JS1},
Doi = {10.1038/ncomms2884},
File = {dodsworth2013_op9_atribacteria_caldatribacterium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21908640}
}
@Article{Dodsworth2014,
Title = {{Thermoflexus hugenholtzii gen. Nov., Sp. Nov., A thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., And description of Thermoflexaceae fam. Nov. And Thermoflexales ord. Nov.}},
Author = {J. A. Dodsworth and J. Gevorkian and F. Despujos and J. K. Cole and S. K. Murugapiran and H. Ming and W.-J. Li and G. Zhang and A. Dohnalkova and B. P. Hedlund},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2014},
Abstract = {Close to Caldilineae and Ardenticatenia},
Doi = {10.1099/ijs.0.055855-0},
File = {dodsworth2014_thermoflexia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24676733}
}
@Article{vonDoehren2008,
Title = {{What Morphology can do to Unravel the Phylogenetic Position of Nemertea}},
Author = {J. von Doehren and T. Bartolomaeus},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {no hint at a sister-group relationship of Nemertea and Annelida},
Doi = {10.1002/jmor.10683},
File = {vondoehren2008.txt}
}
@Article{vonDohren2010,
Title = {{Comparative sperm ultrastructure in Nemertea}},
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Year = {2010},
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Pages = {793 - 813},
Volume = {271},
Abstract = {Heteronemertea and Hoplonemertea are supported as monophyletic by sperm morphology. However, the data do not provide information on the existing contradictions regarding the internal relationships of "Palaeonemertea"},
Doi = {10.1002/jmor.10834},
File = {doehren2010_nemertea_sperms.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20544873}
}
@Article{Doerken2010,
Title = {{Morphology and anatomy of male cones of Pseudotaxus chienii (W.C. Cheng) W.C. Cheng (Taxaceae)}},
Author = {V. M. Doerken and Z. Zhang and I. B. Mundry and T. Stuetzel},
Journal = {Flora},
Year = {2010},
Number = {5},
Pages = {444--450},
Volume = {206},
Abstract = {Transition between Taxaceae and Cephalotax. Flowers = Monoaxial cones},
Doi = {10.1016/j.flora.2010.08.006},
File = {doerken2011_pseudotaxus.pdf},
ISSN = {0367-2530},
Url = {http://dx.doi.org/10.1016/j.flora.2010.08.006}
}
@Article{Dogadina1990,
Title = {Ways of evolution and genetic relations inside yellow-green algae ({X}anthophyta)},
Author = {V. Dogadina},
Journal = {Bot. Zhurn.},
Year = {1990},
Note = {(In Russian)},
Number = {4},
Pages = {462--469},
Volume = {75},
Abstract = {sistematika, Chromophyta},
Annote = {Blizki k Eustigmat., Chlorom.}
}
@Article{Dohrmann2009,
Title = {{New insights into the phylogeny of glass sponges (Porifera, Hexactinellida)}},
Author = {M. Dohrmann and A. G. Collins and G. Woerheide},
Journal = {Molecular Phylogenetics and Evolution},
Year = {2009},
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Pages = {257--262},
Volume = {52},
Abstract = {In favor of sponge monophyly and Demosponge paraphyly (Spongilla etc. closer to Hexact. than Aplysina and others); two groups of Hexact.},
Doi = {10.1016/j.ympev.2009.01.010},
File = {dohrmann2009_hexactinellida.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2009.01.010}
}
@Article{Dohrmann2008,
Title = {{Phylogeny and Evolution of Glass Sponges (Porifera, Hexactinellida)}},
Author = {M. Dohrmann and D. Janussen and J. Reitner and A. G. Collins and G. Wuerheide},
Journal = {Syst. Biol.},
Year = {2008},
Number = {3},
Pages = {388--405},
Volume = {57},
Abstract = {||| Eumetazoa (incl. Trich, Cnid) + ||| Porifera: Homo + Calc || Demo + Hexa},
Doi = {10.1080/10635150802161088},
File = {dohrmann2008.pdf}
}
@Article{Dohrmann2013,
Title = {{Novel scenarios of early animal evolution--is it time to rewrite textbooks?}},
Author = {M. Dohrmann and G. W{\"o}rheide},
Journal = {Integr. Comp. Biol.},
Year = {2013},
Number = {3},
Pages = {503--511},
Volume = {53},
Abstract = {Review},
Doi = {10.1093/icb/ict008},
File = {dorhmann2013_new_scenarios_animal_evol_review.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23539635}
}
@Article{Dojka1998,
Title = {{Microbial Diversity in a Hydrocarbon- and Chlorinated-Solvent- Contaminated Aquifer Undergoing Intrinsic Bioremediation}},
Author = {M. A. Dojka and P. Hugenholtz and S. K. Haack and N. R. Pace},
Journal = {Appl. Environ. Microbiol.},
Year = {1998},
Number = {10},
Pages = {3869--3877},
Volume = {64},
Abstract = {OP11 + WS6},
File = {dojka1998_wsx.pdf}
}
@Article{Dolan2009,
Title = {{Body building on land-morphological evolution of land plants}},
Author = {L. Dolan},
Journal = {Curr. Opin. Plant Biol.},
Year = {2009},
Number = {1},
Pages = {4--8},
Volume = {12},
Abstract = {Roots: evidence for the recruitment of gametophyte genes into the sporophyte; TALE genes evolution is responsible for the increase in sporophyte diversity},
Doi = {10.1016/j.pbi.2008.12.001},
File = {dolan2009_plant_body.pdf}
}
@Article{DomazetLoso2010,
Title = {{Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa}},
Author = {T. Domazet-Loso and D. Tautz},
Journal = {BMC Biol.},
Year = {2010},
Pages = {66},
Volume = {8},
Abstract = {~ Porifera},
Doi = {10.1186/1741-7007-8-66},
File = {domazet-loso2010_cancer_multicell.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20594288}
}
@Article{Dombrowski2017,
Title = {{Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.}},
Author = {N. Dombrowski and K. W. Seitz and A. P. Teske and B. J. Baker},
Journal = {Microbiome},
Year = {2017},
Number = {1},
Pages = {106},
Volume = {5},
Abstract = {WOR-3 are Stahlbacteria},
Doi = {10.1186/s40168-017-0322-2},
File = {dombrowski2017_wor-3_stahlbacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/9254694}
}
@Article{Dombrowski2020,
Title = {{Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution}},
Author = {N. Dombrowski and T. A. Williams and J. Sun and B. J. W. B. Q. Minh and C. Rinke and A. Spang},
Journal = {Nature Communications},
Year = {2020},
Abstract = {3 clusters: Altiarchaeota + (Micra + Diaph) || Undinarchaeota || (Aenigmo + Nanohal) + (Woese + Pace + Nano + Parva)},
Doi = {10.1038/s41467-020-17408-w},
File = {dombrowski2020_undinarchaeota.pdf},
ISSN = {2041-1723}
}
@Article{Donachie2004,
Title = {{The Hawaiian Archipelago: A Microbial Diversity Hotspot}},
Author = {S. P. Donachie and S. Hou and K. S. Lee and C. W. Riley and A. Pikina and C. Belisle and S. Kempe and T. S. Gregory and A. Bossuyt and J. Boerema and J. Liu and T. A. Freitas and A. Malahoff and M. Alam},
Journal = {Microbial Ecol.},
Year = {2004},
Number = {2004},
Pages = {509--520},
Volume = {48},
Abstract = {Deinococci, TM7},
File = {donachie2004.pdf}
}
@Article{Donoghue2000,
Title = {{Conodont affinity and chordate phylogeny}},
Author = {P. C. J. Donoghue and P. L. Forey and R. J. Aldridge},
Journal = {Biol. Rev.},
Year = {2000},
Pages = {191--251},
Volume = {75}
}
@Article{Doolittle2009,
Title = {{The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them}},
Author = {W. F. Doolittle},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2009},
Number = {1527},
Pages = {2221--2228},
Volume = {364},
Abstract = {As stated},
Doi = {10.1098/rstb.2009.0032},
File = {doolittle2009_hgt_evol_theory.pdf}
}
@Article{Dordel2010,
Title = {{Phylogenetic position of Sipuncula derived from multi-gene and phylogenomic data and its implication for the evolution of segmentation}},
Author = {J. Dordel and F. Fisse and G. Purschke and T. H. Struck},
Journal = {J. Zool. Syst. Evol. Res.},
Year = {2010},
Number = {3},
Pages = {197--207},
Volume = {48},
Abstract = {78 ribosome proteins: not sister but inside, after Chaetopteridae; Nemertea ~ Tettaculata s.l., Mollusca separate},
Doi = {10.1111/j.1439-0469.2010.00567.x},
File = {dordel2010_sipuncula.pdf}
}
@Article{Dorken2010,
Title = {{Morphology and anatomy of anomalous cladodes in Sciadopitys verticillata Siebold \& Zucc. (Sciadopityaceae)}},
Author = {V. M. Dorken and T. Stutzel},
Journal = {Trees},
Year = {2010},
Abstract = {Evolve from decidous condition under the pressure of angiosperms (?); gymnosperm leaves amy be not homologous},
Doi = {10.1007/s00468-010-0498-6},
File = {doerken2010_sciadopitys.pdf}
}
@Article{Doud2019,
Title = {{Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere}},
Author = {D. F. R. Doud and others},
Journal = {The ISME Journal},
Year = {2019},
Volume = {5},
Abstract = {Goldbacteria (Cellulosimonas) sister to Elusimicrobia and Firestonebacteria},
Doi = {10.1038/s41396-019-0557-y},
File = {doud2019_goldbacteria.pdf},
ISSN = {1751-7370}
}
@Article{Douglas1998,
Title = {{Further evidence to suggest that archaeal flagella are related to bacterial type {IV} pili}},
Author = {P. B. Douglas and K. F. Jarrell},
Journal = {J. Mol. Evol.},
Year = {1998},
Pages = {370--373},
Volume = {46}
}
@Article{Douglas1999,
Title = {{The plastid genome of the Cryptophyte alga, \textit{Guillardia theta}: complete sequence and conserved synteny groups confirm its common ancestry with red algae}},
Author = {S. E. Douglas and S. L. Penny},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {236--244},
Volume = {48}
}
@Book{Doweld2001,
Title = {{Prosyllabus Tracheophytorum, Tentamen systematis plantarum vascularium (Tracheophyta)}},
Author = {A. Doweld},
Publisher = {GEOS},
Year = {2001},
Address = {Moscow},
ISBN = {5-89118-283-1}
}
@Article{Doyle1996,
Title = {{Seed plant phylogeny and relationships of Gnetales}},
Author = {J. A. Doyle},
Journal = {Int. J. Plant Sci.},
Year = {1996},
Number = {6 Suppl.},
Pages = {S3--S39},
Volume = {57}
}
@Article{Drozdov2012,
Title = {{Morphology of Gametes of Mollusks, Echinoderms, and Brachiopods in Systematics and Phylogeny}},
Author = {A. L. Drozdov and V. V. Vinnikova and O. N. Zezina and S. A. Tyurin},
Journal = {Paleontological Journal},
Year = {2012},
Number = {8},
Pages = {936--944},
Volume = {46},
Abstract = {Brachiopods polyphyletic (inarticulate ~ moll, articulate ~ deuterost)},
Doi = {10.1134/S0031030112080059},
File = {drizdov2013_gametes_mollusks_echinoderms_brachiopods.pdf}
}
@Article{Dubinin1959,
Title = {Chelicers-bearing animals and their position in the classification},
Author = {V. B. Dubinin},
Journal = {Zool. Zhurn.},
Year = {1959},
Note = {(In Russian)},
Number = {8},
Pages = {1163--1189},
Volume = {38},
Abstract = {sistematika, Chelicerata}
}
@Article{Dubuisson2011,
Title = {{Anatomical diversity and regressive evolution in trichomanoid filmy ferns (Hymenophyllaceae): A phylogenetic approach}},
Author = {J.-Y. Dubuisson and S. Hennequin and S. Bary and A. Ebihara and and E. Boucheron-Dubuisson},
Journal = {Comptes Rendus Biologies},
Year = {2011},
Pages = {16},
Volume = {156},
Abstract = {As stated},
Doi = {10.1016/j.crvi.2011.07.009},
File = {dubuisson2011_hymenophyllaceae.pdf},
ISSN = {1631-0691},
Url = {http://dx.doi.org/10.1016/j.crvi.2011.07.009}
}
@Article{Duckett2018,
Title = {{The evolution of the stomatal apparatus: Intercellular spaces and sporophyte water relations in bryophytes-two ignored dimensions.}},
Author = {J. G. Duckett and S. Pressel},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2018},
Number = {1739},
Volume = {373},
Abstract = {... sporophyte desiccation!},
Doi = {10.1098/rstb.2016.0498},
File = {duckett2017_evol_stomatal_app.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20525002}
}
@Article{Duckett2009,
Title = {{Exploding a myth: The capsule dehiscence mechanism and the function of pseudostomata in Sphagnum}},
Author = {J. G. Duckett and S. Pressel and K. M. Y. P'ng and K. S. Renzaglia},
Journal = {New Phytol.},
Year = {2009},
Number = {4},
Pages = {1053 - 1063},
Volume = {183},
Abstract = {As stated},
Doi = {10.1111/j.1469-8137.2009.02905.x},
File = {duckett2009_sphagnum_sporangia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19702775}
}
@Article{Duff1999,
Title = {{Phylogenetic relationships of land plants using mitochondrial small-subunit r{DNA} sequences}},
Author = {R. J. Duff and D. L. Nickrent},
Journal = {Amer. J. Bot.},
Year = {1999},
Pages = {372--386},
Volume = {86(3)}
}
@Article{Duff2007,
Title = {{Progress and challenges toward developing a phylogeny and classification of the hornworts}},
Author = {R. J. Duff and J. C. Villarreal and D. C. Cargill and K. S. Renzaglia},
Journal = {Bryologist},
Year = {2007},
Number = {2},
Pages = {214--243},
Volume = {110},
Abstract = {Leiosporoceros differs by chloroplast morphologies and Nostoc colonies},
File = {duff2007.pdf}
}
@Article{Dumack2017,
Title = {{Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny}},
Author = {K. Dumack and A. P. Mylnikov and M. Bonkowski},
Journal = {Protist},
Year = {2017},
Abstract = {Chlorarachnea | Granophilosea | Thecophilosea | Imbricatea | Kraken + Cercomonadales},
Doi = {10.1016/j.protis.2017.04.004},
File = {dumack2017_kraken_cercomonadales.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2017.04.004}
}
@Article{Dumack2016,
Title = {{A Novel Lineage of ‘Naked Filose Amoebae’; Kraken carinae gen. Nov. Sp. Nov. (Cercozoa) with a Remarkable Locomotion by Disassembly of its Cell Body}},
Author = {K. Dumack and J. Schuster and D. Bass and M. Bonkowski},
Journal = {Protist},
Year = {2016},
Abstract = {Not so similar to Meteora but Meteora could be in the same group, ~ Euglypha; Endomyxa || Tremulida || Chlorarachn || Granofilosea || Cercom. etc. || Thecofilos + Imbricatea},
Doi = {10.1016/j.protis.2016.04.002},
File = {dumack2016_kraken_cercomonad_amoeba_meteora_like.pdf},
Url = {http://dx.doi.org/doi:10.1016/j.protis.2016.04.002}
}
@Article{Dunfield2012,
Title = {{Electing a candidate: A speculative history of the bacterial phylum OP10}},
Author = {P. F. Dunfield and I. Tamas and K. C. Lee and X. C. Morgan and I. R. McDonald and M. B. Stott},
Journal = {Environ. Microbiol.},
Year = {2012},
Volume = {2},
Abstract = {Review: Armatimonadetes},
Doi = {10.1111/j.1462-2920.2012.02742.x},
File = {dunfield2012_op10_armatimonadetes_review.pdf}
}
@Article{Dunlop2010,
Title = {{Geological history and phylogeny of Chelicerata.}},
Author = {J. A. Dunlop},
Journal = {Arthropod structure \& development},
Year = {2010},
Abstract = {Review},
Doi = {10.1016/j.asd.2010.01.003},
File = {dunlop2010_chelicerata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20093195}
}
@Article{Dunn2008,
Title = {{Broad phylogenomic sampling improves resolution of the animal tree of life}},
Author = {C. W. Dunn and A. Hejnol and D. Q. Matus and K. Pang and W. E. Browne and S. A. Smith and E. Seaver and G. W. Rouse and M. Obst and G. D. Edgecombe and M. V. Sorensen and S. H. D. Haddock and A. Schmidt-Rhaesa and A. Okusu and R. M. Kristensen and W. C. Wheeler and M. Q. Martindale and G. Giribet},
Journal = {Nature},
Year = {2008},
Pages = {745--750},
Volume = {452},
Abstract = {Support for Protostomia, Deut. incl. Xeno, Onych || Arthr., supp. for Mollusca, Annel. incl. Ech. and Sip. || ((Phor + Brach) Nemert), Lophotr., Ecdysoz., Capsasp ~ Choano},
Doi = {10.1038/nature06614},
File = {dunn2008.pdf}
}
@Article{Durako2007,
Title = {{A reassessment of Geminella (Chlorophyta) based upon photosynthetic pigments, DNA sequence analyses and electron microscopy}},
Author = {M. R. Durako and C. Bailey},
Journal = {Journal of Phycology},
Year = {2007},
Number = {S1},
Pages = {1--48},
Volume = {42},
Abstract = {Geminella and Microspora may be close to Treboux (weak), may be indep. lineage},
Doi = {10.1111/j.1529-8817.2006.20064201.x},
File = {durako2007.txt}
}
@Article{Dykova2010a,
Title = {{Grellamoeba robusta gen. n., sp. n., A possible member of the family Acramoebidae Smirnov, Nassonova et Cavalier-Smith, 2008}},
Author = {I. Dykova and M. Kostka and H. Peckova},
Journal = {Eur. J. Protistol.},
Year = {2010},
Number = {2},
Pages = {77 - 85},
Volume = {46},
Abstract = {As stated, ~ Filamoeba and Cochliopodium},
Doi = {10.1016/j.ejop.2009.10.004},
File = {dykova2010_grellamoeba.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20347581}
}
@Article{Dykova2010b,
Title = {{Two New Species of the Genus Stenamoeba Smirnov, Nassonova, Chao et Cavalier-Smith, 2007}},
Author = {I. Dykova and M. Kostka and H. Peckova},
Journal = {Acta Protozool.},
Year = {2010},
Pages = {245--251},
Volume = {20},
Abstract = {~ Thecamoeba + Sappinia},
File = {dykova2010_stenamoeba.pdf}
}
@Article{Dykova2008,
Title = {{Introduction of Mayorella gemmifera Schaeffer, 1926 into Phylogenetic Studies of Amoebozoa}},
Author = {I. Dykova and H. Peckova and M. Kostka},
Journal = {Acta Protozoologica},
Year = {2008},
Number = {3},
Pages = {205--210},
Volume = {47},
File = {dykova2008_ref.txt}
}
@Article{Dykova2003,
Title = {{\textit{Nuclearia pattersoni} sp. n. (Filosea), a new species of amphizoic amoeba isolated from gills of roach (Rutilus rutilus), and its rickettsial endosymbiont}},
Author = {I. Dykova and M. Veverkova and I. Fiala and B. Machackova and H. Peckova},
Journal = {Folia Parasitol.},
Year = {2003},
Pages = {161--170},
Volume = {50},
Abstract = {Fungi || Choan + Metazoa || Nuclearia || Capsa || Ichth},
File = {dykova2003.pdf}
}
@Article{Dykstra1977,
Title = {{The Possible Phylogenetic Significance of Mitochondrial Configurations in the Acrasid Cellular Slime Molds with Reference to Members of the Eumycetozoa and Fungi}},
Author = {M. J. Dykstra},
Journal = {Mycologia},
Year = {1977},
Number = {3},
Pages = {579--591},
Volume = {69},
Abstract = {plate-like Acrasis, Pocheina and Guttulinopsis, tubular Copromyxa},
File = {dykstra1977_mitoch_acrasids.pdf},
Url = {http://www.jstor.org/stable/3758561}
}
@Unpublished{Ebersberger2009,
Title = {{A stable backbone for the fungi}},
Author = {I. Ebersberger and M. Gube and S. Strauss and A. Kupczok and A. von Haeseler and M. M. Eckart and K. Voigt and E. Kothe},
Year = {2009},
Abstract = {||| Chytr ||| Zygo + Glom mixed ||| others},
Doi = {10101/npre.2009.2901.1},
File = {ebersberger2009_est_fungi.pdf},
Journal = {Nature Precedings}
}
@Article{Ebersberger2011,
Title = {{A Consistent Phylogenetic Backbone For the Fungi}},
Author = {I. Ebersberger and R. de Matos Simoes and A. Kupczok and M. Gube and E. Kothe and K. Voigt and A. von Haeseler},
Journal = {Bioinformatics},
Year = {2011},
Abstract = {Phylogenomics},
File = {ebersberger2011_fungi_genomic_phyl.pdf}
}
@Article{Ecology2015,
Title = {{Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi}},
Author = {F. Ecology and H.-P. Grossart and C. Wurzbacher and T. Y. James and M. Kagami},
Journal = {Fungal Ecology},
Year = {2015},
Abstract = {Different Rozellomycota},
Doi = {10.1016/j.funeco.2015.06.004},
File = {grossart2015_rozellomycota.pdf},
Url = {www.elsevier.com/locate/funeco}
}
@Article{Edgecombe2009,
Title = {{Palaeontological and Molecular Evidence Linking Arthropods, Onychophorans, and other Ecdysozoa}},
Author = {G. D. Edgecombe},
Journal = {Evo. Edu. Outreach},
Year = {In press},
Abstract = {As stated. Review.},
Doi = {10.1007/s12052-009-0118-3},
File = {edgecombe2009_ecdysozoa.pdf}
}
@Article{Edgecombe2009b,
Title = {{Arthropod phylogeny: An overview from the perspectives of morphology, molecular data and the fossil record.}},
Author = {G. D. Edgecombe},
Journal = {Arthropod Struct. Dev.},
Year = {2009},
Abstract = {Review},
Doi = {10.1016/j.asd.2009.10.002},
File = {F:/ref/os/1/edgecombe2009_arthr_phyl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19854297}
}
@Article{Edgecombe2004,
Title = {{Morphological data, extant Myriapoda, and the myriapod stem-group}},
Author = {G. D. Edgecombe},
Journal = {Contrib. Zool.},
Year = {2004},
Number = {3},
Pages = {1--37},
Volume = {73},
Abstract = {Myriapoda: Chilopoda + Progoneata (incl. Simphyla, Pauropoda, Diplopoda)},
File = {edgecombe2004.pdf}
}
@Article{Edgecombe2010,
Title = {{Higher-level metazoan relationships: Recent progress and remaining questions}},
Author = {G. D. Edgecombe and G. Giribet and C. W. Dunn and A. Hejnol and R. M. Kristensen and R. C. Neves and G. W. Rouse and K. Worsaae and M. V. S{\o}rensen},
Journal = {Org Divers Evol},
Year = {2010},
Pages = {35--40},
Volume = {15},
Abstract = {Review},
Doi = {10.1007/s13127-011-0044-4},
File = {edgecombe2011_metazoa.pdf}
}
@Article{Edgecombe2014,
Title = {{Origins and early evolution of arthropods}},
Author = {G. D. Edgecombe and D. A. Legg},
Journal = {Palaeontology},
Year = {2014},
Pages = {457--468},
Volume = {57},
Abstract = {Chelicerata incl. Pycnog. and Xiphosura; Mandibulata: Myri incl. Chilop and Progoneata (all others) || Oligostraca incl. Ostrac, Mystaco, Branchi, Pentast || Multicrustacea incl. Copep, Thecostr, Malacostr || Allotriocarida incl. Brachiop, Cephal, Remip, Hexap},
Doi = {10.1111/pala.12105},
File = {edgecombe2014_orig_evol_arthropods.pdf}
}
@InCollection{Edvardsen2007,
Title = {{Molecular systematics of Haptophyta}},
Author = {B. Edvardsen and L. K. Medlin},
Booktitle = {Unravelling the algae: the past, present and future of algae systematics. The Systematic Association special volume series 75},
Publisher = {CRC Press},
Year = {2007},
Address = {London},
Editor = {J. Brodie and J. Lewis},
Pages = {183--196},
Abstract = {Pavlovophyceae || Prymnesiophyceae}
}
@Article{Edwards2022,
Title = {{Piecing together the eophytes - a new group of ancient plants containing cryptospores}},
Author = {D. Edwards and P. Kenrick and J. L. Morris and L. Axe and J. G. Duckett and S. Pressel},
Journal = {New Phytologist},
Year = {2022},
Abstract = {Class Embryopsida (tiny axes with floem, microscopic sporangia with spores in dyads or tetrads) || other pteridophytes},
Doi = {10.1111/nph.17703},
File = {edwards2022_eophytes_between_mosses_and_tracheophytes.pdf}
}
@Article{Eeckhaut2003,
Title = {{Larval Development of \textit{Myzostoma cirriferum} (Myzostomida)}},
Author = {I. Eeckhaut and L. Fievez and M. C. M. Muller},
Journal = {J. Morphol.},
Year = {2003},
Pages = {258--269},
Volume = {283},
Abstract = {Myzostoma have trochophora},
File = {eekhout2003.pdf}
}
@Article{Eeckhaut2005,
Title = {{Myzostomida: A review of the phylogeny and ultrastructure}},
Author = {I. Eeckhaut and D. Lanterbecq},
Journal = {Hydrobiologia},
Year = {2005},
Pages = {253--275},
Volume = {535--536},
Abstract = {Morphology > Annelida},
File = {eeckhaut2005.pdf}
}
@Article{Egge2014,
Title = {{Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 pyrosequencing}},
Author = {E. S. Egge and W. Eikrem and B. Edvardsen},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2014},
Abstract = {As stated},
Doi = {10.1111/jeu.12157-4537},
File = {egge2014_haptophytes.pdf}
}
@Article{Ehlers1997,
Title = {{Ultrastructure of the subepidermal musculature of Xenoturbella bocki, the adelphotaxon of the Bilateria}},
Author = {U. Ehlers and B. Sopott-Ehlers},
Journal = {Zoomorphology},
Year = {1997},
Pages = {71--79},
Volume = {117},
Abstract = {Cnidaria || Ctenophora || Xenoturb || Bilateria},
File = {ehlers1997.djvu}
}
@Manual{Eisen2004,
Title = {{Phylogenomics: a genome-level approach to assembling the bacterial branches of the tree of life}},
Author = {J. A. Eisen and N. Ward and K. E. Nelson and J. H. Badger and J. Sakwa and D. Wu and M. Wu and K. Penn and G. Pai and S. Smith and E. M. O. Connor and J. Enticknap and T. Steppe and F. T. Robb},
Year = {2004},
Abstract = {Genomes: (Fuso, Dictyo, Thermot, Deino), Thermodesulfobacter (and ? Thermodesulfovibrio/Nitrospira) ~ Desulfovibrio (d-proteo), Thermomicrobia ~ Chloroflexi},
File = {eisen2004_poster.pdf},
Url = {http://ucjeps.berkeley.edu/bryolab/ATOL/pdf/ATOL_2004_Bacteria_POSTER.pdf}
}
@Article{Eitel2018,
Author = {M. Eitel and W. R. Francis and F. Varoqueaux and J. Daraspe and H.-J. Osigus and S. Krebs and S. Vargas and H. Blum and G. A. Williams},
Journal = {Science},
Year = {2018},
Number = {7},
Pages = {2018},
Volume = {28},
Abstract = {Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus},
Doi = {10.1371/journal.pbio.2005359},
File = {eitel2018_placozoan_species.pdf}
}
@Article{Eitel2011,
Title = {{Pone.0019639 1..9}},
Author = {M. Eitel and L. Guidi and H. Hadrys and M. Balsamo and B. Schierwater},
Journal = {PLoS ONE},
Year = {2011},
Number = {5},
Pages = {e19639},
Volume = {6},
Abstract = {Simple life cycle; no sperms found, only sperm DNA markers},
Doi = {10.1371/journal.pone.0019639},
File = {eitel2011_placozoa.pdf},
Url = {www.plosone.org}
}
@Article{Eitel2013,
Title = {{Global diversity of the placozoa.}},
Author = {M. Eitel and H.-J. Osigus and R. Desalle and B. Schierwater},
Journal = {PLoS ONE},
Year = {2013},
Number = {4},
Pages = {e57131},
Volume = {8},
Abstract = {19 lineages, ecology good but morphology poor},
Doi = {10.1371/journal.pone.0057131},
File = {eital2013_placozoa_diversity.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/14977730}
}
@Article{Eitel2010,
Title = {{The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters.}},
Author = {M. Eitel and B. Schierwater},
Journal = {Mol. Ecol.},
Year = {2010},
Number = {11},
Pages = {2315 - 2327},
Volume = {19},
Abstract = {~ 75 species, maybe also families and orders},
Doi = {10.1111/j.1365-294X.2010.04617.x},
File = {eitel2010_phylogeogr_placozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20604866}
}
@Article{Elgorriaga2018,
Title = {{Origin of Equisetum: Evolution of horsetails (Equisetales) within the major euphyllophyte clade Sphenopsida.}},
Author = {A. Elgorriaga and I. H. Escapa and G. W. Rothwell and A. M. F. Tomescu and N. R. C{\'u}neo},
Journal = {Am. J. Bot.},
Year = {2018},
Number = {8},
Pages = {1286--1303},
Volume = {105},
Doi = {10.1002/ajb2.1125},
File = {elgorriaga2018_orig_equisetum.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30025163}
}
@Article{Elias2016,
Title = {{A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution.}},
Author = {M. Eli{\'a}{\v{s}} and V. Klime{\v{s}} and R. Derelle and R. Petr{\v{z}}elkov{\'a} and J. Tachezy},
Journal = {Biol. Direct},
Year = {2016},
Number = {1},
Pages = {5},
Volume = {11},
Abstract = {Reflects flagella history; Malawi ~ Jacoba},
Doi = {10.1186/s13062-016-0107-8},
File = {elias2016_rabl2_flagella_euk.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25461969}
}
@Article{Elias2008,
Title = {{The guanine nucleotide exchange factors Sec2 and PRONE: candidate synapomorphies for the Opisthokonta and the Archaeplastida}},
Author = {M. Elias},
Journal = {Mol. Biol. and Evolution},
Year = {2008},
Number = {8},
Pages = {1526--1529},
Volume = {25},
Abstract = {As stated (Archeplastida were Rh, Chl \& Charo/Plantae)},
Doi = {doi:10.1093/molbev/msn113},
File = {elias2008.pdf}
}
@Article{Elias2009,
Title = {{The RAB Family GTPase Rab1A from Plasmodium falciparum Defines a Unique Paralog Shared by Chromalveolates and Rhizaria}},
Author = {M. Elias and N. J. Patron and P. J. Keeling},
Journal = {Journal of Eukaryotic Microbiology},
Year = {In press},
Abstract = {As stated; actually, shared with Gymnochlora},
Doi = {10.1111/j.1550-7408.2009.00408.x},
File = {elias2009_rab_genes_plasmodium.pdf}
}
@Article{Elkins2008,
Title = {{A korarchaeal genome reveals insights into the evolution of the Archaea}},
Author = {J. G. Elkins and M. Podar and D. E. Graham and K. S. Makarova and Y. Wolf and L. Randau and B. P. Hedlund and C. Brochier-Armanet and V. Kunin and I. Anderson and A. Lapidus and E. Goltsman and K. Barry and E. V. Koonin and P. Hugenholtz and N. Kyrpides and G. Wanner and P. Richardson and M. Keller and K. O. Stetter},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {23},
Pages = {8102--8107},
Volume = {105},
Abstract = {Nano || Eury || Korarchaeum cryptofilum || Cenarchaeum || other Crenarchaeota},
File = {elkins2008.pdf}
}
@Article{EloeFadrosh2016,
Title = {{Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.}},
Author = {E. A. Eloe-Fadrosh and D. Paez-Espino and J. Jarett and P. F. Dunfield and B. P. Hedlund and A. E. Dekas and S. E. Grasby and A. L. Brady and H. Dong and B. R. Briggs and W.-J. Li and D. Goudeau and R. Malmstrom and A. Pati and J. Pett-Ridge and E. M. Rubin and T. Woyke and N. C. Kyrpides and N. N. Ivanova},
Journal = {Nat Commun},
Year = {2016},
Pages = {10476},
Volume = {7},
Abstract = {Kryptonia ~ Ignavibacteria},
Doi = {10.1038/ncomms10476},
File = {eloe-fadrosh2016_kryptonia_kryptonium_cf_ignavi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24008419}
}
@Article{Elshahed2007,
Title = {{Phylogenetic and Metabolic Diversity of Planctomycetes from Anaerobic, Sulfide- and Sulfur-Rich Zodletone Spring, Oklahoma}},
Author = {M. S. Elshahed and N. H. Youssef and Q. Luo and F. Z. Najar and B. A. Roe and T. M. Sisk and S. I. Buehring and K.-U. Hinrichs and L. R. Krumholz},
Journal = {Appl. Environ. Microbiol.},
Year = {2007},
Number = {15},
Pages = {4707--4716},
Volume = {73},
Abstract = {OP11 ~ OD1, OP3},
File = {elshahed2007.djvu}
}
@Article{Eme2015,
Title = {{Microbial diversity: A bonanza of phyla.}},
Author = {L. Eme and W. F. Doolittle},
Journal = {Curr. Biol.},
Year = {2015},
Number = {6},
Pages = {R227--30},
Volume = {25},
Abstract = {TACK: Euk, Bathyarchaeota, Thaum, Aig, Kor, Cren; Eury; DPANN: Aenigma, Nano, Parva, Nanohalo, Diaph, Woesearchaeota, Pacearchaeota},
Doi = {10.1016/j.cub.2014.12.044},
File = {eme2015_archaea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25784040}
}
@Article{Eme2013,
Title = {{Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota.}},
Author = {L. Eme and L. J. Reigstad and A. Spang and A. Lanz{\'e}n and T. Weinmaier and T. Rattei and C. Schleper and C. Brochier-Armanet},
Journal = {Res. Microbiol.},
Year = {2013},
Abstract = {As stated},
Doi = {10.1016/j.resmic.2013.02.006},
File = {eme2013_thaumarchaeota_new.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23470515}
}
@Article{Emerson2007,
Title = {{A novel lineage of proteobacteria involved in formation of marine fe-oxidizing microbial mat communities}},
Author = {D. Emerson and J. A. Rentz and T. G. Lilburn and R. E. Davis and H. Aldrich and C. Chan and C. L. Moyer},
Journal = {PLoS One},
Year = {2007},
Number = {7},
Pages = {e667},
Volume = {2},
Abstract = {delta || epsilon || zeta || alpha || beta + gamma},
Doi = {10.1371/journal.pone.0000667},
File = {emerson2007_zeta.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17668050}
}
@Article{Emig1997,
Title = {{Les Lophophorates constituent~--- ils un embranchement?}},
Author = {C. C. Emig},
Journal = {Bull. Soc. Zool. Fr.},
Year = {1997},
Number = {3},
Pages = {279--288},
Volume = {122},
Abstract = {"Are the Lophophorata a phylum?"}
}
@Article{Emiliani2009,
Title = {{A horizontal gene transfer at the origin of phenylpropanoid metabolism: A key adaptation of plants to land}},
Author = {G. Emiliani and M. Fondi and R. Fani and S. Gribaldo},
Journal = {Biol. Direct},
Year = {2009},
Pages = {7},
Volume = {4},
Abstract = {As stated},
Doi = {10.1186/1745-6150-4-7},
File = {emiliani2009_hgt_land_plants.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19220881}
}
@Article{Epstein2008,
Title = {{"Missing" protists: A molecular prospective}},
Author = {S. Epstein and P. Lopez-Garcia},
Journal = {Biodivers Conserv},
Year = {2008},
Pages = {261--276},
Volume = {17},
Abstract = {Review},
Doi = {10.1007/s10531-007-9250-y},
File = {epstein2008_missing_protists.pdf}
}
@Article{Erber1998,
Title = {{Molecular phylogeny of Metazoan intermediate filament proteins}},
Author = {A. Erber and D. Riemer and M. Bovenschulte and K. Weber},
Journal = {J. Mol. Evol.},
Year = {1998},
Pages = {751--762},
Volume = {47}
}
@Article{Ereskovsky2006,
Title = {{The problem of germ layers in sponges (Porifera) and some issues concerning early metazoan evolution}},
Author = {A. V. Ereskovsky and A. K. Dondua},
Journal = {Zool. Anz.},
Year = {2006},
Number = {2},
Pages = {65--76},
Volume = {151},
Abstract = {No germ layers; Homoscleromorpha close to Eumetazoa; Hexa || Demo || Calci || Homo || Eumetazoa},
File = {ereskovsky2006.pdf}
}
@Article{Ereskovsky2007,
Title = {{Asexual reproduction in homoscleromorph sponges (Porifera; Homoscleromorpha)}},
Author = {A. V. Ereskovsky and D. B. Tokina},
Journal = {Mar. Biol.},
Year = {2007},
Pages = {425--434},
Volume = {151},
Abstract = {Homo ~ Eumetazoa by epithelial morphogenezis},
File = {ereskovsky2007.pdf}
}
@Article{Eriksson2010,
Title = {{Expression patterns of neural genes in Euperipatoides kanangrensis suggest divergent evolution of onychophoran and euarthropod neurogenesis}},
Author = {J. Eriksson and A. Stollewerk},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2010},
Pages = {2010},
Volume = {28},
Abstract = {neurogenesis in onychophorans largely does not reflect the ancestral pattern of euarthropod neurogenesis, but shows a mixture of derived characters and ancestral character},
Doi = {10.1073/pnas.1008822108},
File = {eriksson2010_euperipatoides_neural.pdf},
Url = {www.pnas.org/cgi/doi/10.1073/pnas.1008822108}
}
@Article{Eriksson2007,
Title = {{Outline of Ascomycota~--- 2007}},
Author = {O. E. Eriksson},
Journal = {Myconet},
Year = {2007},
Pages = {1--58},
Volume = {13}
}
@Article{Eriksson2005,
Title = {{Ascomyceternas ursprung och evolution - Protolichenes-hypotesen}},
Author = {O. E. Eriksson},
Journal = {Svenssk Mykologisk Tidskrift},
Year = {2005},
Number = {1},
Pages = {22--29},
Volume = {26},
Abstract = {Basal higher ascomycetes (with fruit bodies) were ancestrally lichens},
File = {eriksson2005_protolichenes.pdf}
}
@Article{Erpenbeck2007,
Title = {{On the molecular phylogeny of sponges (Porifera)}},
Author = {D. Erpenbeck and G. Woerheide},
Journal = {Zootaxa},
Year = {2007},
Number = {2007},
Pages = {107--126},
Volume = {1668},
Abstract = {Eumetazoa, Homoscleromorpha, Calcarea, "Silicea" (or Hexactinellida + Demospongiae s.s.)},
File = {erpenbeck2007.pdf}
}
@Article{Erseus2003,
Title = {{18S rDNA phylogeny of Clitellata (Annelida)}},
Author = {C. Erseus and M. Kallersjo},
Journal = {Zool. Scr.},
Year = {2003},
Number = {2},
Pages = {187--196},
Volume = {33},
Abstract = {Clitellata are monophyletic},
File = {erseus2004.pdf}
}
@Article{Ertas2009,
Title = {{Hemocyanin suggests a close relationship of Remipedia and Hexapoda}},
Author = {B. Ertas and B. M. von Reumont and J.-W. W{\"a}gele and B. Misof and T. Burmester},
Year = {In press},
Volume = {19},
Abstract = {Malac || Remip + Hexa (Brachiop did not present)},
File = {ertas2009_remipedia.pdf}
}
@Article{Erwin2009,
Title = {{Early origin of the bilaterian developmental toolkit}},
Author = {D. H. Erwin},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2009},
Number = {1527},
Pages = {2253--2261},
Volume = {364},
Abstract = {Ediacarians were probably cnidarians and placozoans},
Doi = {10.1098/rstb.2009.0038},
File = {erwin2009_bilaterian_toolkit.pdf}
}
@Article{Erwin2011,
Title = {{The Cambrian conundrum: Early divergence and later ecological success in the early history of animals.}},
Author = {D. H. Erwin and M. Laflamme and S. M. Tweedt and E. A. Sperling and D. Pisani and K. J. Peterson},
Journal = {Science},
Year = {2011},
Number = {6059},
Pages = {1091--1097},
Volume = {334},
Abstract = {Review},
Doi = {10.1126/science.1206375},
File = {erwin2011_cambrian_conundrum.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22116879}
}
@Article{Escalera2010,
Title = {{Cyanobacterial Endosymbionts in the Benthic Dinoflagellate Sinophysis canaliculata (Dinophysiales, Dinophyceae).}},
Author = {L. Escalera and B. Reguera and K. Takishita and S. Yoshimatsu and K. Koike and K. Koike},
Journal = {Protist},
Year = {2010},
Abstract = {Primary endosymbiosis in dinoflagellates!},
Doi = {10.1016/j.protis.2010.07.003},
File = {escalera2010_sinophysis_cyanob.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20934378}
}
@Article{Escapa2013,
Title = {{Phylogenetic Analysis of Araucariaceae: Integrating Molecules, Morphology, and Fossils}},
Author = {I. H. Escapa and S. A. Catalano},
Journal = {International Journal of Plant Sciences},
Year = {2013},
Number = {8},
Pages = {1153--1170},
Volume = {174},
Abstract = {As stated},
Doi = {10.1086/672369},
File = {escapa2013_araucariaceae.pdf},
Url = {http://www.jstor.org/stable/10.1086/672369}
}
@Article{Esser2007,
Title = {{The origin of mitochondria in light of a fluid prokaryotic chromosome model}},
Author = {C. Esser and W. Martin and T. Dagan},
Journal = {Biol. Lett.},
Year = {2007},
Pages = {180--184},
Volume = {3},
Abstract = {Magnetococcus > a-proteobacteria},
File = {esser2006.pdf}
}
@Article{Esteban2005,
Title = {{\textit{Paraluffisphaera tuba} gen. n., sp. n.~~--- a Newly-discovered Eukaryote}},
Author = {G. F. Esteban and K. J. Clarke and B. J. Finlay},
Journal = {Acta Protozool.},
Year = {2005},
Pages = {265--270},
Volume = {44},
Abstract = {Holozea inside Protista},
File = {esteban2005.pdf}
}
@Article{Ettwig2009,
Title = {{Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum}},
Author = {K. F. Ettwig and T. van Alen and K. T. van de Pas-Schoonen and M. S. M. Jetten and M. Strous},
Journal = {Environ. Microbiol.},
Year = {2009},
Number = {11},
Pages = {3656--3662},
Volume = {75},
Abstract = {Maybe close to Acido},
Doi = {10.1128/AEM.00067-09},
File = {ettwig2009_nc10.pdf}
}
@Article{Euzeby2008,
Title = {{List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet (List of Prokaryotic names with Standing in Nomenclature. Last full update: July 04, 2008. Classification of domains and phyla)}},
Author = {J. P. Euzeby},
Journal = {Int. J. Syst. Bacteriol.},
Year = {1997},
Pages = {590--592},
Volume = {47},
File = {euzeby20080107.txt},
Url = {http://www.bacterio.cict.fr/classifphyla.html}
}
@Article{Evans2014,
Title = {{X-cell disease in Antarctic fishes}},
Author = {C. W. Evans and K. Tupmongkol},
Journal = {Polar Biol},
Year = {2014},
Abstract = {Might be Apicomplexa},
Doi = {10.1007/s00300-014-1518-6},
File = {evans2014_x_cells.pdf}
}
@Article{Evans2010,
Title = {{The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Datasets}},
Author = {N. M. Evans and M. T. Holder and M. S. Barbeitos and B. Okamura and P. Cartwright},
Journal = {Molecular biology and evolution},
Year = {2010},
Abstract = {Or inside Medusozoa, or as a sister to Bilateria},
Doi = {10.1093/molbev/msq159},
File = {evans2010_myxozoa.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20576761}
}
@Article{Evans2009,
Title = {{Correction: Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria}},
Author = {N. M. Evans and A. Lindner and E. V. Raikova and A. G. Collins and P. Cartwright},
Journal = {BMC Evol. Biol.},
Year = {2009},
Pages = {165},
Volume = {9},
Abstract = {Not so close to Cnidaria},
Doi = {10.1186/1471-2148-9-165},
File = {evans2009_polypodium_corr.pdf}
}
@Article{Evans2008,
Title = {{Phylogenetic placement of the enigmatic parasite, \textit{Polypodium hydriforme}, within the Phylum Cnidaria}},
Author = {N. M. Evans and A. Lindner and E. V. Raikova and A. G. Collins and P. Cartwright},
Journal = {BMC Evol. Biol.},
Year = {2008},
Number = {139},
Pages = {1--42},
Volume = {8},
Abstract = {Polypodiozoa || Hydrozoa, Myxozoa unclear (often || Bilateria)},
Doi = {10.1186/1471-2148-8-139},
File = {evans2008.pdf}
}
@Article{Everroad2006,
Title = {{Comparative molecular evolution of newly discovered picocyanobacterial strains reveals a phylogenetically informative variable region of beta-phycoerythrin}},
Author = {R. C. Everroad and A. M. Wood},
Journal = {J. Phycol.},
Year = {2006},
Number = {6},
Pages = {1300--1311},
Volume = {42},
Abstract = {Gloeobacter > cyanobacteria},
File = {everroad2006.pdf}
}
@Article{Exposito2008,
Title = {{Demosponge and sea anemone fibrillar collagen diversity reveals the early emergence of A/C clades and the maintenance of the modular structure of type V/XI collagens from sponge to human}},
Author = {J.-Y. Exposito and C. Larroux and C. Cluzel and U. Valcourt and C. Lethias and B. M. Degnan},
Journal = {J. Biol. Chem.},
Year = {2008},
Number = {42},
Pages = {28226--28235},
Volume = {283},
Abstract = {Porifera (only Demosp.) -> Cnidaria (w/o Ctenophora) -> Bilateria},
Doi = {10.1074/jbc.M804573200},
File = {exposito2008.pdf}
}
@Article{Eyun2017,
Title = {{Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies.}},
Author = {S.-I. Eyun},
Journal = {BMC Evol. Biol.},
Year = {2017},
Number = {1},
Pages = {23},
Volume = {17},
Abstract = {((Malacostraca + Thecostraca) | Copepoda) | Insecta + Brachiopoda},
Doi = {10.1186/s12862-017-0883-5},
File = {eyun2017_copepoda_phylog.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20975721}
}
@Article{Fahrein2007,
Title = {{The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida}},
Author = {K. Fahrein and G. Talarico and A. Braband and L. Podsiadlowski},
Journal = {BMC Genomics},
Year = {2007},
Pages = {386},
Volume = {8},
Abstract = {Solfugida are basal, ~ Limulus},
Doi = {10.1186/1471-2164-8-386},
File = {fahrein2007.pdf}
}
@Article{Falcon2010,
Title = {{Dating the cyanobacterial ancestor of the chloroplast}},
Author = {L. I. Falc{\'o}n and S. Magall{\'o}n and A. Castillo},
Journal = {ISME J},
Year = {2010},
Number = {6},
Pages = {777 - 783},
Volume = {4},
Abstract = {Paleoproterozoic},
Doi = {10.1038/ismej.2010.2},
File = {falcon2010_dating_cyanob_chloropl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20200567}
}
@Article{Faller2012,
Title = {{Comparative neuroanatomy of Caudofoveata, Solenogastres, Polyplacophora, and Scaphopoda (Mollusca) and its phylogenetic implications}},
Author = {S. Faller and B. H. Rothe and C. Todt and A. Schmidt-Rhaesa and R. Loesel},
Journal = {Zoomorphology},
Year = {2012},
Abstract = {Aplacophora should be split},
Doi = {10.1007/s00435-012-0150-7},
File = {faller2012_mollusks.djvu}
}
@Article{Fanenbruck2004,
Title = {{The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships}},
Author = {M. Fanenbruck and S. Harzsch and J. W. Wagele},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2004},
Number = {11},
Pages = {3868--3873},
Volume = {101},
Abstract = {Chelicerata || Maxillopoda + Branchiopoda || Remipedia + Malacostraca + Hexapoda},
File = {fanenbruck2004.pdf}
}
@Article{Fang2021,
Title = {{Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread Sumerlaeota}},
Author = {Y. Fang and Y. Yuan and H. Jianga and J. Liu and G. Wu and J. Yang and Z. Hua and J. Han and X. Zhang and W. Li and c},
Journal = {mBio},
Year = {2021},
Abstract = {~ Latescibacteria},
Doi = {10.1128/mBio.00350-21.},
File = {fang2021_sumerlaeota.pdf}
}
@Article{Farge2000a,
Title = {{Phylogenetic Relationships Within the Haplolepideous Mosses}},
Author = {C. La Farge and B. D. Mishler and J. A. Wheeler and D. P. Wall and K. Johannes and S. Schaffer and A. J. Shaw},
Journal = {Bryologist},
Year = {2000},
Number = {2},
Pages = {257--276},
Volume = {103}
}
@Article{Fawley2013,
Title = {{The diversity and phylogeny of the commercially important algal class Eustigmatophyceae, including the new clade Goniochloridales}},
Author = {K. P. Fawley and M. Eli{\'a}{\v{s}} and M. W. Fawley},
Journal = {J. Appl. Phycol.},
Year = {2013},
Volume = {10},
Abstract = {As stated},
Doi = {10.1007/s10811-013-0216-z},
File = {fawley2013_eustigmatophyceae.pdf}
}
@Article{Fawley2011,
Title = {{Phylogeny of the Pedinophyceae (Chlorophyta)}},
Author = {M. W. Fawley and M. A. Buchheim and F. W. Zechman},
Journal = {J. Phycol.},
Year = {2011},
Pages = {S1--S98},
Volume = {47},
Abstract = {Class comprises the genera Pedinomonas, Resultor, and Marsupiomonas},
Doi = {10.1111/j.1529-8817.2011.01050.x},
File = {fawley2011_pedinophyceae.pdf}
}
@Article{Fedonkin2009,
Title = {{Eukaryotization of the Early Biosphere: A Biogeochemical Aspect}},
Author = {M. A. Fedonkin},
Journal = {Geochemistry International},
Year = {2009},
Number = {13},
Pages = {1265--1333},
Volume = {47},
Abstract = {Looks more like review},
Doi = {10.1134/S0016702909130011},
File = {fedonkin2009_eukariotization_of_biosphere.pdf}
}
@Book{Fedonkin1987,
Title = {The skeleton-less vendian fauna and its place into phanerozoic evolution},
Author = {M. A. Fedonkin},
Publisher = {Nauka},
Year = {1987},
Address = {Moscow},
Note = {(In Russian)},
Volume = {226},
Pages = {176}
}
@Book{Fedonkin2007,
Title = {{The Rise of Animals: Evolution and Diversification of the Kingdom Animalia}},
Author = {M. A. Fedonkin and J. G. Gehling and K. Grey and G. M. Narbonne and P. Vickers-Rich},
Publisher = {JHU Press},
Year = {2007},
Address = {Baltimore},
ISBN = {0801886791},
Pages = {1--326}
}
@Book{Fedotov1966,
Title = {Evoljucija i filogenija bespozvonochnyh zhivotnyh},
Author = {D. M. Fedotov},
Publisher = {Nauka},
Year = {1966},
Address = {Moscow},
Note = {(In Russian)},
Abstract = {evoljucija, Metazoa},
Pages = {404}
}
@Article{FeldmanMuhsama1963,
Title = {{On Adlerocystis n. gen. (Phycomycetes) a symbiote of Ornithodoros ticks}},
Author = {B. Feldman-Muhsama and Y. Havivia},
Journal = {Parasitology},
Year = {1963},
Pages = {183--188},
Volume = {53},
Abstract = {A n.gen. and n.sp. of a yeast-like micro-organism???Adlerocystis ornithodori???is described. This micro-organism is probably a symbiote of sperm cells of Ornithodoros tholozani. Another species, A. parkeri n.sp., is found in O. parkeri.},
Doi = {10.1017/S003118200007267X},
File = {feldman-muhsama1963_adlerocystis.txt}
}
@Article{Fell2000,
Title = {{Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis}},
Author = {J. W. Fell and T. Boekhout and A. Fonseca and G. Scorzetti and A. Statzell-Tallman},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2000},
Pages = {1351--1371},
Volume = {50}
}
@Article{Feller1998,
Title = {{Molecular Evidence for the Early History of Living Amphibians}},
Author = {A. E. Feller and S. B. Hedges},
Journal = {Mol. Phyl. Evol.},
Year = {1998},
Number = {3},
Pages = {509--516},
Volume = {9}
}
@Article{Fenchel2004,
Title = {{``Candidatus \textit{Ovobacter propellens}'': a large conspicuous prokaryote with an unusual motility behaviour}},
Author = {T. Fenchel and R. Thar},
Journal = {FEMS Microbiol. Ecol.},
Year = {2004},
Number = {2004},
Pages = {231--238},
Volume = {48},
Abstract = {Ovobacter i.s., ~ Planctobacteria? (membrane structures)},
File = {fenchel2004_ovobacter.pdf}
}
@Article{Feng1997,
Title = {{Determining divergence times with a protein clock: Update and reevaluation}},
Author = {D.-F. Feng and G. Cho and R. F. Doolittle},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1997},
Pages = {13028--13033},
Volume = {94}
}
@Article{Feng2014,
Title = {{New phylogenomic and comparative analyses provide corroborating evidence that Myxozoa is Cnidaria.}},
Author = {J.-M. Feng and J. Xiong and J.-Y. Zhang and Y.-L. Yang and B. Yao and Z.-G. Zhou and W. Miao},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Pages = {10--18},
Volume = {81C},
Abstract = {sister to Medusozoa, Polypodium absent},
Doi = {10.1016/j.ympev.2014.08.016},
File = {feng2014_myxozoa_cnidaria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25192780}
}
@Article{Fernandez2016,
Title = {{Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction.}},
Author = {R. Fern{\'a}ndez and G. D. Edgecombe and G. Giribet},
Journal = {Syst. Biol.},
Year = {2016},
Abstract = {Pauropoda || Symphyla || Chilo || Diplo},
Doi = {10.1093/sysbio/syw041},
File = {fernandez2016_myriapoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27162151}
}
@Article{Fernandes2019,
Title = {{A multigene timescale and diversification dynamics of Ciliophora evolution.}},
Author = {N. M. Fernandes and C. G. Schrago},
Journal = {Molecular phylogenetics and evolution},
Year = {2019},
Pages = {106521},
Volume = {139},
Abstract = {Protocruziea, SAL (incl. Licnophora sed.m.): Spirotrichea + Lamellicorticata},
Doi = {10.1016/j.ympev.2019.106521},
File = {fernandes2019_ciliophora.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31152779}
}
@Article{Ferrari2009,
Title = {{Remarks on the '`Subcoxa'' hypothesis from Backer - et al. (2008)}},
Author = {F. D. Ferrari},
Journal = {Zoologischer Anzeiger},
Year = {2009},
Pages = {33--34},
Volume = {248},
Abstract = {Against Tracheata},
Doi = {10.1016/j.jcz.2008.10.001},
File = {ferrari2009_subcoxa.pdf}
}
@Article{Ferrera2007,
Title = {{Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales}},
Author = {I. Ferrera and S. Longhorn and A. B. Banta and Y. Liu and D. Preston and A.-L. Reysenbach},
Journal = {Extremophiles},
Year = {2007},
Number = {1},
Pages = {57--64},
Volume = {11},
File = {ferrera2006.pdf}
}
@Article{Ferrier2012,
Title = {{Evolutionary crossroads in developmental biology: Annelids.}},
Author = {D. E. K. Ferrier},
Journal = {Development},
Year = {2012},
Number = {15},
Pages = {2643--2653},
Volume = {139},
Abstract = {Chaetopteridae || Myzo || Sipuncila || Errantia (Nereidae etc.) || Sedentaria (incl. Serpulidae, Echiura) || Clitellata},
Doi = {10.1242/dev.074724},
File = {ferrier2012_annelids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22782719}
}
@Article{Feuda2014,
Title = {{The comb jelly opsins and the origins of animal phototransduction.}},
Author = {R. Feuda and O. Rota-Stabelli and T. H. Oakley and D. Pisani},
Journal = {Genome Biol Evol},
Year = {2014},
Number = {8},
Pages = {1964--1971},
Volume = {6},
Abstract = {Our results are most parsimoniously interpreted assuming a traditional animal phylogeny where Ctenophora are not the sister group of all the other animals.},
Doi = {10.1093/gbe/evu154},
File = {feuda2014_ctenophora_opsins.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/12761335}
}
@Article{Fiala2006,
Title = {{The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis}},
Author = {I. Fiala},
Journal = {Int. J. Parasitol.},
Year = {2006},
Pages = {1521--1534},
Volume = {36},
Abstract = {Marine and freshwater clades},
File = {fiala2006.pdf}
}
@Article{Field2015,
Title = {{Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum.}},
Author = {A. R. Field and W. Testo and P. D. Bostock and J. A. M. Holtum and M. Waycott},
Journal = {Mol. Phylogenet. Evol.},
Year = {2015},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2015.09.024},
File = {field2015_huperzia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26493224}
}
@Article{Field1988,
Title = {{Molecular phylogeny of the animal kingdom}},
Author = {K. G. Field and G. J. Olsen and D. J. Lane and S. J. Giovannoni and M. T. Ghiselin and E. C. Raff and N. R. Pace and R. A. Raff},
Journal = {Science},
Year = {1988},
Pages = {748--753},
Volume = {239}
}
@Article{Fieseler2004,
Title = {{Discovery of the Novel Candidate Phylum ``Poribacteria'' in Marine Sponges}},
Author = {L. Fieseler and M. Horn and M. Wagner and U. Hentschel},
Journal = {Appl. Environ. Microbiol.},
Year = {2004},
Number = {6},
Pages = {3724--3732},
Volume = {70},
File = {fielser2004.pdf}
}
@Article{Fieseler2006,
Title = {{Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics}},
Author = {L. Fieseler and A. Quaiser and C. Schleper and U. Hentschel},
Journal = {Environ. Microbiol.},
Year = {2006},
Number = {4},
Pages = {612--624},
Volume = {8},
File = {fielser2006.pdf}
}
@Article{Figge1999,
Title = {{Glyceraldehyde-3-Phosphate Dehydrogenase Gene Diversity in Eubacteria and Eukaryotes: Evidence for Intra- and Inter-Kingdom Gene Transfer}},
Author = {R. M. Figge and M. Schubert and H. Brinkmann and R. Cerff},
Journal = {Mol. Biol. Evol.},
Year = {1999},
Number = {4},
Pages = {429--440},
Volume = {16}
}
@Article{FigueroaMartinez2018,
Title = {{Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity}},
Author = {F. Figueroa-Martinez and C. Jackson and A. Reyes-Prieto},
Journal = {Genome Biol. Evol.},
Year = {2018},
Number = {1},
Pages = {174 - 188},
Volume = {11},
Abstract = {Closest to cyanobact. but not within},
Doi = {10.1093/gbe/evy268},
File = {figueroa-martinez2018_glaucophyta_plastid_genomes.pdf}
}
@Article{Finet2010,
Title = {{Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants}},
Author = {C. Finet},
Journal = {Current Biology},
Year = {2010},
Pages = {1--6},
Volume = {20},
Abstract = {first multigene phylogenetic evidence that Coleochaetales represent the closest living relatives of land plants},
Doi = {10.1016/j.cub.2010.11.035},
File = {finet2010_land_plants.pdf},
ISSN = {0960-9822},
Url = {http://dx.doi.org/10.1016/j.cub.2010.11.035}
}
@Article{Finet2012,
Title = {{Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants}},
Author = {C. Finet and R. Timme and C. Delwiche and F. MarlEtaz},
Journal = {Current Biology},
Year = {2012},
Month = {7 August},
Pages = {1456--1457},
Volume = {22},
Abstract = {Both Zygnematales and Coleochaete sister},
Doi = {10.1016/j.cub.2012.07.021},
File = {finet2012_orig_land_plants.pdf},
ISSN = {0960-9822},
Url = {http://dx.doi.org/10.1016/j.cub.2012.07.021}
}
@Article{FioreDonno2009b,
Title = {{Semimorula liquescens: A modified echinostelid. Semimorula liquescens is a modified echinostelid myxomycete (Mycetozoa)}},
Author = {A. M. Fiore-Donno and E. F. Haskins and J. Pawlowski and T. Cavalier-Smith},
Journal = {Mycologia},
Year = {In press},
Abstract = {As stated},
Doi = {10.3852/08-075},
File = {F:/ref/os/1/fiore-donno2009_semimorula.pdf}
}
@Article{FioreDonno2010,
Title = {{Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria}},
Author = {A. M. Fiore-Donno and A. Kamono and E. E. Chao and M. Fukui and T. Cavalier-Smith},
Journal = {The Journal of eukaryotic microbiology},
Year = {2010},
Abstract = {To Stemonitida and Physarida},
Doi = {10.1111/j.1550-7408.2009.00466.x},
File = {fiore-donno2010_hyperamoeba_invalidation.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20113379}
}
@Article{FioreDonno2008,
Title = {{Evolution of dark-spored Myxomycetes (slime-molds): Molecules versus morphology}},
Author = {A. M. Fiore-Donno and M. Meyer and S. L. Baldauf and J. Pawlowski},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {6},
Pages = {878--889},
Volume = {46},
Abstract = {Stemonitales paraphyletic},
Doi = {10.1016/j.ympev.2007.12.011},
File = {fiore-donno2008.pdf}
}
@Article{FioreDonno2009a,
Title = {{Deep Phylogeny and Evolution of Slime Moulds (Mycetozoa)}},
Author = {A. M. Fiore-Donno and S. I. Nikolaev and M. Nelson and J. Pawlowski and T. Cavalier-Smith and S. L. Baldauf},
Journal = {Protist},
Year = {In press},
Abstract = {Phalanst + Acram + Multicilia || Filamoeba intermixed with Protostelia || Archamoebae || Macromycetozoa: Dict, Ceratiomyxa, Myxogastria},
Doi = {10.1016/j.protis.2009.05.002},
File = {fiore-donno2009_mycetozoa_phylogeny.pdf},
ISSN = {1434-4610}
}
@Article{FioreDonno2007,
Title = {{Evolutionary pathways in fruiting amoebae (Mycetozoa)}},
Author = {A. M. Fiore-Donno and J. Pawlowski and S. Baldauf and T. Cavalier-Smith},
Journal = {Protistology},
Year = {2007},
Number = {1},
Pages = {9--91},
Volume = {5},
Abstract = {Protostelia (non-monoph?) || Dictyostelia || Ceratiomyxa + other Myxogastria}
}
@Article{FioreDonno2018,
Title = {{A Non-Flagellated Member of the Myxogastria and Expansion of the Echinosteliida.}},
Author = {A. M. Fiore-Donno and A. K. Tice and M. W. Brown},
Journal = {J. Eukaryot. Microbiol.},
Year = {2018},
Abstract = {Dictyost || Protosporangiida (Ceratiomyxa) || Myxogastria},
Doi = {10.1111/jeu.12694},
File = {fiore-donno2018_echinosteliopsis_myxogastria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30329204}
}
@Article{Fitzpatrick2006,
Title = {{A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis}},
Author = {D. A. Fitzpatrick and M. E. Logue and J. E. Stajich and G. Butler},
Journal = {BMC Evol. Biol.},
Year = {2006},
Number = {99},
Pages = {1--15},
Volume = {6},
File = {fitzpatrick2006.pdf}
}
@Article{FizPalacios2013,
Title = {{Did terrestrial diversification of amoebas (Amoebozoa) occur in synchrony with land plants?}},
Author = {O. Fiz-Palacios and M. Romeralo and A. Ahmadzadeh and S. Weststrand and P. E. Ahlberg and S. Baldauf},
Journal = {PLoS ONE},
Year = {2013},
Number = {9},
Pages = {e74374},
Volume = {8},
Abstract = {Macromycetozoa before, Arcellinida in synchrony},
Doi = {10.1371/journal.pone.0074374},
File = {fiz-palacios2013_amoebozoa_timetree.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19004754}
}
@Article{FizPalacios2011,
Title = {{Diversification of land plants: Insights from a family-level phylogenetic analysis.}},
Author = {O. Fiz-Palacios and H. Schneider and J. Heinrichs and V. Savolainen},
Journal = {BMC Evol. Biol.},
Year = {2011},
Pages = {341},
Volume = {11},
Abstract = {concatenated data},
Doi = {10.1186/1471-2148-11-341},
File = {fiz-palacious2011_land_plants_fam_phylog.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22103931}
}
@Article{Flores2017,
Title = {{Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): Towards a robustly diagnosed classification}},
Author = {J. R. Flores and S. A. Catalano and J. Munoz and G. M. Suarez},
Journal = {Cladistics},
Year = {2017},
Abstract = {As stated},
Doi = {10.1111/cla.12225},
File = {flores2017_marchantiidae.pdf}
}
@Article{Foissner1993a,
Title = {{Revision of the Family Spironemidae Doflein (Protista, Hemimastigophora), with Desription of Two Species, \textit{Spironema terricola} N. Sp. and \textit{Stereonema geiseri} N. G., N. Sp.}},
Author = {I. Foissner and W. Foissner},
Journal = {J. Euk. Microbiol.},
Year = {1993},
Number = {4},
Pages = {422--438},
Volume = {40},
Abstract = {Two new hemimastigophoran flagellates are described using light and electron microscopy, and the family Spironemidae is revised. Spironema terricola n. sp. occurs in soil from the Grand Canyon (southwest USA). It moves in a conspicuously euglenoid manner and differs from S. multiciliatum Klebs by its vermiform shape and shorter kinetics. Spironema terricola is similar to Goodey's Spironema multiciliatum from soil in England. However, Goodey's vermiform species has a very elongate nucleus and is thus neither identical with S. terricola, which has a roundish nucleus, nor with Klebs' lanceolate S. multiciliatum; we consider it a new species, Spironema goodeyi n. sp, Stereonema geiseri n. g., n. sp. was discovered in the Aufwuchs (periphyton) of a river in Bavaria, Germany. the new genus differs from Spironema by its a contractility, and from Hemimastix by its shorter kinetics and less plicate cortex. the fine structure of Spironema and Stereonema is very similar to that of Hemimastix Foissner et al., viz., the cortex is composed of two plates having diagonal symmetry and the flagellated basal bodies have associated a short and a long microtubular ribbon. All species have unique extrusomes of the same type. the main differences between the three genera and five species recognized are contractility, length of kinetics, body size, shape of cell and nucleus, and particulars of the cortex and extrusomes. the phylogenetic relationships of the Hemimastigophora are still uncertain. However, the diagonal symmetry of the cortical plates and the pronounced euglenoid movement of Spironema spp. suggest a common ancestor with euglenids.}
}
@Article{Foissner1988,
Title = {{The Hemimastigophora (\textit{Hemimastix amphikineta} nov. gen., nov. spec.), a new protozoan phylum from Gondwanian soils}},
Author = {W. Foissner and H. O. Blatterer and I. Foissner},
Journal = {Eur. J. Protistol.},
Year = {1988},
Pages = {361--383},
Volume = {23}
}
@Article{Foissner1993,
Title = {{The Hemimastigophora, remarkable heterotrophic flagellates possibly related to euglenoid protists}},
Author = {W. Foissner and I. Foissner},
Journal = {Proc. Germ. Zool. Soc.},
Year = {1993},
Number = {1},
Pages = {136},
Volume = {86}
}
@Article{Foret2010,
Title = {{Phylogenomics reveals an anomalous distribution of USP genes in metazoans}},
Author = {S. For{\^e}t and F. Seneca and D. de Jong and A. Bieller and G. Hemmrich and R. Augustin and D. C. Hayward and E. E. Ball and T. C. G. Bosch and K. Agata and M. Hassel and D. J. Miller},
Journal = {Molecular biology and evolution},
Year = {2010},
Abstract = {none were detected in any of the available ecdysozoan or non-urochodate deuterostome},
Doi = {10.1093/molbev/msq183},
File = {foret2010_usp_metazoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20660083}
}
@Article{Forrest2006,
Title = {{Unraveling the evolutionary history of the liverworts (Marchantiophyta): multiple taxa, genomes and analyses}},
Author = {L. L. Forrest},
Journal = {Bryologist
},
Year = {2006},
Number = {3},
Pages = {303--334},
Volume = {109},
Abstract = {Hepaticae: Haplomitriopsida (incl. Treubiaceae), Marchatiopsida (inc. Blasiales), Jungermanniopsida || Anthocerotophytina + Tracheophytes || Bryophytina},
File = {forrest2006.pdf}
}
@Article{Forterre2010a,
Title = {{Defining life: The virus viewpoint}},
Author = {P. Forterre},
Journal = {Orig Life Evol Biosph},
Year = {2010},
Number = {2},
Pages = {151--160},
Volume = {40},
Abstract = {Viruses are capsid-encoded organisms},
Doi = {10.1007/s11084-010-9194-1},
File = {forterre2010_def_life_viruses.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20198436}
}
@Article{Forterre2010b,
Title = {{A new fusion hypothesis for the origin of Eukarya: Better than previous ones, but probably also wrong}},
Author = {P. Forterre},
Journal = {Research in Microbiology},
Year = {2010},
Abstract = {Eukarya originated from the engulfment of a thaumarchaeon by a PCV (Planctomycetes, Verrucomicrobia, Chlamydiae) bacterium, followed by invasions of NCLDV and retroviruses.},
File = {forterre2010_leca_fusion.djvu}
}
@Article{Foster2009,
Title = {{The primary divisions of life: A phylogenomic approach employing composition-heterogeneous methods}},
Author = {P. G. Foster and C. J. Cox and T. M. Embley},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2009},
Number = {1527},
Pages = {2197--2207},
Volume = {364},
Abstract = {Support for eocytes},
Doi = {10.1098/rstb.2009.0034},
File = {foster2009_divisions_of_life.pdf}
}
@Article{Fournier2010b,
Title = {{Evolution of the Archaea: Emerging Views on Origins and Phylogeny}},
Author = {G. P. Fournier and A. A. Dick and D. Williams and J. P. Gogarten},
Journal = {Research in Microbiology},
Year = {2010},
Abstract = {Review},
File = {fournier2010_archaea.djvu}
}
@Article{Fournier2010a,
Title = {{Rooting the Ribosomal Tree of Life}},
Author = {G. P. Fournier and J. P. Gogarten},
Journal = {Molecular biology and evolution},
Year = {2010},
Abstract = {Placing the root of the translation machinery along the bacterial branch},
Doi = {10.1093/molbev/msq057},
File = {fournier2010_translation_root.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20194428}
}
@Article{Fox1980,
Title = {{The phylogeny of procaryotes}},
Author = {G. E. Fox and E. Stackebrandt and R. B. Hespell and J. Gibson and J. Maniloff and T. A. Dyer and R. S. Wolfe and W. E. Balch and R. S. Tanner and L. J. Magrum and L. B. Zablen and R. Blakemore and R. Gupta and L. Bonen and B. J. Lewis and DA Stahl and K. R. Luehrsen and K. N. Chen and C. R. Woese},
Journal = {Science},
Year = {1980},
Number = {4455},
Pages = {457--463},
Volume = {209}
}
@Article{Franceschi2000,
Title = {{Origin of \textit{Ginkgo biloba} L. Phylogenetic approach}},
Author = {D. D. Franceschi and C. Vozenin-Serra},
Journal = {C. R. Acad. Sci. III},
Year = {2000},
Number = {6},
Pages = {583--592},
Volume = {323}
}
@Article{Francis2020,
Title = {{Very few sites can reshape the inferred phylogenetic tree}},
Author = {W. R. Francis and D. E. Canfield},
Journal = {PeerJ},
Year = {2020},
Abstract = {As stated (Animalia roots)},
Doi = {10.7717/peerj.8865},
File = {francis2020_very_few_sites_can_reshape_phylogenetic_tree.pdf}
}
@Article{Francis2018,
Title = {{Very few sites can reshape a phylogenetic tree}},
Author = {W. R. Francis and D. E. Canfield},
Journal = {bioRxiv},
Year = {2018},
Doi = {10.1101/413518},
File = {francis2018_very_few_sites_can_reshape_phylogenetic_tree.pdf},
Url = {http://dx.doi.org/10.1101/413518}
}
@Article{Frenzel1892,
Title = {{Untersuchungen {\"u}ber die mikroskopische Fauna Argentiniens}},
Author = {J. Frenzel},
Journal = {Archiv fuer Naturgeschichte},
Year = {1892},
Pages = {66--96},
Volume = {58},
Abstract = {Salinella salve, later described as a sole member of phylum Monoblastozoa R. Blackwelder, 1963},
File = {frenzel1892_salinella.djvu}
}
@Article{Freund2018,
Title = {{Inferring the evolutionary reduction of corm lobation in Iso{\"e}tes using Bayesian model-averaged ancestral state reconstruction.}},
Author = {F. D. Freund and W. A. Freyman and C. J. Rothfels},
Journal = {Am. J. Bot.},
Year = {2018},
Number = {2},
Pages = {275 - 286},
Volume = {105},
Abstract = {3-lobate ancestral; methods are interesting!},
Doi = {10.1002/ajb2.1024},
File = {freund2018_isoetes_bayes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29573405}
}
@Article{Frey2005,
Title = {A morpho-molecular classification of the liverworts (Hepaticophytina, Bryophyta)},
Author = {W. Frey and M. Stech},
Journal = {Nova Hedwigia},
Year = {2005},
Pages = {55--78(24)},
Volume = {81},
Abstract = {Superclass I: Treubiops., Haplomitr.; II: Blasiops., Marchantiops.; III: _Fossombroniops._, Pallaviciniops., Pelliops. + families i.s.; IV: Jungermanniops.},
Doi = {10.1127/0029-5035/2005/0081-0055}
}
@Article{Friedl2002,
Title = {{Phylogenetic relationships of green algae assigned to the genus Planophila (Chlorophyta) : evidence from 18S rDNA sequence data and ultrastructure}},
Author = {T. Friedl and C. O'Kelly},
Journal = {Eur. J. Phycol.},
Year = {2002},
Pages = {373--384},
Volume = {37},
Abstract = {Chlorodendr || Treboux || Chloro || Ulvo},
File = {friedl2002.pdf}
}
@Article{Friedl2012,
Title = {{Systematics of the Green Algae: A Brief Introduction to the Current Status}},
Author = {T. Friedl and N. Rybalka},
Journal = {Progress in Botany},
Year = {2012},
Volume = {73},
Abstract = {Mamiello || Nephrosel || Chlorod || Trebouxia incl. Prasiola || Chloroph + Ulv},
Doi = {10.1007/978-3-642-22746-2_10},
File = {friedl2011_green_algae_syst.pdf}
}
@Article{Friedman2015,
Title = {{Development and evolution of the female gametophyte and fertilization process in Welwitschia mirabilis (Welwitschiaceae).}},
Author = {W. E. Friedman},
Journal = {Am. J. Bot.},
Year = {2015},
Number = {2},
Pages = {312--324},
Volume = {102},
Abstract = {No double fertilization},
Doi = {10.3732/ajb.1400472},
File = {friedman2015_welwitschia_fert.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25667083}
}
@Article{Friedman2014,
Title = {{Fertilization in Welwitschia mirabilis: It Doesn't Get Any Weirder (or Apomorphic)!}},
Author = {W. E. Friedman},
Year = {2014},
Abstract = {No double fertilization},
Annote = {Boise, Idaho},
Booktitle = {{Botany 2014}},
File = {friedman2014_welwitschia_no_double_fertilization.txt},
Url = {http://www.2014.botanyconference.org/engine/search/index.php?func=detail&aid=469}
}
@Article{Friis2007,
Title = {{Phase-contrast X-ray microtomography links Cretaceous seeds with Gnetales and Bennettitales}},
Author = {E. M. Friis and P. R. Crane and K. R. Pedersen and S. Bengtson and P. C. J. Donoghue and G. W. Grimm and M. Stampanoni},
Journal = {Nature},
Year = {2007},
Pages = {549--553},
Volume = {450},
Abstract = {Gnetales ~ Bennettitales},
File = {friis2007.pdf}
}
@Article{Fritzsch2008,
Title = {{PCR Survey of Xenoturbella bocki Hox Genes}},
Author = {G. Fritzsch and M. U. Bohme and M. Thorndyke and H. Nakano and O. Israelsson and T. Stach and M. Schlegel and T. Hankeln and P. F. Stadler},
Journal = {J. Exp. Zool.},
Year = {2008},
Pages = {278--284},
Volume = {310B},
Abstract = {An alternative explanation for the small number of Hox genes would be a more basal phylogenetic position of Xenoturbella},
Doi = {10.1002/jez.b.21208},
File = {fritzsch2008.pdf}
}
@Article{Frohlich2007,
Title = {{After a dozen years of progress the origin of angiosperms is still a great mystery}},
Author = {M. W. Frohlich and M. W. Chase},
Journal = {Nature},
Year = {2007},
Pages = {1184--1189},
Volume = {450},
Abstract = {As stated},
File = {frohlich2007.pdf}
}
@Article{Frohlich2000,
Title = {{The Mostly Male Theory of Flower Evolutionary Origins: from Genes to Fossils}},
Author = {M. W. Frohlich and D. S. Parker},
Journal = {Syst. Bot.},
Year = {2000},
Number = {2},
Pages = {155--170},
Volume = {25}
}
@Article{Frommolt2008,
Title = {{Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis}},
Author = {R. Frommolt and S. Werner and H. Paulsen and R. Goss and C. Wilhelm and S. Zauner and U. G. Maier and A. R. Grossman and D. Bhattacharya and M. Lohr},
Journal = {Mol. Biol. Evol.},
Year = {2008},
Number = {12},
Pages = {2653--2667},
Volume = {25},
Abstract = {As stated, pre-endosymb? or ancient genes?},
Doi = {10.1093/molbev/msn206},
File = {frommolt2008_chromista.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18799712}
}
@Article{Fu2014,
Title = {{Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.}},
Author = {C.-J. Fu and S. Sheikh and W. Miao and S. G. E. Andersson and S. L. Baldauf},
Journal = {Genome Biol Evol},
Year = {2014},
Number = {9},
Pages = {2240--2257},
Volume = {6},
Abstract = {As stated},
Doi = {10.1093/gbe/evu180},
File = {fu2014_heterolobosea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17483454}
}
@Article{Fuchs2010,
Title = {{The first internal molecular phylogeny of the animal phylum Entoprocta (Kamptozoa)}},
Author = {J. Fuchs and T. Iseto and M. Hirose and P. Sundberg and M. Obst},
Journal = {Molecular phylogenetics and evolution},
Year = {2010},
Abstract = {Tentaculata || Cyclioph || Coloniales + Solitaria},
Doi = {10.1016/j.ympev.2010.04.009},
File = {fuchs2010_kamptozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20398775}
}
@Article{Fuchs2009,
Title = {{The first comprehensive molecular phylogeny of Bryozoa (Ectoprocta) based on combined analyses of nuclear and mitochondrial genes}},
Author = {J. Fuchs and M. Obst and P. Sundberg},
Journal = {Molecular Phylogenetics and Evolution},
Year = {In press},
Abstract = {Phylactolemata -- basal branch},
Doi = {10.1016/j.ympev.2009.01.021},
File = {fuchs2009_bryozoa.pdf}
}
@Article{Fucikova2014,
Title = {{New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data}},
Author = {K. Fucikova and F. Leliaert and E. Cooper and P. Skaloud and S. D'hondt and O. De Clerck and F. Gurgel and L. Lewis and P. Lewis and J. Lopez-Bautista and C. F. Delwiche and H. Verbruggen},
Year = {2014},
Abstract = {Pedinophyceae || Chlorodendrophyceae incl. Oltmannsielliopsis || others, Ulvophyeae is probably not monophyletic},
Doi = {10.3389/fevo.2014.00063},
File = {fucikova2014_chlorophyta.pdf}
}
@InCollection{Fuerst2007,
Title = {{Semantides and Modern Bacterial Systematics}},
Author = {J. A. Fuerst},
Booktitle = {{Encyclopedia of Life Sciences}},
Publisher = {Whiley \& Sons},
Year = {2007},
Abstract = {OP5, TM7, OD2, ZB2, OP11, and OP10, AD3 ~ Chloroflexi; TM6, Marine_group_A ~ Endomicrobia; WS3, OP3 ~ PVC; Halanaerob ~ Thermot; Acido !Nitrospir; OP1 ~ Fuso; Deferrib. ~ Aminanaer.},
Doi = {10.1002/9780470015902.a0000464.pub2},
File = {fuerst2007.txt}
}
@Article{Fuerst2005,
Title = {{Intracellular Compartmentation in Planctomycetes}},
Author = {J. A. Fuerst},
Journal = {Annu. Rev. Microbiol.},
Year = {2005},
Pages = {299--328},
Volume = {59},
File = {fuerst2005.pdf}
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@Article{Fuerst2004,
Title = {{Planctomycetes~--- a phylum of emerging interest for microbial evolution and ecology}},
Author = {J. A. Fuerst},
Journal = {WFCC Newsletter},
Year = {2004},
Pages = {1--11},
Volume = {38},
File = {fuerst2004.pdf}
}
@Article{Fujita2008,
Title = {{Convergent evolution of shoots in land plants: lack of auxin polar transport in moss shoots}},
Author = {T. Fujita and H. Sakaguchi and Y. Hiwatashi and S. J. Wagstaff and M. Ito and H. Deguchi and T. Sato and M. Hasebe},
Journal = {Evolution and Development},
Year = {2008},
Number = {2},
Pages = {176--186},
Volume = {10},
Abstract = {Shoots in mosses and vascular plants are not homologous},
File = {fujita2008.pdf}
}
@Article{Fukuda2008,
Title = {{Phylogenetic analyses of the dinoflagellate \textit{Noctiluca scintillans} based on b-tubulin and Hsp90 genes}},
Author = {Y. Fukuda and H. Endoh},
Journal = {Eur. J. Protistol.},
Year = {2008},
Pages = {27--33},
Volume = {44},
Abstract = {Perkinsus || Oxyrrhis || Noctiluca || others},
Doi = {10.1016/j.ejop.2007.07.001},
File = {fukuda2008.pdf}
}
@Article{Fukuda2007,
Title = {{Life cycle and phylogenetic position of noctilucid dinoflagellate (\textit{Noctiluca scintillans})}},
Author = {Y. Fukuda and H. Endoh},
Journal = {Protistology},
Year = {2007},
Pages = {9--91},
Volume = {5},
Abstract = {Oxyrris || Noctiluca || other dino}
}
@Article{Fukunaga2008,
Title = {{Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum `Acidobacteria'}},
Author = {Y. Fukunaga and M. Kurahashi and K. Yanagi and A. Yokota and S. Harayama},
Journal = {Int. J. Syst. Appl. Microbiol.},
Year = {2008},
Pages = {2597--2601},
Volume = {58},
Abstract = {Halophagae = Subdivision 8 of Acidobacteria, Acidobacterium belongs to Subd. 1},
Doi = {10.1099/ijs.0.65589-0},
File = {fukunaga2008.pdf}
}
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Title = {{Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids}},
Author = {N. J. Fuller and C. Campbell and D. J. Allen and F. D. Pitt and K. Zwirglmaier and F. L. Gall and D. Vaulot and D. J. Scanlan},
Journal = {Aquat. Micr. Ecol.},
Year = {2006},
Pages = {79--93},
Volume = {43},
Abstract = {PLASTID 16S: Dictyoch. sep. from Pelago; Eustig. sep. from Chryso; Pingu || Raphido; Prasino deeply polyphyletic with sep. II,VI: Micromonas/Ostreococcus/Prasinoderma (~Eugl) and I,III: Nephroselmis/Pyramimonas (~ Strep); Glau || Rhodo},
File = {fuller2006.pdf}
}
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Title = {{Piwi expression in archeocytes and choanocytes in demosponges: Insights into the stem cell system in demosponges}},
Author = {N. Funayama and M. Nakatsukasa and K. Mohri and Y. Masuda and K. Agata},
Journal = {Evol. Dev.},
Year = {2010},
Number = {3},
Pages = {275--287},
Volume = {12},
Abstract = {the possibility that choanocytes might represent the ancestral stem cells},
Doi = {10.1111/j.1525-142X.2010.00413.x},
File = {funayama2010_demosp_stem_cells.pdf}
}
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Title = {{On the phylogenetic position of Rotifera~--- have we come any further?}},
Author = {P. Funch and M. V. S. rensen and M. Obst},
Journal = {Hydrobiologia},
Year = {2005},
Pages = {11--28},
Volume = {546},
Abstract = {Cycliophora may be Gnathifera, or may be close to Entoprocta},
Doi = {10.1007/s10750-005-4093-6},
File = {funch2005.pdf}
}
@Article{Funes2003,
Title = {{Response to Comment on ``A Green Algal Apicoplast Ancestor''}},
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Journal = {Science},
Year = {2003},
Pages = {49b},
Volume = {301}
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@Book{Fursenko1978,
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Author = {G. Poinar, Jr},
Journal = {Hydrobiologia},
Year = {2008},
Pages = {79--83},
Volume = {595},
Doi = {10.1007/s10750-007-9112-3},
File = {pojnar2008.pdf}
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@Article{Gomez2009,
Title = {{The crustacean parasites Ellobiopsis Caullery, 1910 and Thalassomyces Niezabitowski, 1913 form a monophyletic divergent clade within the Alveolata}},
Author = {F. G{\'o}mez and P. L{\'o}pez-Garc{\'i}a and A. Nowaczyk and D. Moreira},
Journal = {Syst. Parasitol.},
Year = {2009},
Number = {1},
Pages = {65--74},
Volume = {74},
Abstract = {Perkins || Ellob, MAG I || others},
Doi = {10.1007/s11230-009-9199-1},
File = {gomez2009_ellobiopsea.pdf}
}
@Article{Gomez2011,
Title = {{Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST-3.}},
Author = {F. G{\'o}mez and D. Moreira and K. Benzerara and P. L{\'o}pez-Garc{\'i}a},
Journal = {Environ. Microbiol.},
Year = {2011},
Number = {1},
Pages = {193--202},
Volume = {13},
Abstract = {(MAST-4,7 + (MAST-8,6,9 + Labyr) || Bicoec || Placid || (Blasto + MAST-12) || Solenicolida) || others incl. Pirsonia + MAST-1},
Doi = {10.1111/j.1462-2920.2010.02320.x},
File = {gomez2012_solenicola_mast3.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20722698}
}
@Article{Gabaldon2010,
Title = {{Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes}},
Author = {T. Gabaldon and S. Capella-Gutierrez},
Journal = {Gene},
Year = {2010},
Abstract = {As stated},
Doi = {10.1016/j.gene.2010.06.004},
File = {gabaldon2010_peroxisomes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20600706}
}
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Title = {{Giant Higgins-larvae with paedogenetic reproduction from the deep sea of the Angola Basin? Evidence for a new life cycle and for abyssal gigantism in Loricifera?}},
Author = {G. Gad},
Journal = {Organisms, Diversity \& Evolution},
Year = {2005},
Pages = {59--75},
Volume = {5},
Abstract = {As stated},
Doi = {10.1016/j.ode.2004.10.005},
File = {gad2005b.pdf}
}
@Article{Gai2008,
Title = {{\textit{Symphylella} sp. (Myriapoda: Symphyla): Extensive gene order rearrangement and evidence in favor of Progoneata}},
Author = {Y. Gai and D. Song and H. Sun and Q. Yang and K. Zhou},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {2},
Pages = {574--585},
Volume = {49},
Abstract = {Diplopoda + Symphyla; no clear placement of Myriapoda},
Doi = {10.1016/j.ympev.2008.08.010},
File = {gai2008.pdf}
}
@Article{Gai2006,
Title = {{Myriapod Monophyly and Relationships Among Myriapod Classes Based on Nearly Complete 28S and 18S rDNA Sequences}},
Author = {Y.-H. Gai and D.-X. Song and H.-Y. Sun and K.-Y. Zhou},
Journal = {Zool. Sci.},
Year = {2006},
Number = {2006},
Pages = {86--25},
Volume = {23},
Abstract = {Symphyla + Pauropoda [but have extremely long branches], Chilopoda often sister, then Diplo},
Doi = {10.2108/zsj.23.1101},
File = {gai2006.pdf}
}
@Article{Galindo2021,
Title = {{Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota}},
Author = {L. J. Galindo and P. L{\'o}pez-Garc{\'i}a and G. Torruella and S. Karpov and D. Moreira},
Journal = {Nature Communications},
Year = {2021},
Abstract = {Chitr || Blastolc + Sanchytr || Zygo || Dikarya},
Doi = {10.1038/s41467-021-25308-w},
File = {galindo2021_sanchytriomycota_sist_blastoclad.pdf},
ISSN = {2041-1723}
}
@Article{Galindo2019,
Title = {Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi},
Author = {Galindo, Luis Javier and Torruella, Guifr{\'e} and Moreira, David and Eglit, Yana and Simpson, Alastair GB and V{\"o}lcker, Eckhard and Clau{\ss}, Steffen and L{\'o}pez-Garc{\'\i}a, Purificaci{\'o}n},
Journal = {Philosophical Transactions of the Royal Society B},
Year = {2019},
Number = {1786},
Pages = {20190094},
Volume = {374},
File = {galindo2019_pompholyxophrys_lithocolla.pdf}
}
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Title = {{Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium.}},
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Journal = {Genome Biol Evol},
Year = {2018},
Number = {10},
Pages = {2736--2748},
Volume = {10},
Abstract = {Similar to Corsaro et al. (2018)},
Doi = {10.1093/gbe/evy205},
File = {galindo2018_metchnikoviella.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17051209}
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Year = {2007},
Number = {3},
Pages = {1118--1130},
Volume = {43},
Doi = {10.1016/j.ympev.2006.11.012},
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File = {galperin2008.pdf}
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@Article{Ganesan2008,
Title = {{Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester}},
Author = {A. Ganesan and S. Chaussonnerie and A. Tarrade and C. Dauga and T. Bouchez and E. Pelletier and P. D. Le and A. Sghir},
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Pages = {2003--2012},
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Author = {B. Gao and R. S. Gupta},
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Year = {2007},
Pages = {86},
Volume = {8},
Abstract = {4 groups of Euryarcheota: sugnatures in Gupta-style},
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Title = {{Phylogenomic analyses support the bifurcation of ciliates into two major clades that differ in properties of nuclear division.}},
Author = {F. Gao and L. A. Katz},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Pages = {240--243},
Volume = {70},
Abstract = {Postcilio || Litostomatea (Didinium), Armophorea (Metopus) ~ (weak) Licnophorida (Licnophora), Spirotrichea, Protocruzia, Ventrata},
Doi = {10.1016/j.ympev.2013.10.001},
File = {gao2013_ciliates.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24121125}
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@Article{gao2016all,
Title = {The all-data-based evolutionary hypothesis of ciliated protists with a revised classification of the phylum Ciliophora (Eukaryota, Alveolata)},
Author = {Gao, Feng and Warren, Alan and Zhang, Qianqian and Gong, Jun and Miao, Miao and Sun, Ping and Xu, Dapeng and Huang, Jie and Yi, Zhenzhen and Song, Weibo},
Journal = {Scientific Reports},
Year = {2016},
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Publisher = {Nature Publishing Group}
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@Article{Gao2007,
Title = {{Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology}},
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Journal = {Sci. China Ser. C: Life Sci.s},
Year = {2007},
Number = {5},
Pages = {587--599},
Volume = {50},
Abstract = {Spiro (excl. Leptosp) + Chlamyd; Cyano || Actino || Dein/Th || Aquific + Chloroflexi; Mollucites || Archaea, Plancto + Acido},
Doi = {10.1007/s11427-007-0084-3},
File = {gao2007b.pdf}
}
@Article{Gao2008,
Title = {{Phylogenetic Relationships of Basal Hexapods Reconstructed from Nearly Complete 18S and 28S rRNA Gene Sequences}},
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Year = {2008},
Number = {11},
Pages = {1139--1145},
Volume = {25},
Abstract = {Insecta || Colle || protu || Diplu},
Doi = {10.2108/zsj.25.1139},
File = {gao2008_basal_hexapods.pdf}
}
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@InCollection{Garrity2006,
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@Book{Garrity2004,
Title = {{Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology}},
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Publisher = {Springer-Verlag},
Year = {2004},
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Edition = {2nd},
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@Manual{Garrity2007,
Title = {{Taxonomic Outline of the Bacteria and Archaea (Formerly the Taxonomic Outline of the Prokaryotes). Release 7.7. March 6, 2007}},
Author = {G. M. Garrity and T. G. Lilburn and J. R. Cole and S. H. Harrison and J. Euzeby and B. J. Tindall},
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@Article{Gasiorowski2017,
Title = {{Morphology and evolution of the nervous system in Gnathostomulida (Gnathifera, Spiralia)}},
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Journal = {Org Divers Evol},
Year = {2017},
Abstract = {~ Micrognathozoa},
Doi = {10.1007/s13127-017-0324-8},
File = {gsiorowski2017_nerv_syst_gnathostom.pdf}
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@Article{Gasmi2014,
Title = {{Evolutionary history of Chaetognatha inferred from molecular and morphological data: A case study for body plan simplification}},
Author = {S. Gasmi and G. N{\`e}ve and N. Pech and S. Tekaya and A. Gilles and Y. Perez},
Journal = {Frontiers in Zoology},
Year = {2014},
Pages = {84},
Abstract = {As stated},
Doi = {10.1186/s12983-014-0084-7},
File = {gasmi2014_chaetognatha.pdf},
Url = {http://www.frontiersinzoology.com/content/11/1/84}
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@Article{Gaucher2010,
Title = {{Deep Phylogeny -- How a Tree Can Help Characterize Early Life on Earth}},
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@Article{Gawryluk2019,
Title = {{Non-photosynthetic predators are sister to red algae.}},
Author = {R. M. R. Gawryluk and D. V. Tikhonenkov and E. Hehenberger and F. Husnik and A. P. Mylnikov and P. J. Keeling},
Journal = {Nature},
Year = {2019},
Number = {7768},
Pages = {240 - 243},
Volume = {572},
Abstract = {Cryptista (Palpitomonas, Roombia, others) || ((Rhodelphidia + Rhodophyta) || (Glaucophyta + Chlorophyta)) || (Ancoracysta | Centroh + Haptoph) || Telonema, Alv, SR},
Doi = {10.1038/s41586-019-1398-6},
File = {gawryluk2019_rhodelphidia.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31316212}
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@Article{Gazave2008,
Title = {{NK homeobox genes with choanocyte-specific expression in homoscleromorph sponges}},
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Journal = {Dev. Genes Evol.},
Year = {2008},
Number = {9},
Pages = {479--489},
Volume = {218},
Abstract = {Hompscl separated from Demosp.; choanocytes may be homologs of neurosensory cells},
Doi = {10.1007/s00427-008-0242-z},
File = {gazave2008.pdf}
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@Article{Gazave2010,
Title = {{Molecular Phylogeny Restores the Supra-Generic Subdivision of Homoscleromorph Sponges (Porifera, Homoscleromorpha)}},
Author = {E. Gazave and P. Lapebie and E. Renard and J. Vacelet and C. Rocher and A. V and Ereskovsky and D. V. Lavrov and C. Borchiellini},
Journal = {PLoS ONE},
Year = {2010},
Number = {12},
Pages = {e14290},
Volume = {5},
Abstract = {Plakinidae + Oscarellidae},
Doi = {10.1371/journal.pone.0014290},
File = {gazave2010_homoscleromorpha.pdf},
Url = {www.plosone.org}
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Journal = {Hydrobiologia},
Year = {2011},
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Year = {2016},
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Year = {2014},
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Volume = {48},
Abstract = {Review},
Chapter = {On Aculifera: a review of hypotheses in tribute to Christoffer Schander},
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@Article{Giribet2000,
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Pages = {61--79},
Volume = {1668},
Abstract = {Porif+Placo+Cten+Cnid || Aco, Nemer || Deuter || Chaeto, Ecdyso, Spiralia; Ecdyso: Lori, Kino+Priap, Nem+Nem, Ony, Tard, Arthr; Spir: Myzo, Plath+Gastr+Rotif+Gnath+Micr, Cycl, Bryoz, Ento+ Nemer+ (Phor|| Brach)+ Moll+Ann+Sipun},
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Pages = {167--186},
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Pages = {319--340},
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Pages = {7723--7728},
Volume = {103},
Abstract = {Scapho+Soleno+Caudo+Gephalo || Biv || Poly+Mono || Gastro},
File = {giribet2006.pdf}
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Abstract = {Chelicer || Myriapoda || Hexa || Remipedia || Cephalo || Malaco || Maxillo+Branchio},
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}
@Article{Giribet2004b,
Title = {{Investigations into the phylogenetic position of Micrognathozoa using four molecular loci}},
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File = {giribet2004a.pdf}
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Journal = {Gene},
Year = {2008},
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Pages = {20 - 26},
Volume = {421},
Abstract = {As stated},
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File = {digiulio2008a.pdf}
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Journal = {Gene},
Year = {2008},
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Pages = {39--46},
Volume = {426},
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}
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Journal = {Gene},
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Abstract = {As stated},
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@Article{Glenner2008,
Title = {{Induced metamorphosis in crustacean y-larvae: towards a solution to a 100-year-old riddle}},
Author = {H. Glenner and J. T. Hoeg and M. J. Grygier and Y. Fujita},
Journal = {BMC Biol.},
Year = {2008},
Pages = {21},
Volume = {6},
Abstract = {Convergent with Rhizocephala; unique},
Doi = {10.1186/1741-7007-6-21},
File = {glenner2008.pdf}
}
@Article{Gluecksman2010,
Title = {{The Novel Marine Gliding Zooflagellate Genus Mantamonas (Mantamonadida ord. N.: Apusozoa).}},
Author = {E. Gluecksman and E. A. Snell and C. Berney and E. E. Chao and D. Bass and T. Cavalier-Smith},
Journal = {Protist},
Year = {2010},
Abstract = {Apusomonadida: Manchomonas, Thecamonas (Amastigomonas), Apusom, Mantamonas sister to them; close to Amoebozoa or Chromobionta; far from Planomonas (Ancyromponas); Breviata + Micronuclearia also close here},
Doi = {10.1016/j.protis.2010.06.004},
File = {glueksman2010_mantamonadida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20884290}
}
@Article{Godon2005,
Title = {{Rarity associated with specific ecological niches in the bacterial world: the Synergistes example}},
Author = {J.-J. Godon and J. Moriniere and M. Moletta and M. Gaillac and V. Bru and J.-P. Delgenes},
Journal = {Environ. Microbiol.},
Year = {2005},
Number = {2},
Pages = {213--224},
Volume = {7},
Abstract = {Synergistes || Flexistipes},
File = {godon2005.pdf}
}
@Article{Goertzen2003,
Title = {{Effect of taxon sampling, character weighting, and combined data on the interpretation of relationships among the heterokont algae}},
Author = {L. R. Goertzen and E. C. Theriot},
Journal = {J. Phycol.},
Year = {2003},
Pages = {423--439},
Volume = {39},
Abstract = {Support for Dia + Bolid; Phaeot + Ph + Xan; Chry + Eu + Syn; (Pelago + Sarcinochrysidales) + Dictyo},
File = {goertzen2003.pdf}
}
@InProceedings{Goffinet2004,
Title = {{Systematics of the Bryophyta (mosses): from molecules to a revised classification}},
Author = {B. Goffinet and W. R. Buck},
Booktitle = {{Monographs in Systematics Botany}},
Year = {2004},
Volume = {38}
}
@InCollection{Goffinet2008,
Title = {{Morphology, anatomy, and classification of the Bryophyta}},
Author = {B. Goffinet and W. R. Buck and A. J. Shaw},
Booktitle = {Bryophyte Biology},
Publisher = {Oxford University Press},
Year = {2008},
Address = {Cambridge},
Editor = {B. Goffinet and A. J. Shaw},
Pages = {55--138},
Abstract = {Takakiops., Sphagnops., Andraeops., Andraeobryops., Polytrichops., Tetraphidops., Bryops.}
}
@Article{Goffinet2000a,
Title = {{Phylogenetic Relationships Among Basal-most Arthrodontous Mosses with Special Emphasis on the Evolutionary Significance of the Funariineae}},
Author = {B. Goffinet and C. J. Cox},
Journal = {Bryologist},
Year = {2000},
Number = {2},
Pages = {212--223},
Volume = {103}
}
@Article{Goldmann2018,
Title = {{Molecular phylogeny of the Laboulbeniomycetes (Ascomycota).}},
Author = {L. Goldmann and A. Weir},
Journal = {Fungal Biol},
Year = {2018},
Number = {2 - 3},
Pages = {87 - 100},
Volume = {122},
Abstract = {Sister to Sordariomycetes},
Doi = {10.1016/j.funbio.2017.11.004},
File = {goldman2017_laboulbeniomycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29458722}
}
@Article{Goloboff2009,
Title = {{Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups}},
Author = {P. A. Goloboff and S. A. Catalano and J. M. Mirande and C. A. Szumik and J. S. Arias and M. Kallersjo and J. S. Farris},
Journal = {Cladistics},
Year = {2009},
Pages = {1--20},
Volume = {25},
Abstract = {As stated},
Doi = {10.1111/j.1096-0031.2009.00255.x},
File = {goloboff2009_73060_taxa.pdf}
}
@Article{Golombek2013,
Title = {{Mitochondrial genomes to the rescue - Diurodrilidae in the myzostomid trap.}},
Author = {A. Golombek and S. Tobergte and M. P. Nesnidal and G. Purschke and T. H. Struck},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Abstract = {Diurodrilus is an LBA},
Doi = {10.1016/j.ympev.2013.03.026},
File = {golombek2013_diurodrilidae_lba.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23563272}
}
@Article{Golombek2015,
Title = {{Elucidating the phylogenetic position of Gnathostomulida and first mitochondrial genomes of Gnathostomulida, Gastrotricha and Polycladida (Platyhelminthes).}},
Author = {A. Golombek and S. Tobergte and T. H. Struck},
Journal = {Mol. Phylogenet. Evol.},
Year = {2015},
Pages = {49--63},
Volume = {86},
Abstract = {Gnath + Synderm || Platyh},
Doi = {10.1016/j.ympev.2015.02.013},
File = {golombek2015_gnathostomulida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25796325}
}
@Article{Gomaa2013,
Title = {{Amphitremida (Poche, 1913) is a new major, ubiquitous labyrinthulomycete clade.}},
Author = {F. Gomaa and E. A. D. Mitchell and E. Lara},
Journal = {PLoS ONE},
Year = {2013},
Number = {1},
Pages = {e53046},
Volume = {8},
Abstract = {Class of Labyr.},
Doi = {10.1371/journal.pone.0053046},
File = {gomaa2013_amphitremida_labyr.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/11411837}
}
@Article{Gonez2010,
Title = {{A new definition and a lectotypification of the genus Cooksonia Lang 1937}},
Author = {P. Gonez and P. Gerrienne},
Journal = {Int. J. Plant Sci.},
Year = {2010},
Number = {2},
Pages = {199 - 215},
Volume = {171},
Abstract = {mosses || Horneopohytopsida || Cooksonia, Paratracheophytes (Rhynia) -> Lycophytina, Euphyllophytina},
Doi = {10.1086/648988},
File = {gonez2010_cooksonia.pdf}
}
@Article{Gong2009,
Title = {{Small Subunit rRNA Phylogenies Show that the Class Nassophorea is Not Monophyletic (Phylum Ciliophora}},
Author = {J. Gong and T. Stoeck and Z. Yi and M. Miao and Q. Zhang and D. McRoberts and A. Warren and W. Song},
Journal = {Journal of Eukaryotic Microbiology},
Year = {In press},
Abstract = {Nassoph. incl. Nassulina and Microthoracina; Phyllopharingea incl. Synchimeniida},
Doi = {10.1111/j.1550-7408.2009.00413.x},
File = {gong2009_nassophorea.pdf}
}
@Article{Gong2015,
Title = {{Vernalophrys algivore gen. Nov., Sp. Nov. (Rhizaria: Cercozoa: Vampyrellida), a New Algal Predator Isolated from Outdoor Mass Culture of Scenedesmus dimorphus.}},
Author = {Y. Gong and D. J. Patterson and Y. Li and Z. Hu and M. Sommerfeld and Y. Chen and Q. Hu},
Journal = {Appl. Environ. Microbiol.},
Year = {2015},
Number = {12},
Pages = {3900--3913},
Volume = {81},
Abstract = {As stated},
Doi = {10.1128/AEM.00160-15},
File = {gong2015_vernalophrys_vampyrellida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25819973}
}
@Article{Gonobobleva2009,
Title = {{Choanocyte ultrastructure in Halisarca dujardini (Demospongiae, Halisarcida)}},
Author = {E. Gonobobleva and M. Maldonado},
Journal = {J. Morphol.},
Year = {2009},
Number = {5},
Pages = {615--627},
Volume = {270},
Abstract = {Structure varies in sponges},
Doi = {10.1002/jmor.10709},
File = {gonobobleva2009_halisarca_choanocytes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19107941}
}
@Article{Gontcharov2010,
Title = {{Problems of taxonomy of the Conjugates (Zygnematophyceae, Streptophyta) in relation to molecular-phylogenetic data}},
Author = {A. A. Gontcharov},
Journal = {Botanicheskij Zhurnal},
Year = {2010},
Number = {10},
Pages = {1417--1458},
Volume = {94},
Abstract = {Review; Genus Conjugata},
File = {goncharov2009_zygnematophyceae.pdf}
}
@Article{GonzalezRomero2009,
Title = {{Histone genes of the razor clam Solen marginatus unveil new aspects of linker histone evolution in protostomes}},
Author = {R. Gonzalez-Romero and J. Ausio and J. Mendez and J. M. Eirin-Lopez},
Journal = {Genome},
Year = {2009},
Pages = {597--607},
Volume = {52},
Abstract = {Unique histones},
Doi = {10.1139/G09-034},
File = {gonzalez-romero2009_hist_protost.pdf}
}
@Article{Gooday2018,
Title = {{Xenophyophores (Rhizaria, Foraminifera) from the Eastern Clarion-Clipperton Zone (equatorial Pacific): The Genus Psammina.}},
Author = {A. J. Gooday and M. Holzmann and A. Goineau and O. Kamenskaya and V. F. Melnik and R. B. Pearce and A. A.-T. Weber and J. Pawlowski},
Journal = {Protist},
Year = {2018},
Number = {6},
Pages = {926--957},
Volume = {169},
Doi = {10.1016/j.protis.2018.09.003},
File = {gooday2018_xenophyophores_eastern_pacific.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30453273}
}
@Article{Gooday2011,
Title = {{Xenophyophores (Rhizaria, Foraminifera) from the Nazare Canyon (Portuguese margin, NE Atlantic)}},
Author = {A. J. Gooday and A. A. da Silva and J. Pawlowski},
Journal = {Deep-Sea Research II},
Year = {2011},
Pages = {2401--2419},
Volume = {58},
Abstract = {~ Textulariida},
Doi = {10.1016/j.dsr2.2011.04.005},
File = {gooday2011_xenophyophores.djvu},
Url = {www.elsevier.com/locate/dsr2}
}
@Article{Goodkov2004,
Title = {{The concept of pelobionts (Peloflagellata class): a brief history and current status}},
Author = {A. V. Goodkov and I. V. Chistyakova and L. N. Seravin and A. O. Frolov},
Journal = {Zoologicheskij Zhurnal},
Year = {2004},
Number = {6},
Pages = {643--654},
Volume = {83},
Abstract = {Review},
File = {gudkov2004_pelobionty.djvu}
}
@Article{Goodman1998,
Title = {{Toward a Phylogenetic Classification of Primates Based on {DNA} Evidence Complemented by Fossil Evidence}},
Author = {M. Goodman and C. A. Porter and J. Czelusniak and S. L. Page and H. Schneider and J. Shoshani and G. Gunnell and C. P. Groves},
Journal = {Mol. Phyl. Evol.},
Year = {1998},
Number = {3},
Pages = {585--598},
Volume = {9}
}
@Article{Goods2014,
Title = {{Tetraradial symmetry in early poriferans}},
Author = {C. P. Goods and J. P. Botting and X. Yuan and O. Content},
Journal = {Chin. Sci. Bull.},
Year = {2014},
Abstract = {As stated},
Doi = {10.1007/s11434-013-0099-z},
File = {botting2014_tetraradial_porifera.txt}
}
@Article{Goodson2006,
Title = {{Multiplying myosins}},
Author = {H. V. Goodson and S. C. Dawson},
Journal = {Biochemistry},
Year = {2006},
Number = {10},
Pages = {3498--3499},
Volume = {103},
Abstract = {Plants have unique myosins, not comparable with Excavata and Alveolata},
File = {goodson2006.pdf}
}
@Article{Gophna2005,
Title = {{Weighted Genome Trees: Refinements and Applications}},
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Journal = {J. Bacteriol.},
Year = {2005},
Number = {4},
Pages = {1305},
Volume = {187},
File = {gophna2005.pdf}
}
@Book{Gorbunova1991,
Title = {{Algology}},
Author = {N. P. Gorbunova},
Publisher = {Vysshaja Shkola},
Year = {1991},
Address = {Moscow},
Pages = {1--256}
}
@Article{Gothe1999,
Title = {{Ultrastructural Details of the Plasmodial Rhizopod Synamoeba arenaria Grell}},
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Journal = {Acta Protozool.},
Year = {1999},
Pages = {49--59},
Volume = {38}
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@Article{Goto2013,
Title = {{Molecular phylogeny of echiuran worms (Phylum: Annelida) reveals evolutionary pattern of feeding mode and sexual dimorphism.}},
Author = {R. Goto and T. Okamoto and H. Ishikawa and Y. Hamamura and M. Kato},
Journal = {PLoS ONE},
Year = {2013},
Number = {2},
Pages = {e56809},
Volume = {8},
Abstract = {Capitellidae sister},
Doi = {10.1371/journal.pone.0056809},
File = {goto2013_echiura.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/9021275}
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@Article{Gottschling2013,
Title = {{New home for tiny symbionts: Dinophytes determined as Zooxanthella are Peridiniales and distantly related to Symbiodinium.}},
Author = {M. Gottschling and T. I. McLean},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Number = {1},
Pages = {217--222},
Volume = {67},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2013.01.003},
File = {gottschling2013_zooxantella.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23333735}
}
@Article{Gould2008,
Title = {{Alveolins, a new family of cortical proteins that define the Infrakingdom Alveolata}},
Author = {S. B. Gould and W.-H. Tham and A. F. Cowman and G. I. McFadden and R. F. Waller},
Journal = {Mol. Biol. and Evolution},
Year = {2008},
Number = {6},
Pages = {1219--1230},
Volume = {25},
Abstract = {Synapomorphy!},
File = {gould2008.pdf}
}
@Article{Govindarajan2010,
Title = {{A molecular phylogeny of the Thaliacea}},
Author = {A. F. Govindarajan and A. Bucklin and L. P. Madin},
Journal = {JOURNAL OF PLANKTON RESEARCH},
Year = {2010},
Pages = {1--11},
Abstract = {Append || Stolidobranchia || Phlebobranchia || Pyrosomatida || Doliolida + Salpida},
Doi = {10.1093/plankt/fbq157},
File = {govindarajan2010_thaliacea.pdf},
Url = {www.plankt.oxfordjournals.org}
}
@Article{deGraaf2009,
Title = {{The hydrogenosomes of Psalteriomonas lanterna}},
Author = {R. M. de Graaf and I. Duarte and T. A. van Alen and J. W. P. Kuiper and K. Schotanus and J. Rosenberg and M. A. Huynen and J. H. P. Hackstein},
Journal = {BMC Evol. Biol.},
Year = {2009},
Pages = {287},
Volume = {9},
Abstract = {confirms the relationship of P. lanterna with its aerobic relative, the heterolobosean amoeboflagellate Naegleria gruberi, corroborating the evolution of hydrogenosomes from a common, mitochondriate ancestor.},
Doi = {10.1186/1471-2148-9-287},
File = {degraaf2009_psalteriomonas_hydrogenosomes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20003182}
}
@Article{Graf2019,
Title = {{Further investigations on the Phaeothamniophyceae using multigene phylogeny, with descriptions of five new species.}},
Author = {L. Graf and E. C. Yang and G. H. Boo and R. A. Andersen and H. S. Yoon},
Journal = {Journal of phycology},
Year = {2019},
Abstract = {Raph || Aurea + Phaeoth || !Chrysoparadox | Chrysomer + Xantho || !Schizo + Phaeoph},
Doi = {10.1111/jpy.12950},
File = {graf2019_phaeothamniophyceae.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31762049}
}
@Article{Graf2021,
Title = {{Multigene Phylogeny, Morphological Observation and Re-examination of the Literature Lead to the Description of the Phaeosacciophyceae classis nova and Four New Species of the Heterokontophyta SI Clade}},
Author = {L. Graf and E. C. Yang and K. Y. Han and F. C. Kupper and K. M. Benes and J. K. Oyadomari and R. J. H. Herbert and H. Verbruggen and R. Wetherbee and R. A. Andersen and H. S. Yoon},
Journal = {Protist},
Year = {2021},
Abstract = {Raphid || Aurea+Phaeo || Schizocl+Phaeo || Phaeosacciophyceae [Phaeosaccion, Antarctosaccion, Tetraspopsis, Psammochrysis: initially thalloid brown algae] || Chrysoparad + Phaeobotrys, Pleurochloridella i.s. + Xanthophyceae},
Doi = {10.1016/j.protis.2020.125781},
File = {graf2020_phaeosacciophyceae_cl_xanthoph.pdf},
ISSN = {1434-4610}
}
@Article{Graham2000,
Title = {{Evolution An archaeal genomic signature}},
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@Article{Grandcolas2004,
Title = {{Abstracts of the 23rd Annual Meeting of the Willi Hennig Society. ``Phylogenetics and Evolutionary Biology''}},
Author = {P. Grandcolas},
Journal = {Cladistics},
Year = {2004},
Pages = {583--608},
Volume = {20},
Abstract = {Pentastomida+Branchiura=Ichthyostraca, maybe || Ostracoda; morphol: Ctenophora || Bilateria wheraas 18S: Ct (Cnid, Bilat)},
File = {grandcolas2004_23whs.pdf}
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@Article{Grande2014,
Title = {{Evolution, divergence and loss of the Nodal signalling pathway: New data and a synthesis across the Bilateria.}},
Author = {C. Grande and J. M. Mart{\'i}n-Dur{\'a}n and N. J. Kenny and M. Truchado-Garc{\'i}a and A. Hejnol},
Journal = {Int. J. Dev. Biol.},
Year = {2014},
Number = {6--8},
Pages = {521--532},
Volume = {58},
Abstract = {Acoelomorpha diatant from core Deuterost},
Doi = {10.1387/ijdb.140133cg},
File = {grande2014_nodal_metazoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25690967}
}
@Article{Grant2009,
Title = {{Multigene Evidence for the Placement of a Heterotrophic Amoeboid Lineage Leukarachnion sp. Among Photosynthetic Stramenopiles}},
Author = {J. Grant and Y. I. Tekle and O. R. Anderson and D. J. Patterson and L. A. Katz},
Journal = {Protist},
Year = {In press},
Abstract = {(Bolid + Bacill) || (Ping + Eust) || (Raph || (Phaeot + Xa) || (Schiz + Phaeo)) || Dicty || Pelag || Picophagus || Leuk, Chlamyd, Synchroma || other Chryso},
Doi = {10.1016/j.protis.2009.01.001},
File = {grant2009_leukarachnion.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2009.01.001}
}
@Article{Grasshoff2002,
Title = {{The Origin of Metazoa and the Main Evolutionary Lineages of the Animal Kingdom: The Gallertoid Hypothesis in the light of Modern Research}},
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Year = {2002},
Number = {1},
Pages = {295--314},
Volume = {82},
Abstract = {Basal lineages (Radialia) are independent},
File = {grasshoff2002.html}
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@Article{Graur1997,
Title = {{Evolutionary Affinities of the Order Perissodactyla and the Phylogenetic Status of the Superordinal Taxa Ungulata and Altungulata}},
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Year = {1997},
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Pages = {195--200},
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@Article{Gray1998a,
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@Article{Gray1998,
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@Article{Green2011,
Title = {{After the primary endosymbiosis: An update on the chromalveolate hypothesis and the origins of algae with Chl c}},
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Year = {2011},
Pages = {103--115},
Volume = {107},
Abstract = {Review},
Doi = {10.1007/s11120-010-9584-2},
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@Article{Grela2008,
Title = {{Structural Relationships Among the Ribosomal Stalk Proteins from the Three Domains of Life.}},
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Year = {2008},
Number = {2},
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Volume = {67},
Abstract = {Ribo proteins are not homologous},
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File = {grela2008.pdf}
}
@Article{Grell1994,
Title = {{Thalassomyxa canariensis n. sp. from a Tide Pool of Tenerife (Canary Islands)}},
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Year = {1994},
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Pages = {319--324},
Volume = {144}
}
@Article{Grell1994a,
Title = {{Reticulamoeba gemmipara n. gen., n. sp., an ``Amoebo-flagellate'' with Reticulopodia and Zoosporogenesis}},
Author = {K. G. Grell},
Journal = {Arch. Protistenkd.},
Year = {1994},
Number = {1},
Pages = {55--61},
Volume = {144}
}
@Article{Grell1994b,
Title = {{The Feeding Community of Synamoeba arenaria n. gen., n. sp.}},
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Journal = {Arch. Protistenkd.},
Year = {1994},
Number = {2},
Pages = {143--146},
Volume = {144}
}
@Article{Grell1991,
Title = {{Corallomyxa nipponica n. sp. and the phylogeny of plasmodial protists}},
Author = {K. G. Grell},
Journal = {Arch. Protistenkd.},
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Pages = {303--390},
Volume = {140}
}
@Article{Grell1991a,
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Volume = {140}
}
@Article{Grell1990,
Title = {{The ultrastructure of \textit{Reticulosphaera socialis} Grell (Heterokontophyta)}},
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@Article{Grewe2013,
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Journal = {BMC Evol. Biol.},
Year = {2013},
Pages = {8},
Volume = {13},
Abstract = {Spermatophyta || (((Psil + Ophio) || Equis) || Maratt || Pterid); molecular apomorphies found},
Doi = {10.1186/1471-2148-13-8},
File = {grewe2013_equisetales.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/11214320}
}
@Article{Gribaldo2009,
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Abstract = {Review},
Doi = {10.1016/j.resmic.2009.07.006},
File = {gribaldo2009_prok_phylog.pdf}
}
@Article{Gribaldo2006,
Title = {{The origin and evolution of Archaea: a state of the art}},
Author = {S. Gribaldo and C. Brochier-Armanet},
Journal = {Phil. Trans. R. Soc. B},
Year = {2006},
Number = {1470},
Pages = {1007--1022},
Volume = {361},
File = {gribaldo2006.pdf}
}
@Article{Gribaldo1999,
Title = {{Discontinuous Occurrence of the hsp70 (dnaK) Gene among Archaea and Sequence Features of HSP70 Suggest a Novel Outlook on Phylogenies Inferred from This Protein}},
Author = {S. Gribaldo and V. Lumia and R. Creti and E. Conway de Macario and A. Sanangelantoni and P. Cammarano},
Journal = {J. Bacteriol.},
Year = {1999},
Number = {2},
Pages = {434--443},
Volume = {181}
}
@Article{Griffiths2007,
Title = {{Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae}},
Author = {E. Griffiths and R. S. Gupta},
Journal = {Microbiology},
Year = {2007},
Pages = {2648--2654},
Volume = {153},
Abstract = {11 conserved proteins: Verru || Chlam, Spiro + Plancto, Thermot + Aquif},
File = {griffits2007.pdf}
}
@Article{Grimaldi2009,
Title = {{400 Million years on six legs: On the origin and early evolution of Hexapoda}},
Author = {D. A. Grimaldi},
Journal = {Arthropod Struct. Dev.},
Year = {2009},
Abstract = {Review},
Doi = {10.1016/j.asd.2009.10.008},
File = {grimaldi2009_hexapoda_origin.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19883792}
}
@Article{Grobben1908,
Title = {{Die systematische Einteilung des Teirreichs}},
Author = {K. Grobben},
Journal = {Verh. Zool.-bot. Ges. Wien},
Year = {1908},
Pages = {491--511},
Volume = {58},
File = {grobben1908.djvu}
}
@Article{Grobe2008,
Title = {{The Development and Phylogenetic Position of the Phoronida}},
Author = {P. Grobe and T. Bartolomaeus},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {correspondences in the formation of the coelom in the craniid larva and the larva of P. ovalis indicate that a lecithotrophic larva represents the primary type of larva in Phoronida and Brachiopoda},
Doi = {10.1002/jmor.10683},
File = {grobe2008.txt}
}
@Article{Groisillier2006,
Title = {{Genetic diversity and habitats of two enigmatic marine alveolate lineages}},
Author = {A. Groisillier and R. Massana and K. Valentin and D. Vaulot and L. Guillou},
Journal = {Aquat. Micr. Ecol.},
Year = {2006},
Pages = {37--49},
Volume = {42},
Abstract = {AGI || other Dino; AGII = Syndiniales},
File = {groisillier2006.pdf},
Url = {www.int-res.com}
}
@Article{Gross2008,
Title = {{Evidence of a chimeric genome in the cyanobacterial ancestor of plastids}},
Author = {J. Gross and J. Meurer and D. Bhattacharya},
Journal = {BMC Evol. Biol.},
Year = {2008},
Number = {117},
Pages = {1--29},
Volume = {8},
Abstract = {Plastids closer to gamma-p and Chlorobi -> ancestral cyano were mixtures},
Doi = {10.1186/1471-2148-8-117},
File = {gross2008.pdf}
}
@Article{Groth2011,
Title = {{AGAMOUS subfamily MADS-box genes and the evolution of seed cone morphology in Cupressaceae and Taxodiaceae}},
Author = {E. Groth and A. K. Tandre and P. Engstrom and F. Vergara-Silva},
Journal = {EVOLUTION \& DEVELOPMENT},
Year = {2011},
Pages = {159--170},
Volume = {2},
Abstract = {Much less homology},
Doi = {10.1111/j.1525-142X.2011.00466.x},
File = {groth2011_cupress_taxod.pdf}
}
@Article{GrothMalonek2007,
Title = {{Evolution of a pseudogene: Exclusive survival of a functional mitochondrial nad7 gene supports \textit{Haplomitrium} as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae}},
Author = {M. Groth-Malonek and U. Wahrmund and M. Polsakiewicz and V. Knoop},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Pages = {1--22},
Volume = {5},
Abstract = {Haplomitrium || other Hepaticae},
File = {groth-malonek2007.pdf}
}
@Article{Grothman2017,
Title = {{Gilbert Rahm and the Status of Mesotardigrada Rahm, 1937.}},
Author = {G. T. Grothman and C. Johansson and G. Chilton and H. Kagoshima and M. Tsujimoto and A. C. Suzuki},
Journal = {Zool. Sci.},
Year = {2017},
Number = {1},
Pages = {5--10},
Volume = {34},
Abstract = {nomen dubium},
Doi = {10.2108/zs160109},
File = {grothman2017_rahm_mesotardigrada.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28148217}
}
@Article{Groussin2011a,
Title = {{Adaptation to Environmental Temperature is a Major Determinant of Molecular Evolutionary Rates in Archaea}},
Author = {M. Groussin and M. Gouy},
Journal = {Molecular Biology and Evolution},
Year = {2011},
Volume = {15},
Abstract = {As stated},
File = {groussin2011_archaea_and_temper.djvu}
}
@Article{Groussin2011b,
Title = {{Bayesian Relaxed Clock Estimation of Divergence Times in Foraminifera}},
Author = {M. Groussin and J. Pawlowski and Z. Yang},
Journal = {MOLECULAR PHYLOGENETICS AND EVOLUTION},
Year = {2011},
Abstract = {Monothalamiids || Milliolids || Textulariids + Rotaliids},
Doi = {10.1016/j.ympev.2011.06.008},
File = {groussin2011_foraminifera.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2011.06.008}
}
@Article{Grube2007,
Title = {{Trouble with lichen: the re-evaluation and re-interpretation of thallus form and fruit body types in the molecular era}},
Author = {M. Grube and D. L. Hawksworth},
Journal = {Mycol. Res.},
Year = {2007},
Pages = {1116--1132},
Volume = {111},
Abstract = {"non-lichenised lichens"},
File = {grube2007.pdf}
}
@Article{Gruhl2009a,
Title = {{Ultrastructure of mesoderm formation and development in Membranipora membranacea (Bryozoa: Gymnolaemata)}},
Author = {A. Gruhl},
Year = {2009},
Abstract = {Ectodermal, remains other spiralian taxa and Phoronida},
Doi = {10.1007/s00435-009-0099-3},
File = {gruhl2009_bryozoan_mesodem.pdf}
}
@Article{Gruhl2008b,
Title = {{Serotonin and FMRFamide in the Nervous Systems of Gymnolaemate Bryozoan Larvae}},
Author = {A. Gruhl},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {The distribution of neurotransmitters in the apical organ is more comparable to that of Entoprocta, Polychaeta, and Mollusca than to that of Phoronida and Brachiopoda.},
Doi = {10.1002/jmor.10683},
File = {gruhl2008.txt}
}
@Article{Gruhl2008,
Title = {{Ganglion Ultrastructure in Phylactolaemate Bryozoa: Evidence for a Neuroepithelium}},
Author = {A. Gruhl and T. Bartolomaeus},
Journal = {J. Morphol.},
Year = {2008},
Pages = {594--603},
Volume = {269},
Abstract = {Far from Deuterost, Kamptoz and Phoron, unclear about Brachiop},
Doi = {10.1002/jmor.10607},
File = {gruhl2008.pdf}
}
@Article{Gruhl2005,
Title = {{Fine structure of the epistome in Phoronis ovalis: significance for the coelomic organization in Phoronida}},
Author = {A. Gruhl and P. Grobe and T. Bartolomaeus},
Journal = {Invert. Biol.},
Year = {2005},
Number = {4},
Pages = {332--343},
Volume = {124},
Abstract = {No tripartite coelom -- no similarity with Deutero},
File = {gruhl2005.pdf}
}
@Article{Gruhl2012,
Title = {{Development and myogenesis of the vermiform Buddenbrockia (Myxozoa) and implications for cnidarian body plan evolution}},
Author = {A. Gruhl and B. Okamura},
Journal = {EvoDevo},
Year = {2012},
Pages = {10},
Volume = {3},
Abstract = {Convergence with Bilateria},
File = {gruhl2012_buddenbrockia_dev_myogenesis.pdf},
Url = {http://www.evodevojournal.com/content/3/1/10}
}
@InProceedings{Gruhl2009b,
Title = {{Muscular architecture of Buddenbrockia plumatellae and its significance for the phylogenetic position of Myxozoa}},
Author = {A. Gruhl and B. Okamura},
Booktitle = {{Systematics 2009. Leiden, August 11-14. Abstracts}},
Year = {2009},
Abstract = {The muscular system shows a distinct tetraradial symmetry, supporting an affinity to the cnidarian taxon Medusozoa},
File = {gruhl2009_buddenbrockia.txt}
}
@Article{Gruhl2009,
Title = {{Ultrastructure of the body cavities in Phylactolaemata (Bryozoa}},
Author = {A. Gruhl and I. Wegener and T. Bartolomaeus},
Journal = {J. Morphol.},
Year = {2009},
Number = {3},
Pages = {306--318},
Volume = {270},
Abstract = {... no further support for a primary homology of the epistomes in phylactolaemate Bryozoa, Phoronida, and Brachiopoda can be found. This renders an independent origin of the epistomes in these groups possible, therefore weakening the idea of a common ancestry of these taxa.},
Doi = {10.1002/jmor.10691},
File = {gruhl2009_body_cavities_phylactolaem.pdf}
}
@Article{Gryganskyi2013,
Title = {{Phylogenetic lineages in Entomophthoromycota}},
Author = {A. P. Gryganskyi and R. A. Humber and M. E. Smith and K. Hodge and B. Huang and K. Voigt and R. Vilgalys},
Journal = {Persoonia},
Year = {2013},
Pages = {94--105},
Volume = {30},
Abstract = {Kickxellomycotima, Zoopagomycotina, Mucoromycotina, Glomerulomycota, Enth: Basidiobolomycetes, Neozygitomycetes (Neozygites), Entomophthoromycetes},
Doi = {10.3767/003158513X666330},
File = {gryganskyi2013_entomophthoromycota.pdf},
Url = {www.ingentaconnect.com/content/nhn/pimj}
}
@Article{Gryganskyi2012,
Title = {{Molecular phylogeny of the Entomophthoromycota.}},
Author = {A. P. Gryganskyi and R. A. Humber and M. E. Smith and J. Miadlikovska and S. Wu and K. Voigt and G. Walther and I. M. Anishchenko and R. Vilgalys},
Journal = {Mol. Phylogenet. Evol.},
Year = {2012},
Abstract = {Olpidium || Glomerulo + Mucoro + Mortierell || Kickxell + Zoopag || Entomph + Basidiobol},
Doi = {10.1016/j.ympev.2012.07.026},
File = {gryganskyj2012_entomophtoromycota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22877646}
}
@InCollection{Grygier1983,
Title = {{Ascothoracida and the unity of Maxillopoda}},
Author = {M. J. Grygier},
Booktitle = {{Crustacean phylogeny}},
Publisher = {A.A.Balkema},
Year = {1983},
Editor = {F. R. Schram},
Pages = {73--104},
Abstract = {Probably not monophyletic},
File = {schram1983_crust_phylogeny_sel_3_papers.djvu}
}
@Article{Grzebyk2003,
Title = {{The mesozoic radiation of eucaryotic algae: the portable plastid hypothesis}},
Author = {D. Grzebyk and O. Schofield and C. Vetriani and P. G. Falkowski},
Journal = {J. Phycol.},
Year = {2003},
Pages = {259--267},
Volume = {39}
}
@Article{Guan2016,
Title = {{Draft genome of the living fossil Ginkgo biloba.}},
Author = {R. Guan and Y. Zhao and H. Zhang and G. Fan and X. Liu and W. Zhou and C. Shi and J. Wang and W. Liu and X. Liang and Y. Fu and K. Ma and L. Zhao and F. Zhang and Z. Lu and S. M.-Y. Lee and X. Xu and J. Wang and H. Yang and C. Fu and S. Ge and W. Chen},
Journal = {Gigascience},
Year = {2016},
Number = {1},
Pages = {49},
Volume = {5},
Abstract = {Pinus (Ginkgo + Cycas)},
Doi = {10.1186/s13742-016-0154-1},
File = {guan2016_ginkgo_draft_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27871309}
}
@Unpublished{Gudo2008,
Title = {{100 Years of Deuterostomia (GROBBEN, 1908): Cladogenetic and Anagenetic Relations within the Notoneuralia Domain}},
Author = {M. Gudo and T. Syed},
Year = {2008},
Abstract = {Chordata are basal},
File = {gudo2008_deuterostomia.pdf},
Journal = {ArXiv}
}
@Article{Guermazi2008,
Title = {{Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach}},
Author = {S. Guermazi and P. Daegelen and C. Dauga and D. Riviere and T. Bouchez and J. J. Godon and G. Gyapay and A. Sghir and E. Pelletier and J. Weissenbach and D. Le Paslier},
Journal = {Environ. Microbiol.},
Year = {2008},
Number = {8},
Pages = {2111--2123},
Volume = {10},
Abstract = {TM7 || OD1 || OP11 ~ SR1 (Harris, 2004) || WS6 || WWE3 (new)},
Doi = {10.1111/j.1462-2920.2008.01632.x},
File = {guermazi2008_wwe3.pdf}
}
@Article{Guersoy2000,
Title = {{The Vertebrate 7S K RNA Separates Hagfish (\textit{Myxine glutinosa}) and Lamprey (\textit{Lampetra fluviatilis})}},
Author = {H.-C. Guersoy and D. Koper and B.-J. Benecke},
Journal = {J. Mol. Evol.},
Year = {2000},
Pages = {456--464},
Volume = {50}
}
@Article{Guil2012,
Title = {{A comprehensive molecular phylogeny of tardigrades adding genes and taxa to a poorly resolved phylumlevel phylogeny}},
Author = {N. Guil and G. Giribet},
Journal = {Cladistics},
Year = {2012},
Pages = {21--49},
Volume = {28},
Abstract = {As stated; Mesotardigrada with questioned validity},
Doi = {10.1111/j.1096-0031.2011.00364.x},
File = {guil2012_tardigrada.pdf}
}
@Article{Guil2018,
Title = {{An upgraded comprehensive multilocus phylogeny of the Tardigrada tree of life}},
Author = {N. Guil and A. J{\o}rgensen and R. Kristensen},
Journal = {Zoologica Scripta},
Year = {2018},
Abstract = {Class Apotargigrada comb.n.},
Doi = {10.1111/zsc.12321},
File = {guil2018_apotardigrada.pdf}
}
@Article{Guillou1999,
Title = {{\textit{Bolidomonas}: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta)}},
Author = {L. Guillou},
Journal = {J. Phycol.},
Year = {1999},
Number = {2},
Pages = {368--381},
Volume = {35}
}
@Article{Guillou1999b,
Title = {{\textit{Symbiomonas scintillans} gen. et sp. nov. and \textit{Picophagus flagellatus} gen. et sp. nov. (Heterokonta): Two New Heterotrophic Flagellates of Picoplanktonic Size}},
Author = {L. Guillou and M.-J. Chretiennot-Dinet and S. Boulben and S. Y. Moon-van der Staay and D. Vaulot},
Journal = {Protist},
Year = {1999},
Pages = {383--398},
Volume = {150}
}
@Article{Guillou2004,
Title = {{Diversity of Picoplanktonic Prasinophytes Assessed by Direct Nuclear SSU rDNA Sequencing of Environmental Samples and Novel Isolates Retrieved from Oceanic and Coastal Marine Ecosystems}},
Author = {L. Guillou and W. Eikrem and M.-J. Chritiennot-Dinet and F. L. Gald and R. Massana and K. Romari and C. Pedros-Alio and D. Vaulot},
Journal = {Protist},
Year = {2004},
Pages = {193--214},
Volume = {155},
Abstract = {Prasinophyceae -- paraphyletic unit},
File = {guillou2004.pdf}
}
@Article{Guillou1999a,
Title = {{Diversity and Abundance of Bolidophyceae (Heterokonta) in Two Oceanic Regions}},
Author = {L. Guillou and Seung-Y. Moon-van der Staay and H. Claustre and F. Partensky and D. Vaulot},
Journal = {Appl. Environ. Microbiol.,},
Year = {1999},
Number = {10},
Pages = {4528--4536},
Volume = {65}
}
@Article{Guillou2008,
Title = {{Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata)}},
Author = {L. Guillou and M. Viprey and A. Chambouvet and R. M. Welsh and A. R. Kirkham and R. Massana and D. J. Scanlan and A. Z. Worden},
Journal = {Environ. Microbiol.},
Year = {2008},
Number = {12},
Pages = {3349--3365},
Volume = {10},
Abstract = {MAG I and II = Syndiniales},
Doi = {10.1111/j.1462-2920.2008.01731.x},
File = {guillou2008.pdf}
}
@Article{Gulbrandsen2021,
Title = {{Phylogenomic analysis restructures the Ulvophyceae}},
Author = {{\O}. S. Gulbrandsen and I. J. Andresen and A. K. Krabber{\o}d and J. Br},
Journal = {J. Phycol.},
Year = {2021},
Pages = {1223 - 1233},
Volume = {57},
Abstract = {Supports synat 6.24},
Doi = {10.1111/jpy.13168-20-145},
File = {gulbrandsen2021_ulvophyceae.pdf}
}
@Article{Gupta2012b,
Title = {{Molecular Evolution of Translin Superfamily Proteins Within the Genomes of Eubacteria, Archaea and Eukaryotes}},
Author = {G. D. Gupta and A. Kale and V. Kumar},
Journal = {J Mol Evol},
Year = {2012},
Pages = {155--167},
Volume = {75},
Abstract = {TRAX in euk, arch and Chloroflexi},
Doi = {10.1007/s00239-012-9534-z},
File = {gupta2012_trax_chloroflexi.pdf}
}
@Article{Gupta2015,
Title = {{Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates.}},
Author = {R. S. Gupta},
Journal = {Mol. Phylogenet. Evol.},
Year = {2015},
Number = {Pt--A},
Pages = {383--391},
Volume = {94},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2015.09.019},
File = {gupta2015_tunicata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26419477}
}
@Article{Gupta2011c,
Title = {{Origin of diderm (Gram-negative) bacteria: Antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes}},
Author = {R. S. Gupta},
Journal = {Biochemistry},
Year = {2011},
Abstract = {As stated; G+ give Thermotog, "atypical diderms" (Negativicutes, Fuso, Synerg, Elusimicr) and Chloroflexi -> Dein-Therm -> G-},
Doi = {10.1007/s10482-011-9616-8},
File = {gupta2011_origin_of_g_neg.pdf}
}
@Article{Gupta2010b,
Title = {{Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups}},
Author = {R. S. Gupta},
Journal = {Photosyn. Res.},
Year = {2010},
Number = {2 - 3},
Pages = {357 - 372},
Volume = {104},
Abstract = {No Chloroflexi yet},
Doi = {10.1007/s11120-010-9553-9},
File = {gupta2010_photos_bact_signatures.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20414806}
}
@Unpublished{Gupta2007b,
Title = {{Branching Order of Bacterial Phyla}},
Author = {R. S. Gupta},
Note = {http://www.bacterialphylogeny.com/index.html},
Year = {2007},
Abstract = {Firm, Acti, Fuso + Thermot, Deino, Chlorofl, Cya, Fib+Chlorob+CFB, PVC, Aqui, (d, e), (a, (g, b))},
File = {gupta2007_site.jpg},
Url = {http://www.bacterialphylogeny.com/index.html}
}
@Article{Gupta2004,
Title = {{The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi and Bacteroidetes}},
Author = {R. S. Gupta},
Journal = {Crit. Rev. Microbiol.},
Year = {2004},
Pages = {123--143},
Volume = {30}
}
@Article{Gupta2000,
Title = {{The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes.}},
Author = {R. S. Gupta},
Journal = {FEMS Microbiol. Rev.},
Year = {2000},
Number = {4},
Pages = {367--402},
Volume = {24}
}
@Article{Gupta1998,
Title = {{Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes}},
Author = {R. S. Gupta},
Journal = {Microbiology and Mol. Biol. Reviews},
Year = {1998},
Number = {4},
Pages = {1435--1491},
Volume = {62}
}
@Article{Gupta2011b,
Title = {{Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups}},
Author = {R. S. Gupta and V. Bhandari},
Journal = {Antonie van Leeuwenhoek},
Year = {2011},
Abstract = {Early branching ~ Firmi and Actino whereas Aquifi ~ epsilon},
Doi = {10.1007/s10482-011-9576-z)},
File = {gupta2011_thermotogae.djvu}
}
@Article{Gupta2012a,
Title = {{Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. Nov. Into the suborder Chloroflexineae subord. Nov., Consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. Nov., And the suborder Roseiflexineae subord. Nov., Containing the family Roseiflexaceae fam. Nov.}},
Author = {R. S. Gupta and P. Chander and S. George},
Journal = {Antonie Van Leeuwenhoek},
Year = {2012},
Abstract = {Thermomicrobia + Chloroflexi cl. nov.},
Doi = {10.1007/s10482-012-9790-3},
File = {gupta2012_chloroflexi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22903492}
}
@Article{Gupta2007a,
Title = {{Phylogeny and Molecular Signatures (Conserved Proteins and Indels) that are Specific for the Bacteroidetes and Chlorobi Species.}},
Author = {R. S. Gupta and E. Lorenzini},
Journal = {BMC Evol. Biol.},
Year = {2007},
Number = {1},
Pages = {71},
Volume = {7},
Abstract = {Signature support for Fibro (Chlorobi ( Salini (Sphingo ( Bacteroidetes, Flavo))))},
File = {gupta2007b.pdf}
}
@Article{Gupta2013,
Title = {{A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: Proposal for a taxonomic revision of the phylum.}},
Author = {R. S. Gupta and S. Mahmood and M. Adeolu},
Journal = {Front Microbiol},
Year = {2013},
Pages = {217},
Volume = {4},
Abstract = {As stated},
Doi = {10.3389/fmicb.2013.00217},
File = {gupta2013_spirochaetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23908650}
}
@Article{Gupta2010,
Title = {{Signature proteins for the major clades of Cyanobacteria.}},
Author = {R. S. Gupta and D. W. Mathews},
Journal = {BMC Evol. Biol.},
Year = {2010},
Pages = {24},
Volume = {10},
Abstract = {3 clades/classes, Synechococcus strains dispersed among them; A: Gloeobacter etc., C: Synech. + Prochlorococc., B: Acaryochloris, Oscillatoriales, Nostocineae etc.},
Doi = {10.1186/1471-2148-10-24},
File = {gupta2010_cyanob_signat.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20100331}
}
@Article{Gupta1999,
Title = {{Evolutionary relationships among photosynthetic prokaryotes (\textit{Heliobacterium chlorum}, \textit{Chloroflexus aurantiacus}, cyanobacteria, \textit{Chlorobium tepidum} and proteobacteria): implications regarding the origin of photosynthesis.}},
Author = {R. S. Gupta and T. Mukhtar and B. Singh},
Journal = {Mol. Microbiol.},
Year = {1999},
Number = {5},
Pages = {893--906},
Volume = {32}
}
@Article{Gupta2014,
Title = {{Phylogenomic Analyses and Molecular Signatures for the Class Halobacteria and its Two Major Clades: A Proposal for Division of the Class Halobacteria into an emended order Halobacteriales and Two New Orders, Haloferacales ord. Nov. And Natrialbales ord. Nov.}},
Author = {R. S. Gupta and S. Naushad and S. Baker},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2014},
Abstract = {As stated},
Doi = {10.1099/ijs.0.070136-0},
File = {gupta2014_halobacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25428416}
}
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Author = {R. S. Gupta and M. Sethi},
Journal = {Anaerobe},
Year = {2014},
Pages = {182--198},
Volume = {28},
Abstract = {As stated},
Doi = {10.1016/j.anaerobe.2014.06.007},
File = {gupta2014_fusobacteria.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24969840}
}
@Article{Gupta2011a,
Title = {{Molecular signatures for the Crenarchaeota and the Thaumarchaeota}},
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Journal = {Antonie van Leeuwenhoek},
Year = {2011},
Pages = {133--157},
Volume = {99},
Abstract = {Thaumarchaeota distinct},
Doi = {10.1007/s10482-010-9488-3},
File = {gupta2011_signatures_crenarch_thaumarch.pdf}
}
@Article{Gupta2007c,
Title = {{Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions.}},
Author = {R. S. Gupta and P. H. A. Sneath},
Journal = {J. Mol. Evol.},
Year = {2007},
Number = {1},
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Volume = {64},
Abstract = {e(d(a(b,y))) where b ~ y},
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@Book{Gusev1980,
Title = {Free oxygen and cell evolution},
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Note = {(In Russian)},
Abstract = {evoljucija, Bacteria},
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@Article{Guy2014,
Title = {{'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum.}},
Author = {L. Guy and A. Spang and J. H. Saw and T. J. G. Ettema},
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Volume = {8},
Abstract = {As stated},
Doi = {10.1038/ismej.2014.6},
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@Article{Haag2014,
Title = {{Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites.}},
Author = {K. L. Haag and T. Y. James and J.-F. Pombert and R. Larsson and T. M. M. Schaer and D. Refardt and D. Ebert},
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Year = {2014},
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Pages = {15480--15485},
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Abstract = {Mitosporidium: basal to Microsporidia},
Doi = {10.1073/pnas.1410442111},
File = {haag2014_mitosporidium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25313038}
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@Article{Haas2003,
Title = {{\textit{Devonohexapodus bocksbergensis}, a new marine hexapod from the Lower Devonian Hunsrueck Slates, and the origin of Atelocerata and Hexapoda}},
Author = {F. Haas and D. Waloszek and R. Hartenberger},
Journal = {Org. Divers. Evol.},
Year = {2003},
Pages = {39--54},
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@Article{Hackett2007,
Title = {{Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of ``Rhizaria'' with chromalveolates}},
Author = {J. D. Hackett and H. S. Yoon and S. Li and A. Reyes-Prieto and S. E. Ruemmele and D. Bhattacharya},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {8},
Pages = {1702--1713},
Volume = {24},
Abstract = {Amoeboz sep. from Opi and Rhiza; Hapt + Crypto || Rhiza || Chro + Alv; Rho || Glau || Chlo; Malawi || oth. Excavata; Jac || Meta OR Eug},
File = {hackett2007.pdf}
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@Book{Hadzi1963,
Title = {{The Evolution of the Metazoa}},
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Publisher = {Pergamon Press},
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Pages = {1--499}
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@Article{Haelewaters2019,
Title = {{Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales.}},
Author = {D. Haelewaters and W. P. Pfliegler and M. Gorczak and D. H. Pfister},
Journal = {Mol. Phylogenet. Evol.},
Year = {2019},
Pages = {286 - 301},
Volume = {133},
Abstract = {sister},
Doi = {10.1016/j.ympev.2019.01.007},
File = {haelewaters2019_harpomycetales_laboulb.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30625361}
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@Article{Haen2007,
Title = {{Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?}},
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Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {7},
Pages = {1518--1527},
Volume = {24}
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@Article{Haering2005,
Title = {{Independent virus development outside a host}},
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Abstract = {As stated},
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@Article{Haese2008,
Title = {{Phylogeny of Collembola: Were the first springtails semiaquatic?}},
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Journal = {Cladistics},
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Abstract = {May have aquatic ancestors},
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@Article{Hagemann2008,
Title = {{The sterols of calcareous sponges (Calcarea, Porifera)}},
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Year = {2008},
Number = {1--2},
Pages = {26--32},
Volume = {156},
Abstract = {Sterols: Calcarea ~ Demosp., but no overlap with Hexact.},
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File = {hagemann2008.pdf}
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@Article{Hahn2017,
Title = {{Silvanigrella aquatica gen. Nov., Sp. Nov., Isolated from a freshwater lake, description of Silvanigrellaceae fam. Nov. And Silvanigrellales ord. Nov., Reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. Nov., And reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales.}},
Author = {M. W. Hahn and J. Schmidt and U. Koll and M. Rohde and S. Verbarg and A. Pitt and R. Nakai and T. Naganuma and E. Lang},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2017},
Number = {8},
Pages = {2555 - 2568},
Volume = {67},
Abstract = {~ Delta},
Doi = {10.1099/ijsem.0.001965},
File = {hahn2017_oligoflexia.txt},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25406234}
}
@Article{Hahnke2016,
Title = {{Genome-Based Taxonomic Classification of Bacteroidetes}},
Author = {R. L. Hahnke and J. P. Meier-Kolthoff and M. Garc{\'i}a-L{\'o}pez and S. Mukherjee and M. Huntemann and N. N. Ivanova and T. Woyke and N. C. Kyrpides and H.-P. Klenk and M. G{\"o}ker},
Journal = {Front Microbiol},
Year = {2016},
Volume = {7},
Abstract = {Balneola ~ Chlorobium, Ignavibact; Saprospiria, Chitinophagia ~ Sphingobacteria; Bacteroides-Chlorobi superphylum: Rhodothermaeota (cl. Rhodothermia: Rhodothermus, Salinibacter, Salisaeta), Balneolaeota (cl. Balneolia: Balneola, Gracilimonas), Bacteroides: Cytophagia, Sphingobacteria, Flavobacteria, Bacteroidea, Saprospiria, Chitinophagia},
Doi = {10.3389/fmicb.2016.02003},
File = {hahnke2016_balneolaeota_saprospiria_bacteroidetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19567576}
}
@PhdThesis{Hai2015,
Title = {{Taxonomy, phylogeny and genomics of the Wallemiomycetes and a newly discovered class of extremophilic fungi}},
Author = {N. Hai},
Year = {2015},
Address = {Ottawa},
Abstract = {Geminibasidium + Basidioascus || Wallemia},
File = {hai2015_geminibasidiomycetes.djvu},
Organization = {University of Ottawa}
}
@Article{Haig2010,
Title = {{What do we know about charophyte (Streptophyta) life cycles?}},
Author = {D. Haig},
Journal = {J. Phycol.},
Year = {2010},
Abstract = {Not so simple},
Doi = {10.1111/j.1529-8817.2010.00874.x},
File = {haig2010_streptophyla_life_cycles.pdf}
}
@Article{Haig2008,
Title = {{Homologous Versus Antithetic Alternation of Generations and the Origin of Sporophytes}},
Author = {D. Haig},
Journal = {Bot. Rev.},
Year = {2008},
Number = {3},
Pages = {395--418},
Volume = {74},
Abstract = {History of discussion and theories},
Doi = {10.1007/s12229-008-9012-x},
File = {haig2008.pdf}
}
@Article{Hajibabaei2006,
Title = {{Seed plant phylogeny: Gnetophytes are derived conifers and a sister group to Pinaceae}},
Author = {M. Hajibabaei and J. Xia and G. Drouin},
Journal = {Mol. Phyl. Evol.},
Year = {2006},
Number = {1},
Pages = {208--217},
Volume = {40},
Abstract = {Subj},
File = {hajibabaei2006.pdf}
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@Article{Hakariya2009,
Title = {{Molecular phylogeny of terrestrial holocarpic endoparasitic peronosporomycetes, Haptoglossa spp., Inferred from 18S rDNA}},
Author = {M. Hakariya and D. Hirose and S. Tokumasu},
Journal = {Science},
Year = {2009},
Pages = {130--136},
Volume = {50},
Abstract = {Pirsonia || Developayella || Eurychasma + Haptoglossa || others},
Doi = {10.1007/s10267-008-0458-9},
File = {hakariya2009_haptoglossa.pdf}
}
@Article{Halanych2004,
Title = {{The new view of animal phylogeny}},
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Journal = {Annu. Rev. Ecol. Evol. Syst.},
Year = {2004},
Pages = {229--256},
Volume = {35},
Abstract = {Hexactin || Demo || Calci; Gnathifera (Synderm, Gnath, Micr); Platyzoa (Plath, Cycl, Ent, Gastrotr)},
File = {halanych2004.pdf}
}
@Article{Halanych1995,
Title = {{The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data.}},
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@Article{Hall2008,
Title = {{Phylogeny of the conjugating green algae based on chloroplast and mitochondrial nucleotide sequence data}},
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Journal = {Science},
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Pages = {467--477},
Volume = {44},
Abstract = {Spirogyra basal},
Doi = {10.1111/j.1529-8817.2008.00485.x},
File = {hall2008.pdf}
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@Article{Hall2004,
Title = {{Further phylogenetic studies of the Polychaeta using 18S rDNA sequence data}},
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@Article{Hamann2016,
Title = {{Environmental Breviatea harbour mutualistic Arcobacter epibionts.}},
Author = {E. Hamann and H. Gruber-Vodicka and M. Kleiner and H. E. Tegetmeyer and D. Riedel and S. Littmann and J. Chen and J. Milucka and B. Viehweger and K. W. Becker and X. Dong and C. W. Stairs and K.-U. Hinrichs and M. W. Brown and A. J. Roger and M. Strous},
Journal = {Nature},
Year = {2016},
Number = {7606},
Pages = {254 - 258},
Volume = {534},
Abstract = {Amoeb || Apus + Brev (Lenisia limosa nov.) || Opist},
Doi = {10.1038/nature18297},
File = {hamann2016_lenisia_breviatea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27279223}
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@Article{Hampl2009,
Title = {{Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ``supergroups''}},
Author = {V. Hampl and L. Hug and J. W. Leigh and J. B. Dacks and B. F. Lang and A. G. B. Simpson and A. J. Roger},
Journal = {Proceedings of the National Academy of Sciences},
Year = {2009},
Number = {10},
Pages = {3859--3864},
Volume = {106},
Abstract = {"Excavata forms a monophyletic suprakingdom-level group that is one of the 3 primary divisions within eukaryotes, along with unikonts and a megagroup of Archaeplastida, Rhizaria, and the chromalveolate lineages". Some support for Bikonta.},
Doi = {10.1073/pnas.0807880106},
Eprint = {http://www.pnas.org/content/106/10/3859.full.pdf+html},
File = {hampl2009_supergroups.pdf},
Keywords = {pr1},
Url = {http://www.pnas.org/content/106/10/3859.abstract}
}
@Conference{Hampl2008,
Title = {{Taxon-rich Phylogenomic Analyses Support the Monophyly of Excavata and Robustly Resolve Relationships among Eukaryotic "Supergroups"}},
Author = {V. Hampl and L. Hug and J. W. Leigh and J. B. Dacks and B. F. Lang and A. G. B. Simpson and A. J. Roger},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {||| Preaxostyla + Diplo + Parabas ||| Discoba: Andalucia || Jacob. || Eugl. + Heterolob.; between Unik. and Arch., Rhiz. and Chomalv.},
File = {hamp2008.txt}
}
@Article{Hampl2011,
Title = {{The tangled past of eukaryotic enzymes involved in anaerobic metabolism}},
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Journal = {Mobile Genetic Elements},
Year = {2011},
Pages = {71--74},
Volume = {1},
Abstract = {Many LGTs},
Doi = {10.4161/mge.1.1.15588},
File = {hampl2011_anaer_euk_enz.pdf},
Url = {www.landesbioscience.com}
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@Article{Hanelt1996,
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@Article{Hannaert2000,
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@Article{Hansmann2000,
Title = {{Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across procaryotic genomes: influence of excluding poorly alignable sites from analysis}},
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@Article{Hao2008,
Title = {{Prokaryotic branch of the Tree of Life: A composition vector approach}},
Author = {B. L. Hao and L. Gao},
Journal = {Journal of Systematics and Evolution},
Year = {2008},
Number = {3},
Pages = {258--262},
Volume = {46},
Abstract = {(Proteo + Acido + Plancto) || (Chlorobi + Bacteroi + Deino) || Cyano || (Chlorof + Aquif + Thermot) + Firmic incl. Fuso || Actino || Spiro + Molluc + Chlamy || Archaea + Euk},
Doi = {10.3724/SP.J.1002.2008.08008},
File = {hao2008.pdf}
}
@Article{Hao2008b,
Title = {{Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences}},
Author = {D. Hao and P. G. Xiao and B. Huang and G. B. Ge and L. Yang},
Journal = {Plant Syst. Evol.},
Year = {2008},
Pages = {89--104},
Volume = {276},
Abstract = {Cephalotaxus distant, then Amenthotax + Torreya || Austro || Pseudotax || Taxus},
Doi = {10.1007/s00606-008-0069-0},
File = {hao2008.pdf}
}
@Article{Hao2009,
Title = {{Evolution of the Chloroplast trnL-trnF Region in the Gymnosperm Lineages Taxaceae and Cephalotaxaceae}},
Author = {D. C. Hao and B. L. Huang and S. L. Chen and J. Mu},
Journal = {Biochem. Genet.},
Year = {2009},
Pages = {351--369},
Volume = {47},
Doi = {10.1007/s10528-009-9233-7},
File = {hao2009_taxaceae.pdf}
}
@Article{Harada2007,
Title = {{Species of the Parasitic Genus \textit{Duboscquella} are Members of the Enigmatic Marine Alveolate Group I}},
Author = {A. Harada and S. Ohtsuka and T. Horiguchi},
Journal = {Protist},
Year = {2007},
Number = {3},
Pages = {337--347},
Volume = {158},
Abstract = {Dubosquella > MAGI || Syndiniales = MAGII},
File = {harada2007.pdf}
}
@Article{Harder2014,
Title = {{Ultrastructure and phylogenetic position of Regin rotiferus and Otto terricolus genera et species novae (Bicosoecida, Heterokonta/Stramenopiles).}},
Author = {C. B. Harder and F. Ekelund and S. A. Karpov},
Journal = {Protist},
Year = {2014},
Number = {2},
Pages = {144--160},
Volume = {165},
Abstract = {Rictus || Placididea || MAST-3 + MAST-12 + Blastocystea || Bicosoecida},
Doi = {10.1016/j.protis.2014.01.004},
File = {harder2014_bicosoecida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24637333}
}
@Article{Harding2012,
Title = {{Amoeba Stages in the Deepest Branching Heteroloboseans, Including Pharyngomonas: Evolutionary and Systematic Implications}},
Author = {T. Harding and M. W. Brown and A. Plotnikov and E. Selivanova and J. S. Park and J. H. Gunderson and M. Baumgartner and J. D. Silberman and A. J. Roger and A. G. B. Simpson},
Journal = {Protist},
Year = {2012},
Abstract = {As stated},
Doi = {10.1016/j.protis.2012.08.002},
File = {harding2012_pharyngomonas.pdf},
Url = {http://www.elsevier.de/protis}
}
@Article{Harholt2016,
Title = {{Why Plants Were Terrestrial from the Beginning.}},
Author = {J. Harholt and {\O}. Moestrup and P. Ulvskov},
Journal = {Trends Plant Sci.},
Year = {2016},
Number = {2},
Pages = {96--101},
Volume = {21},
Abstract = {The current hypothesis is that land plants originated from a charophycean green alga and that a prominent feature for adaptation to land was their development of alternating life cycles. Our work on cell wall evolution and morphological and physiological observations in the charophycean green algae challenged us to reassess how land plants became terrestrial. Our hypothesis is simple in that the charophycean green algae ancestors were already living on land and had been doing so for some time before the emergence of land plants. The evolution of alternate life cycles merely made the ancestral land plants evolutionary successful and had nothing to do with terrestrialization per se.},
Doi = {10.1016/j.tplants.2015.11.010},
File = {harholt2015_plants_primarily_terrestrial.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26706443}
}
@Article{Harish2017,
Title = {{Mitochondria are not captive bacteria.}},
Author = {A. Harish and C. G. Kurland},
Journal = {J. Theor. Biol.},
Year = {2017},
Pages = {88 - 98},
Volume = {434},
Abstract = {Because mt tree rooted at LUCA},
Doi = {10.1016/j.jtbi.2017.07.011},
File = {harish2017_mt_are_not_bacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28754286}
}
@Article{Harish2013,
Title = {{Rooted Phylogeny of the Three Superkingdoms}},
Author = {A. Harish and A. Tunlid and C. G. Kurland},
Journal = {Biochimie},
Year = {2013},
Abstract = {(Bac + Ar) || Euk},
Doi = {10.1016/j.biochi.2013.04.016},
File = {harish2013_rooted_phylogeny_superkingdoms.pdf},
ISSN = {0300-9084},
Url = {http://dx.doi.org/10.1016/j.biochi.2013.04.016}
}
@Article{Harper2017,
Title = {{Brachiopods: Origin and early history}},
Author = {D. A. T. Harper and L. E. Popov and L. E. Holmer},
Journal = {Palaeontology},
Year = {2017},
Abstract = {Review},
Doi = {10.1111/pala.12307},
File = {harper2017_brachiopoda_orig_evol_review.pdf}
}
@Article{Harper2005,
Title = {{On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes}},
Author = {J. T. Harper and E. Waanders and P. J. Keeling},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2005},
Pages = {487--496},
Volume = {55},
Abstract = {Hapto+Crypto(+Chlorara) || Chloro || Alv + Chro},
File = {harper2005.pdf}
}
@Article{Harrison2018,
Title = {{The origin and early evolution of vascular plant shoots and leaves.}},
Author = {C. J. Harrison and J. L. Morris},
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Year = {2018},
Number = {1739},
Volume = {373},
Abstract = {Review; branching sporophytes of Physcomytrella},
Doi = {10.1098/rstb.2016.0496},
File = {harrison2017_orig_evol_shoots_leaves_rhynie_review.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26687813}
}
@Article{Hart1994,
Title = {{Form and feeding mechanism of a living \textit{Planctosphaera pelagica} (phylum Hemichordata)}},
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Year = {1994},
Pages = {521--533},
Volume = {120},
Abstract = {Planctosphaera ~ Enteropneusta},
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@Article{Harta2009,
Title = {{Caterpillars did not evolve from onychophorans by hybridogenesis}},
Author = {M. W. Harta and R. K. Grosbergb},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2009},
Pages = {15786--15790},
Volume = {106},
Abstract = {As stated},
File = {hart2009_against_williamson.pdf}
}
@Article{Hartikainen2014,
Title = {{Diversification and repeated morphological transitions in endoparasitic cnidarians (Myxozoa: Malacosporea).}},
Author = {H. Hartikainen and A. Gruhl and B. Okamura},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Pages = {261--269},
Volume = {76},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2014.03.010},
File = {hartikainen2014_malacosporea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24675700}
}
@Article{Hartmann2012,
Title = {{Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data.}},
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Year = {2012},
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Pages = {e29843},
Volume = {7},
Abstract = {Basal to Annelida},
Doi = {10.1371/journal.pone.0029843},
File = {hartmann2012_myzostomid_transcriptome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22276131}
}
@Article{Harvey2010,
Title = {{Are palaeoscolecids ancestral ecdysozoans?}},
Author = {T. H. P. Harvey and X. Dong and P. C. J. Donoghue},
Journal = {Evol. Dev.},
Year = {2010},
Number = {2},
Pages = {177 - 200},
Volume = {12},
Abstract = {Stem priapulids},
Doi = {10.1111/j.1525-142X.2010.00403.x},
File = {harvey2010_palaeoscolecids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20433458}
}
@Article{Harzsch2006,
Title = {{Neurophylogeny: Architecture of the nervous system and a fresh view on arthropod phyologeny}},
Author = {S. Harzsch},
Journal = {Integr. Comp. Biol.},
Year = {2006},
Number = {2},
Pages = {162--194},
Volume = {46},
Abstract = {Xipho || Chilo+Progoneata || Branchio+Maxillo+Mystaco || Cephalo+Pterygota+(Remip+Malacostr)},
File = {harzsch2006.pdf}
}
@Article{Harzsch2006b,
Title = {{Evolution of eye development in arthropods: Phylogenetic aspects}},
Author = {S. Harzsch and G. Hafner},
Journal = {Arthropod Struct. Devel.},
Year = {2006},
Pages = {319--340},
Volume = {35},
Abstract = {Xipho || Progoneata || Chilo || Tetraconata},
File = {halanych2005.pdf}
}
@Article{Harzsch2007,
Title = {{A new look at the ventral nerve centre of \textit{Sagitta}: implications for the phylogenetic position of Chaetognatha (arrow worms) and the evolution of the bilaterian nervous system}},
Author = {S. Harzsch and C. H. Mueller},
Journal = {Front. Zool.},
Year = {2007},
Number = {14},
Pages = {1--15},
Volume = {4},
Abstract = {Chaetoghatha between Ecdyso and Lophotro},
File = {harzsch2007.pdf}
}
@Article{Harzsch2010,
Title = {{Evolution of invertebrate nervous systems: The Chaetognatha as a case study}},
Author = {S. Harzsch and A. Wanninger},
Journal = {Acta Zoologica},
Year = {2010},
Pages = {35--43},
Volume = {91},
Abstract = {Two concentration events: proto- and deutero-, Chaetogn. is early stage of protostomes nervous system concentration},
Doi = {10.1111/j.1463-6395.2009.00423.x},
File = {harzsch2010_chaetognatha_nervous_system.pdf}
}
@Article{Hashimoto2006,
Title = {{Phylogeny and evolution of eukaryotes}},
Author = {T. Hashimoto and Y. Inagaki and M. Sakaguchi},
Journal = {Genes Genet. Syst.},
Year = {2006},
Pages = {420},
Volume = {81},
Abstract = {Hetero+Eugleno},
File = {hashimoto2006.pdf}
}
@Article{Hashimoto1998,
Title = {{Secondary absence of mitochondria in \textit{Giardia lamblia} and \textit{Trichomonas vaginalis} revealed by valyl-tRNA synthetase phylogeny}},
Author = {T. Hashimoto and Lidya B. Srnchez and T. Shirakura and M. Mueller and M. Hasegawa},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1998},
Number = {12},
Pages = {6860--6865},
Volume = {95}
}
@Article{Haskins1983,
Title = {{Semimorula: New Genus with Myxomycete and Protostelid Affinities}},
Author = {E. F. Haskins and M. D. McGuinness and C. S. Berry},
Journal = {Mycologia},
Year = {1983},
Number = {1},
Pages = {153--158},
Volume = {75},
Abstract = {As stated},
File = {haskins1983_semimorula.pdf},
Url = {http://www.jstor.org/stable/3792929}
}
@Article{Haszprunar2016,
Title = {{Review of data for a morphological look on Xenacoelomorpha (Bilateria incertae sedis)}},
Author = {G. Haszprunar},
Journal = {Organisms Diversity \& Evolution},
Year = {2016},
Abstract = {Separate group},
Doi = {10.1007/s13127-015-0249-z},
File = {haszprunar2015_xenoacoelomorpha.pdf}
}
@InCollection{Haszprunar1997,
Title = {{Monoplacophora}},
Author = {G. Haszprunar and K. Schaefer},
Booktitle = {{Microscopic Anatomy of Invertebrates}},
Publisher = {Wiley-Liss},
Year = {1997},
Address = {New York},
Editor = {F. W. Harrison and A. J. Kohn},
Pages = {415--457},
Volume = {6B},
Abstract = {Stem lineage, 7 genera (incl. Monoplacophorus), 20 species}
}
@Article{Haszprunar2008,
Title = {{On the fine structure of the creeping larva of \textit{Loxosomella murmanica}: additional evidence for a clade of Kamptozoa (Entoprocta) and Mollusca}},
Author = {G. Haszprunar and A. Wanninger},
Journal = {Acta Zoologica},
Year = {2008},
Pages = {137--148},
Volume = {89},
Abstract = {Kamptozoa ~ Solenogastres},
Doi = {10.1111/j.1463-6395.2007.00301.x},
File = {hasrupnar2008.pdf}
}
@Article{Haszprunar2008c,
Title = {{Mollusca and Entoprocta Are Sister Groups: Implications for the Origin of Both Phyla}},
Author = {G. Haszprunar and A. Wanninger},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {remarkable number of synapomorphic characters of Mollusca and Entoprocta},
Doi = {10.1002/jmor.10683},
File = {haszprunar2008.txt}
}
@InCollection{Haszrupnar2008b,
Title = {{Monoplacophora (Tryblidiida)}},
Author = {G. Haszrupnar},
Booktitle = {{Phylogeny and evolution of the Mollusca}},
Publisher = {University of California Press},
Year = {2008},
Address = {Berkeley},
Editor = {W. F. Ponder and D. R. Lindberg},
Pages = {97--104},
Abstract = {Segmentation is an apomorphy, Giribet et al. (2007) data mismatch with Polyplac.},
File = {haszrupnar2008b.djvu}
}
@InCollection{Haszrupnar2008a,
Title = {{Relatioships of higher molluscan taxa}},
Author = {G. Haszrupnar and C. Schander and K. M. Halanych},
Booktitle = {{Phylogeny and evolution of the Mollusca}},
Publisher = {University of California Press},
Year = {2008},
Address = {Berkeley},
Editor = {W. F. Ponder and D. R. Lindberg},
Pages = {19--32},
Abstract = {Solenog || Caudof ||Polyplac || Conchifera: Monoplac || Bivalv || Scaph || Cyrtosoma: Gastr || Ceph},
File = {haszrupnar2008a.djvu}
}
@Article{Hausdorf2007,
Title = {{Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta}},
Author = {B. Hausdorf and M. Helmkampf and A. Meyer and A. Witek and H. Herlyn and I. Bruchhaus and T. Hankeln and T. H. Struck and B. Lieb},
Journal = {Mol. Biol. and Evolution},
Year = {2007},
Number = {12},
Pages = {2723--2729},
Volume = {24},
Abstract = {Synder + Platyh + (Ecto + Ento) || Moll || Annel},
File = {hausdorf2007.pdf}
}
@Article{Hausdorf2009,
Title = {{Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida)}},
Author = {B. Hausdorf and M. Helmkampf and M. P. Nesnidal and I. Bruchhaus},
Journal = {Molecular phylogenetics and evolution},
Year = {2009},
Abstract = {ribosomal proteins: Brachiopoda + Pho ~ Nemert and separate from Ento + Ecto},
Doi = {10.1016/j.ympev.2009.12.022},
File = {hausdorf2010_lophophorate.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20045074}
}
@Article{Hausmann2010,
Title = {{Ultrastructural and functional aspects of static and motile systems in two taxa of the Alveolata: Dinoflagellata and Ciliata}},
Author = {K. Hausmann and N. H{\"u}lsmann},
Journal = {Protistology},
Year = {2010},
Number = {3},
Pages = {139--146},
Volume = {6},
Abstract = {Review, nice figures :)},
File = {hausmann2011_dinofl_ciliata_morph.pdf}
}
@Article{Hausmann1994,
Title = {{Towards to a new perspective in protozoan evolution}},
Author = {K. Hausmann and N. Huelsmann},
Journal = {Eur. J. Protistol.},
Year = {1994},
Number = {4},
Pages = {365--482},
Volume = {30}
}
@Article{Hausmann2002,
Title = {{\textit{Meteora sporadica} gen. nov. et sp. nov. (Protista incertae sedis) ~--- an exttraordinary free-living protist from the Mediterranean deep sea}},
Author = {K. Hausmann and M. Weitere and M. Wolf and H. Arndt},
Journal = {Eur. J. Protistol.},
Year = {2002},
Pages = {171--177},
Volume = {38}
}
@Article{Hawksworth2017,
Title = {{Fungal Diversity Revisited: 2.2 To 3.8 Million Species.}},
Author = {D. L. Hawksworth and R. L{\"u}cking},
Journal = {Microbiol Spectr},
Year = {2017},
Number = {4},
Volume = {5},
Abstract = {As stated in the title},
Doi = {10.1128/microbiolspec.FUNK-0052-2016},
File = {hawksworth2017_fungal_div_revisited.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28752818}
}
@Article{He2014,
Title = {{An alternative root for the eukaryote tree of life.}},
Author = {D. He and O. Fiz-Palacios and C.-J. Fu and J. Fehling and C.-C. Tsai and S. L. Baldauf},
Journal = {Curr. Biol.},
Year = {2014},
Number = {4},
Pages = {465--470},
Volume = {24},
Abstract = {nuclear proteins of close bacterial ancestry: Discoba/Excavata || SARP/Panalgae/Bikonta + Amorphea/Panmycota/Unikonta (incl. Thecamonas || Opisto)},
Doi = {10.1016/j.cub.2014.01.036},
File = {he2014_alt_root_euk_tol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24556435}
}
@Article{He2015,
Title = {{Multiple origins of eukaryotic cox15 suggest a horizontal gene transfer from bacteria to jakobid mitochondrial DNA}},
Author = {D. He and C.-J. Fu and S. L. Baldauf},
Journal = {Mol. Biol. Evol.},
Year = {2015},
Abstract = {As stated (Andalucia)},
File = {he2015_andalucia_jacobida_mt_lgt.pdf},
Url = {http://mbe.oxfordjournals.org/}
}
@Article{He2016,
Title = {{Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria.}},
Author = {D. He and R. Sierra and J. Pawlowski and S. L. Baldauf},
Journal = {Mol. Phylogenet. Evol.},
Year = {2016},
Pages = {1--7},
Volume = {101},
Abstract = {S || A + R; Haptophyta || Crypto || Rhod + Glauc || Chloroplastida},
Doi = {10.1016/j.ympev.2016.04.033},
File = {he2016_alveolata_and_rhizaria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27132173}
}
@Article{He2015a,
Title = {{Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle.}},
Author = {X. He and J. S. McLean and A. Edlund and S. Yooseph and A. P. Hall and S.-Y. Liu and P. C. Dorrestein and E. Esquenazi and R. C. Hunter and G. Cheng and K. E. Nelson and R. Lux and W. Shi},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2015},
Number = {1},
Pages = {244--249},
Volume = {112},
Abstract = {Saccharibacteria: Saccharimonas aalborgensis},
Doi = {10.1073/pnas.1419038112},
File = {he2015_tm7_cultivation.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22939375}
}
@InProceedings{Healy2009,
Title = {{Phylogenetic implications of septal pore ultrastructure in the basal Ascomycete Neolecta irregularis}},
Author = {R. Healy and T. K. A. Kumar and D. J. McLaughlin},
Booktitle = {{Botany and Mycology 2009. Snowbird, Utah, July 25-29. Abstracts}},
Year = {2009},
Abstract = {pattern is unlike any of the various septal pore plugs reported in the Pezizomycotina},
File = {healy2009_neolecta.txt}
}
@Article{Hedges1998,
Title = {{A Molecular Phylogeny of Reptiles}},
Author = {S. B. Hedges and L. L. Poling},
Journal = {Science},
Year = {1998},
Number = {5404},
Pages = {998--1001},
Volume = {283}
}
@Article{Heger2010,
Title = {{Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent}},
Author = {T. J. Heger and E. A. D. Mitchell and M. Todorov and V. Golemansky and E. Lara and B. S. Leander and J. Pawlowski},
Journal = {Mol. Phylogenet. Evol.},
Year = {2010},
Number = {1},
Pages = {113 - 122},
Volume = {55},
Abstract = {Thaum || Paulinell || others},
Doi = {10.1016/j.ympev.2009.11.023},
File = {F:/ref/os/1/heger2010_euglyphida_phyl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20004728}
}
@Article{Hehenberger2017,
Title = {{Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals.}},
Author = {E. Hehenberger and D. V. Tikhonenkov and M. Kolisko and J. Del Campo and A. S. Esaulov and A. P. Mylnikov and P. J. Keeling},
Journal = {Curr. Biol.},
Year = {2017},
Number = {13},
Pages = {2043 - 2050 - e6},
Volume = {27},
Abstract = {Ichthy || Pluriformea: Corallochy + Syssomonas || (Filasterea: Ministeria | Capsaspora | Pigoraptor) || Choano || Animalia},
Doi = {10.1016/j.cub.2017.06.006},
File = {hehenberger2017_filasterea_pluriformea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28648822}
}
@Article{Heimberg2010,
Title = {{MicroRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate.}},
Author = {A. M. Heimberg and R. C.-S. Lari and M. S{\'e}mon and P. C. J. Donoghue and K. J. Peterson},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2010},
Abstract = {Cyclostomata monophyletic},
Doi = {10.1073/pnas.1010350107},
File = {heimberg2010_microrna_chordata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20959416}
}
@Article{Heiner2009,
Title = {{The spermiogenesis and the early spermatozoa of Armorloricus elegans (Loricifera, Nanaloricidae)}},
Author = {I. Heiner},
Journal = {Zoomorphology},
Year = {In press},
Abstract = {some similarities with especially Kinorhyncha and Priapulida. These similarities are thought to be plesiomorphic.},
File = {heiner2009_loricifera.pdf}
}
@Article{Heiner2008,
Title = {{Urnaloricus gadi nov. gen. et nov. sp. (Loricifera, Urnaloricidae nov. fam.), an aberrant Loricifera with a viviparous pedogenetic life cycle}},
Author = {I. Heiner and R. M. Kristensen},
Journal = {J. Morphol.},
Year = {2009},
Number = {2},
Pages = {129--153},
Volume = {270},
Abstract = {As stated},
Doi = {10.1002/jmor.10671},
File = {heiner2008.pdf}
}
@Article{Heiss2017,
Title = {{The flagellar apparatus of the glaucophyte Cyanophora cuspidata.}},
Author = {A. A. Heiss and A. W. Heiss and K. Lukacs and E. Kim},
Journal = {J. Phycol.},
Year = {2017},
Number = {6},
Pages = {1120 - 1150},
Volume = {53},
Abstract = {Paradoxicaql combination of characters; more research needed},
Doi = {10.1111/jpy.12569},
File = {heiss2017_cyanophora_cuspidata_flagell_app.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28741699}
}
@Article{Heiss2018,
Title = {{Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes.}},
Author = {A. A. Heiss and M. Kolisko and F. Ekelund and M. W. Brown and A. J. Roger and A. G. B. Simpson},
Journal = {R. Soc. open sci.},
Year = {2018},
Abstract = {Malaw is Excavata; Malaw + Metamon},
Doi = {10.1098/rsos.171707},
File = {heiss2018_malawimonads.pdf},
Url = {http://rsos.royalsocietypublishing.org/}
}
@Article{Heiss2015,
Title = {{Cultivation and Characterisation of New Species of Apusomonads (the Sister Group to Opisthokonts), Including Close Relatives of Thecamonas (Chelonemonas n. Gen.)}},
Author = {A. A. Heiss and W. J. Lee and K.-i. Ishida and A. G. B. Simpson},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2015},
Abstract = {Apuso incl. Chelonemonas, Ancyro || Mantamonas || Breviat || Micronucl + Rigifila || Collod + Diphy},
Doi = {10.1111/jeu.12220-4597},
File = {heiss2015_chelonemonas_apusom.pdf}
}
@Conference{Heiss2008,
Title = {{The ultrastructure of Ancyromonas, a eukaryote without supergroup affiliation}},
Author = {A. A. Heiss and G. Walker and A. G. B and Simpson},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {Homologies with the apusomonads are possible but not obvious.},
File = {heiss2008.txt}
}
@Article{Heiss2013,
Title = {{The microtubular cytoskeleton of the apusomonad Thecamonas, a sister lineage to the opisthokonts.}},
Author = {A. A. Heiss and G. Walker and A. G. B. Simpson},
Journal = {Protist},
Year = {2013},
Number = {5},
Pages = {598--621},
Volume = {164},
Abstract = {Similarities between apuso, ancyro and Breviata},
Doi = {10.1016/j.protis.2013.05.005},
File = {heiss2013_thecamonas_morph.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23872341}
}
@Article{Heiss2013a,
Title = {{The flagellar apparatus of Breviata anathema, a eukaryote without a clear supergroup affinity.}},
Author = {A. A. Heiss and G. Walker and A. G. B. Simpson},
Journal = {Eur. J. Protistol.},
Year = {2013},
Abstract = {Unclear but unikont},
Doi = {10.1016/j.ejop.2013.01.001},
File = {heiss2013_breviata_fragellar_app.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23523042}
}
@Article{Heiss2011,
Title = {{The Ultrastructure of Ancyromonas; a Eukaryote without Supergroup Affinities}},
Author = {A. A. Heiss and G. Walker and A. G. B. Simpson},
Journal = {Protist},
Year = {2011},
Abstract = {Maybe equally similar to excavates and Apusom, slightly more distant from Micronuclearia podoventralis},
Doi = {10.1016/j.protis.2010.08},
File = {heiss2011_ancyromonas.djvu},
Url = {http://www.elsevier.de/protis}
}
@Article{Heiss2010,
Title = {{Clarifying the Taxonomic Identity of a Phylogenetically Important Group of Eukaryotes: Planomonas is a Junior Synonym of Ancyromonas}},
Author = {A. A. Heiss and G. Walker and A. G. B. Simpson},
Journal = {The Journal of eukaryotic microbiology},
Year = {2010},
Abstract = {As stated, 7 species},
Doi = {10.1111/j.1550-7408.2010.00477.x},
File = {heiss2010_ancyromonas.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20384907}
}
@Article{Heiss,
Title = {{Description of Imasa heleensis, gen. Nov., Sp. Nov. (Imasidae, fam. Nov.), A Deep-Branching Marine Malawimonad and Possible Key Taxon in Understanding Early Eukaryotic Evolution}},
Author = {A. A. Heiss and S. D. Warring and K. Lukacs and J. Favate and A. Yang and Y. Gyaltshen and C. Filardi and A. G. B. Simpson and E. Kim},
Journal = {Journal of Eukaryotic Microbiology},
Number = {2021},
Abstract = {As stated; position of the whole Malawim. near Discoba or Collod.},
Doi = {10.1111/jeu.12837},
File = {heiss2020_imasa_malawimon_phylog.pdf}
}
@Article{Hejnol2010,
Title = {{A Twist in Time-The Evolution of Spiral Cleavage in the Light of Animal Phylogeny}},
Author = {A. Hejnol},
Journal = {Integrative and Comparative Biology},
Year = {2010},
Abstract = {(Gnathi || Gast || Platy) + (Bry || Cyc || Ent) || Moll || Ann || Neme || Phor + Brach},
Doi = {10.1093/icb/icq103},
File = {hejnol2010_spiral_cleavage.pdf},
Url = {http://icb.oxfordjournals.org}
}
@Article{Hejnol2008,
Title = {{Acoel development supports a simple planula-like urbilaterian}},
Author = {A. Hejnol and M. Q. Martindale},
Journal = {Phil. Trans. R. Soc. B},
Year = {2008},
Number = {1496},
Pages = {1493--1501},
Volume = {363},
Abstract = {stem Urbilateria were simple, ancestors of Eubilateria ("Nephrozoa") deployed old genes},
Doi = {10.1098/rstb.2007.2239},
File = {hejnol2008.pdf}
}
@Article{Hejnol2008b,
Title = {{Acoel development indicates the independent evolution of the bilaterian mouth and anus}},
Author = {A. Hejnol and M. Q. Martindale},
Journal = {Nature},
Year = {2008},
Pages = {382--387},
Volume = {456},
Abstract = {Against trochaea (but no Platyh., Gnathost., Xenot.)},
Doi = {10.1038/nature07309},
File = {hejnol2008.pdf}
}
@Article{Hejnol2008c,
Title = {{From Nerve Net to CNS--Evolutionary Impacts from the Development of an Acoel}},
Author = {A. Hejnol and M. Q. Martindale},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {The dorsal-ventral patterning genes however, are more similar to the situation found in hemichordates},
Doi = {10.1002/jmor.10683},
File = {hejnol2008.txt}
}
@Article{Hejnol2009,
Title = {{Assessing the root of bilaterian animals with scalable phylogenomic methods.}},
Author = {A. Hejnol and M. Obst and A. Stamatakis and M. Ott and G. W. Rouse and G. D. Edgecombe and P. Martinez and J. Bagu{\~n}{\`a} and X. Bailly and U. Jondelius and M. Wiens and W. E. G. M{\"u}ller and E. Seaver and W. C. Wheeler and M. Q. Martindale and G. Giribet and C. W. Dunn},
Journal = {Proc. Biol. Sci.},
Year = {2009},
Number = {1677},
Pages = {4261 - 4270},
Volume = {276},
Abstract = {Improvement of EST data and taxon sampling from Dunn et al. (2008) paper: Symbion, Microgn, Trichoplax, 2 ctenophores. Ctenoph. sister (short branches!), sponges (Homoscl. separate), then? Trich., Cnidaria, (Xenot + (Acoel + Nemert)), Deuter, Ecdyso, Chaet + Phoron, Protost.: (Annelida || Kryptrochozoa (Nemertini + Brachiopoda) + Mollusca) || Platyzoa (no support, incl.? Microgn.) + Polyzoa (Bryoz || Cycl. + Entopr)},
Doi = {10.1098/rspb.2009.0896},
File = {hejnol2009_bilaterian_root_.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19759036}
}
@Article{Hejnol2004,
Title = {{The eutardigrade Thulinia stephaniae has an indeterminate development and the potential to regulate early blastomere ablations}},
Author = {A. Hejnol and R. Schnabel},
Journal = {Development},
Year = {2004},
Pages = {1349--1361},
Volume = {132},
Abstract = {Not enterocoel; more or less "free" development},
Doi = {10.1242/dev.01701},
File = {hejnol2005.pdf}
}
@Article{Helm2012,
Title = {{Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida}},
Author = {C. Helm and S. H. Bernhart and C. H. z. Siederdissen and B. Nickel and C. Bleidorn},
Journal = {Mol. Phyl. Evol.},
Year = {2012},
Abstract = {~ Errantia},
Doi = {10.1016/j.ympev.2012.03.017},
File = {helm2012_myzostomida.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2012.03.017}
}
@Article{Helm2013,
Title = {{Immunohistochemical investigations of Myzostoma cirriferum and Mesomyzostoma cf. Katoi (Myzostomida, Annelida) with implications for the evolution of the myzostomid body plan}},
Author = {C. Helm and {\'A}. C. Bleidorn and P. A. Stevenson and G. W. Rouse},
Journal = {Zoomorphology},
Year = {2013},
Volume = {33},
Abstract = {segmented ancestry},
Doi = {10.1007/s00435-014-0221-z},
File = {helms2014_myzostomids.pdf}
}
@Article{Helm2014,
Title = {{Immunohistochemical investigations of Myzostoma cirriferum and Mesomyzostoma cf. Katoi (Myzostomida, Annelida) with implications for the evolution of the myzostomid body plan}},
Author = {C. Helm and P. A. Stevenson and G. W. Rouse and C. Bleidorn},
Journal = {Zoomorphology},
Year = {2014},
Pages = {257--271},
Volume = {133},
Abstract = {Secondary bilateral},
Doi = {10.1007/s00435-014-0221-z},
File = {helm2014_myzostomida.pdf}
}
@Article{Helm2013a,
Title = {{Myoanatomy of Myzostoma cirriferum (Annelida, Myzostomida): Implications for the evolution of the Myzostomid body plan.}},
Author = {C. Helm and A. Weigert and G. Mayer and C. Bleidorn},
Journal = {J. Morphol.},
Year = {2013},
Number = {4},
Pages = {456--466},
Volume = {274},
Abstract = {In line with Annelida, radial is secondary},
Doi = {10.1002/jmor.20107},
File = {helm2013_myzostoma_myoanatomy.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23280634}
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@Article{Helmkampf2008a,
Title = {{Multigene analysis of lophophorate and chaetognath phylogenetic relationships}},
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Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {2008},
Pages = {206--214},
Volume = {46},
Abstract = {Chaeto+Priapul (but unstable); Platy || Brachiop || Bryoz+(Anne+Phoron) || Nemert || Mollusca},
Doi = {10.1016/j.ympev.2007.09.004},
File = {helmkampf2008.pdf}
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Title = {{Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept}},
Author = {M. Helmkampf and I. Bruchhaus and B. Hausdorf},
Journal = {Proc. R. Soc. B},
Year = {2008},
Number = {1645},
Pages = {1927--1933},
Volume = {275},
Abstract = {Brachiozoa (!): Brachiopoda + Phoronida; Ecto + Entom but no Cycl. in analysis},
Doi = {10.1098/rspb.2008.0372},
File = {helmkampf2008.pdf}
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@Article{Hendriks1991,
Title = {{The evolutionary position of the rhodophyte \textit{Porphyra umbilicalis} and the basidiomycete \textit{Leucosporidium scottii} among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA.}},
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@Article{Henz2005,
Title = {{Whole-genome prokaryotic phylogeny.}},
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Pages = {2329--2335},
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@Article{Hering2012,
Title = {{Opsins in Onychophora (Velvet Worms) Suggest a Single Origin and Subsequent Diversification of Visual Pigments in Arthropods.}},
Author = {L. Hering and M. J. Henze and M. Kohler and A. Kelber and C. Bleidorn and M. Leschke and B. Nickel and M. Meyer and M. Kircher and P. Sunnucks and G. Mayer},
Journal = {Molecular biology and evolution},
Year = {2012},
Abstract = {Onychophora sister},
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@Article{Herlemann2007,
Title = {{The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment}},
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Year = {2007},
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Pages = {6682--6685},
Volume = {73},
Abstract = {TG1 has 5 environmental lines in addition to "Endomicrobia"},
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File = {herlemann2007.pdf}
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Title = {{Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1).}},
Author = {D. P. R. Herlemann and O. Geissinger and W. Ikeda-Ohtsubo and V. Kunin and H. Sun and A. Lapidus and P. Hugenholtz and A. Brune},
Journal = {Appl. Environ. Microbiol.},
Year = {2009},
Number = {9},
Pages = {2841--2849},
Volume = {75},
Abstract = {Synergistetes + (Endom. + Elusim.); Fuso, Termotog, Thermi, Coprothermobacter; Acido, Deferri ~ Proteo; Thermodesulfo ~ Aquific},
Doi = {10.1128/AEM.02698-08},
File = {herlemann2009_elusimicrobia.pdf}
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Title = {{Enigmatic Gnathostomulida (Gnathifera, Spiralia): About monociliated pharyngeal receptors and the pharyngeal nervous system}},
Author = {H. Herlyn},
Journal = {Zoomorphology},
Year = {2017},
Abstract = {As stated},
Doi = {10.1007/s00435-017-0369-4},
File = {/home/alexey/coll/ref/os/1/herlin2017_gnathostomulida.pdf},
ISSN = {1432-234X},
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Title = {{The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences}},
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Year = {2003},
Pages = {155--164},
Volume = {26},
Abstract = {Eurotatoria || Seison || Acanthocephala},
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Title = {{The symbiont \textit{Capsaspora owczarzaki}, nov. gen. nov. sp., isolated from three strains of the pulmonate snail Biomphalaria glabrata is related to members of the Mesomycetozoea}},
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Title = {{The mystery of clade X: Orciraptor gen. Nov. And Viridiraptor gen. Nov. Are highly specialised, algivorous amoeboflagellates (Glissomonadida, Cercozoa).}},
Author = {S. Hess and M. Melkonian},
Journal = {Protist},
Year = {2013},
Number = {5},
Pages = {706--747},
Volume = {164},
Abstract = {Cercomonadida || Pansomonadida || Glissomonadida},
Doi = {10.1016/j.protis.2013.07.003},
File = {ess2013_orciraptor_viridiraptor_glissomonadida.djvu},
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Title = {{Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited}},
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Abstract = {Endomyxa: Filoreta, Gromiidea, Asceto || Phytomyxea || Vampyrellidae || Leptophrydae incl. Theratomyxa, "Arachnula impatiens", Platyreta, Leptophrys},
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Keywords = {pr1}
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@InProceedings{Holton2009,
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Pages = {723--739},
Volume = {48}
}
@Article{Honda2007,
Title = {{Taxonomic rearrangement of the genus Schizochytrium sensu lato based on morphology, chemotaxonomic characteristics, and 18S rRNA gene phylogeny (Thraustochytriaceae, Labyrinthulomycetes): Emendation for Schizochytrium and erection of Aurantiochytrium and Oblongichytrium gen. nov.}},
Author = {R. Y.-. D. Honda},
Journal = {Mycoscience},
Year = {2007},
Pages = {199--211},
Volume = {48},
Abstract = {Oblongichytrium sister to other Labyr.},
Doi = {10.1007/s10267-006-0362-0},
File = {yokoyama2007_oblongicgytrium.pdf}
}
@Article{Honegger2018,
Title = {{Fertile Prototaxites taiti: A basal ascomycete with inoperculate, polysporous asci lacking croziers}},
Author = {R. Honegger and D. Edwards and L. Axe and C. Strullu-Derrien},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2018},
Number = {1739},
Volume = {373},
Abstract = {As stated},
Doi = {10.1098/rstb.2017.0146},
File = {honegger2017_prototaxites_is_sporophore.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17486975}
}
@Article{Hongoh2006,
Title = {{Phylogenetic Diversity, Localization, and Cell Morphologies of Members of the Candidate Phylum TG3 and a Subphylum in the Phylum Fibrobacteres, Recently Discovered Bacterial Groups Dominant in Termite Guts}},
Author = {Y. Hongoh and P. Deevong and S. Hattori and T. Inoue and S. Noda and N. Noparatnaraporn and T. Kudo and M. Ohkuma},
Journal = {Appl. Environ. Microbiol.},
Year = {2006},
Number = {10},
Pages = {6780--6788},
Volume = {72},
Abstract = {TG3 ~ Fibrobacteres, comprises of 2 subphyla},
File = {hongoh2006.pdf}
}
@Article{Hongoh2007,
Title = {{The Motility Symbiont of the Termite Gut Flagellate Caduceia versatilis Is a Member of the ``Synergistes'' Group}},
Author = {Y. Hongoh and T. Sato and M. F. Dolan and S. Noda and S. Ui and T. Kudo and M. Ohkuma},
Journal = {Appl. Environ. Microbiol.},
Year = {2007},
Number = {19},
Pages = {6270--6276},
Volume = {73},
Abstract = {Contain two kinds of symbionts: Bacteroidetes and Synergistes (Tammella caduceiae)},
Doi = {10.1128/AEM.00750-07},
File = {hongoh2007.pdf}
}
@Article{Hongoh2008,
Title = {{Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell.}},
Author = {Y. Hongoh and V. K. Sharma and T. Prakash and S. Noda and T. D. Taylor and T. Kudo and Y. Sakaki and A. Toyoda and M. Hattori and M. Ohkuma},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {14},
Pages = {5555--5560},
Volume = {105},
Abstract = {Firmi | Chloroflexi | Cyano; ||| Aquifex + Thermot + Deino; Spiro | TG1 | Bactero | PVC},
Doi = {10.1073/pnas.0801389105},
File = {hongoh2008.pdf}
}
@Article{Hoppe2009,
Title = {{In the shadow of Darwin: Anton de Bary's origin of myxomycetology and a molecular phylogeny of the plasmodial slime molds}},
Author = {T. Hoppe and U. Kutschera},
Journal = {Theory Biosci.},
Year = {2009},
Abstract = {Elements of history (latest things are not reflected)},
Doi = {10.1007/s12064-009-0079-7},
File = {hoppe2009_myxomyc_history.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19997788}
}
@Article{Hoppenrath2016,
Title = {{Dinoflagellate taxonomy -- a review and proposal of a revised classification}},
Author = {M. Hoppenrath},
Journal = {Marine Biodiversity},
Year = {2016},
Abstract = {Internal to the class},
Doi = {10.1007/s12526-016-0471-8},
File = {hoppenrath2016_dinoflagell_taxonomy.pdf},
ISSN = {1867-1616},
Url = {http://dx.doi.org/10.1007/s12526-016-0471-8}
}
@Article{Hoppenrath2009,
Title = {{Molecular Phylogeny of Parvilucifera prorocentri (Alveolata, Myzozoa): Insights into Perkinsid Character Evolution}},
Author = {M. Hoppenrath and B. S. Leander},
Journal = {Journal of Eukaryotic Microbiology},
Year = {In press},
Abstract = {Parv + Perk || Dinok + Oxyrr + Syndi + Dubosquella},
Doi = {10.1111/j.1550-7408.2009.00395.x},
File = {hoppenrath2009_parvilucifera.pdf}
}
@Article{Hoppenrath2010,
Title = {{Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences.}},
Author = {M. Hoppenrath and B. S. Leander},
Journal = {PLoS ONE},
Year = {2010},
Number = {10},
Pages = {e13220},
Volume = {5},
Abstract = {Noctiluca inside, Oxyrrhis sister},
Doi = {10.1371/journal.pone.0013220},
File = {hoppenrath2010_dinoflagellates.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20949037}
}
@Article{Hoppenrath2006,
Title = {{Ebriid Phylogeny and the Expansion of the Cercozoa}},
Author = {M. Hoppenrath and B. S. Leander},
Journal = {Protist},
Year = {2006},
Number = {3},
Pages = {279--290},
Volume = {157},
Abstract = {Retaria || Chlorara || Sarco* || Eugly + Thauma, (Phaeoda (Pseudodiffl + Cryo inc. Protaspis, Ebri))},
File = {hoppenrath2006.pdf}
}
@Article{Hoppenrath2006b,
Title = {{Dinoflagellate, Euglenid, or Cercomonad? The Ultrastructure and Molecular Phylogenetic Position of Protaspis grandis n. sp.}},
Author = {M. Hoppenrath and B. S. Leander},
Journal = {J. Euk. Microbiol.},
Year = {2006},
Number = {5},
Pages = {1--16},
Volume = {53},
Abstract = {Protaspis > Cryo},
File = {hoppenrath2006b.pdf}
}
@Article{Horiike2009,
Title = {{Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs}},
Author = {T. Horiike and D. Miyata and K. Hamada and S. Saruhashi and T. Shinozawa and S. Kumar and R. Chakraborty and T. Komiyama and Y. Tateno},
Journal = {Gene},
Year = {2009},
Pages = {59--64},
Volume = {429},
Abstract = {Thermot || Aquific || Chlorofl || Chlam + Bacteroid + Chlorob + Spiro + ?Fuso (or ~ Firmi) || Proteo + ?Plancto (or ~ Actino) || Actino + Deino || Firmi + ?Cyano (or ~ Actino)},
Doi = {10.1016/j.gene.2008.10.006},
File = {horiike2009.pdf}
}
@Article{Horn2007,
Title = {{\textit{Synchroma grande} spec. nov. (Synchromophyceae class. nov., Heterokontophyta): An Amoeboid Marine Alga with Unique Plastid Complexes}},
Author = {S. Horn and K. Ehlers and G. Fritzsch and M. C. Gil-Rodriguez and C. Wilhelm and R. Schnetter},
Journal = {Protist},
Year = {2007},
Number = {3},
Pages = {277--293},
Volume = {158},
Abstract = {Xanth mixed with Phaeo; Pelago can be not related with Dictyoch; Eust sep. from other Chryso, Synchroma grande basal to Chrysoph},
File = {horn2007.pdf}
}
@Article{Horne2002,
Title = {{Taxonomy, morphology and biology of Quaternary and living Ostracoda}},
Author = {D. J. Horne and A. Cohen and K. Martens},
Journal = {Geophysical monograph},
Year = {2002},
Pages = {5--36},
Volume = {131},
Abstract = {Review},
File = {horne2002_ostracoda.pdf}
}
@Article{Horner2000,
Title = {{Iron Hydrogenases and the Evolution of Anaerobic Eukaryotes}},
Author = {D. S. Horner and P. G. Foster and T. M. Embley},
Journal = {Mol. Biol. Evol.},
Year = {2000},
Number = {11},
Pages = {1695--1709},
Volume = {17}
}
@Article{Horner1999,
Title = {{A Single Eubacterial Origin of Eukaryotic Pyruvate:Ferredoxin Oxidoreductase Genes: Implications for the Evolution of Anaerobic Eukaryotes}},
Author = {D. S. Horner and R. P. Hirt and T. M. Embley},
Journal = {Mol. Biol. Evol.},
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Pages = {1280--1291},
Volume = {16}
}
@Article{Hoshino2018,
Title = {{On the origin of isoprenoid biosynthesis.}},
Author = {Y. Hoshino and E. A. Gaucher},
Journal = {Mol. Biol. Evol.},
Year = {2018},
Abstract = {CPR might be closer to archaea},
Doi = {10.1093/molbev/msy120},
File = {hoshino2018_isoprenoid_biosynth_candidate_phyla_rad_archaea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23184964}
}
@Article{Hou2015,
Title = {{New insights into the evolutionary history of Gnetum (Gnetales)}},
Author = {C. Hou and A. M. Humphreys and O. Thureborn and C. Rydin},
Journal = {Taxon},
Year = {2015},
Abstract = {Sister to conifers},
File = {hou2015_gnetum.pdf}
}
@Article{Hou2008,
Title = {{Complete genome sequence of the extremely acidophilic methanotroph isolate V4, "Methylacidiphilum infernorum", a representative of the bacterial phylum Verrucomicrobia.}},
Author = {S. Hou and K. S. Makarova and J. H. Saw and P. Senin and B. V. Ly and Z. Zhou and Y. Ren and J. Wang and M. Y. Galperin and M. V. Omelchenko and Y. I. Wolf and N. Yutin and E. V. Koonin and M. B. Stott and B. W. Mountain and M. A. Crowe and A. V. Smirnova and P. F. Dunfield and L. Feng and L. Wang and M. Alam},
Journal = {Biol. Direct},
Year = {2008},
Number = {1},
Pages = {26},
Volume = {3},
Abstract = {51 ribos:( Aquif + Dein + Therm), (Actino || Fuso + Firm || Chlorofl + Cyano), ((Acido+Delta || Epsilon || Alpha || Beta+Gamma),(Spir + Bact/Chlorobi || PVC: Planct || Chl || Lenti || Verru)); subunits: Spiro, (Fuso || Mycopl || Thermot || Dein-Th || Cyano || Firm || Actino + Chlorofl w/o supp.), ((Epsi+Aquif || Acido || Delta || Alpha || Beta + Gamma), ((Chlorobi + Bacteroid), (P || C || L || V)))},
Doi = {10.1186/1745-6150-3-26},
File = {hou2008.pdf}
}
@Article{Hou2013,
Title = {{Molecular evidence for beta-tubulin neofunctionalization in Retaria (Foraminifera and radiolarians)}},
Author = {Y. Hou and R. Sierra and D. Bassen and N. K. Banavali and A. Habura and J. Pawlowski and S. S. Bowser},
Journal = {Mol. Biol. Evol.},
Year = {2013},
Pages = {1--20},
Abstract = {Unusual beta2 tubulin is a synapomorphy for Retaria},
File = {hou2013_retaria.pdf},
Url = {http://mbe.oxfordjournals.org/}
}
@Article{Howard2020,
Title = {{Ancestral morphology of Ecdysozoa constrained by an early Cambrian stem group ecdysozoan}},
Author = {R. J. Howard and G. D. Edgecombe and X. Shi and X. Hou and X. Ma},
Journal = {BMC Evolutionary Biology},
Year = {2020},
Abstract = {Acosmia || Scalidophora and then others},
Doi = {10.1186/s12862-020-01720-6},
File = {howard2020_acosmia_cambrian_stem_ecdysozoa.pdf},
ISSN = {1471-2148}
}
@Article{Howe2011b,
Title = {{New Genera, Species, and Improved Phylogeny of Glissomonadida (Cercozoa)}},
Author = {A. T. Howe and D. Bass and E. E. Chao and T. Cavalier-Smith},
Journal = {Protist},
Year = {2011},
Pages = {13},
Abstract = {As stated},
Doi = {10.1016/j.protis.2011.06.002},
File = {howe2011_glissomonadida.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2011.06.002}
}
@Article{Howe2011a,
Title = {{Novel Cultured Protists Identify Deep-branching Environmental DNA Clades of Cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrini}},
Author = {A. T. Howe and D. Bass and J. M. Scoble and R. Lewis and K. Vickerman and H. Arndt and T. Cavalier-Smith},
Journal = {Protist},
Year = {2011},
Pages = {41},
Volume = {1},
Abstract = {Endomyxa || Tremulida || Chrorarachn || Granofilosea (incl Massisteridae, Leucodictyda) || MONADOFILOSA (glide only on posterior flagella): Metromonadea (incl. Metopion, Micrometopion) || Sarcomonadea || Thecofilosea (incl. Ventricleftida etc.) || Imbricatea (incl. Eugl, Marinomonadidae: Aurant, Clautr, Taum, Peregrinidae, Spongom, Discomonas)},
Doi = {10.1016/j.protis.2010.10.002},
File = {howe2011_new_cercozoa.pdf},
Url = {http://www.elsevier.de/protis}
}
@Article{Howe2009,
Title = {{Phylogeny, Taxonomy, and Astounding Genetic Diversity of Glissomonadida ord. Nov., The Dominant Gliding Zooflagellates in Soil (Protozoa: Cercozoa)}},
Author = {A. T. Howe and D. Bass and K. Vickerman and E. E. Chao and T. Cavalier-Smith},
Journal = {Protist},
Year = {In press},
Abstract = {Chlorar | Granofilosea ||| Cercomonadida ||| Spongomonadida, Thecofilosea, Thaumato, Euglyph, Pseudopirsonia || Pansomonadida (Aurigamonas, Cercobodo) || Glissomonadida; Classis Sarcomonadea: Ordines Cercom, Glisso (inc. ?Allantion), Panso, Metopiida},
Doi = {10.1016/j.protis.2008.11.007},
File = {howe2009_glissomonadida.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2008.11.007}
}
@Conference{Howe2008,
Title = {{Phylogeny, taxonomy, and genetic diversity of Glissomonadida ord. nov., the dominant gliding zooflagellates in soil (Protozoa: Cercozoa)}},
Author = {A. T. Howe and D. Bass and K. Vickerman and E. E. Chao and T. Cavalier-Smith},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {we establish a new order "Glissomonadida" (as yet unpublished) for Heteromitidae sensu Cavalier-Smith and Chao, 2003},
File = {howe2008.txt}
}
@Article{Hrda2016,
Title = {{Mitochondrial Genome of Prasinophyte Alga Pyramimonas parkeae}},
Author = {{\v{S}}. Hrd{\'a} and M. Hroudov{\'a} and {\v{C}}. Vl{\v{c}}ek and V. Hampl},
Journal = {Journal of Eukaryotic Microibiology},
Year = {2016},
Abstract = {Controversial Prasinoderma + Picnococcus; others more or less similar to synat},
Doi = {10.1111/jeu.12371-4856},
File = {hrda2016_pyramimonas_mt.pdf}
}
@Article{Huang2008,
Title = {{Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding}},
Author = {D. Huang and R. Meier and P. A. Todd and L. M. Chou},
Journal = {J. Mol. Evol.},
Year = {2008},
Number = {2},
Pages = {167--174},
Volume = {66},
Abstract = {Porifera and Anthozoa slowwer than Medusozoa},
Doi = {10.1007/s00239-008-9069-5},
File = {huang2008.pdf}
}
@Article{Huang2004,
Title = {{The novel organization and complete sequence of the ribosomal RNA gene of Nosema bombycis}},
Author = {W.-F. Huang and S.-J. Tsai and C.-F. Lo and Y. Soichi and C.-H. Wang},
Journal = {Fungal Genet. Biol.},
Year = {2004},
Number = {5},
Pages = {473--481},
Volume = {41},
Abstract = {The organization of the N. bombycis rRNA gene is LSUrRNA-ITS-SSUrRNA-IGS-5S. This novel arrangement, in which the LSU is 5' of the SSU, is the reverse of the organizational sequence (i.e., SSU-ITS-LSU) found in all previously reported microsporidian rRNAs.},
Doi = {10.1016/j.fgb.2003.12.005}
}
@Article{Huber2002,
Title = {{A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont}},
Author = {Harald Huber and Michael J. Hohn and Reinhard Rachel and Tanja Fuchs and Verena C. Wimmer and Karl O. Stetter},
Journal = {Nature},
Year = {2002},
Pages = {63--67},
Volume = {417}
}
@Article{Hueber2013,
Title = {{Analysis of central Hox protein types across bilaterian clades: On the diversification of central Hox proteins from an Antennapedia/Hox7-like protein.}},
Author = {S. D. Hueber and J. Rauch and M. A. Djordjevic and H. Gunter and G. F. Weiller and T. Frickey},
Journal = {Dev. Biol.},
Year = {2013},
Number = {2},
Pages = {175--185},
Volume = {383},
Abstract = {Hox "portraits" of phyla},
Doi = {10.1016/j.ydbio.2013.09.009},
File = {hueber2013_hox_bilateria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24055174}
}
@Article{HuertaCepas2007,
Title = {{The human phylome}},
Author = {J. Huerta-Cepas and H. Dopazo and J. Dopazo and T. Gabaldon},
Journal = {Genome Biol.},
Year = {2007},
Number = {6},
Pages = {R109},
Volume = {2007},
Abstract = {Slight support to Unikonta; more to Coelomata than Ecdysozoa},
File = {huerta-cepas2007.pdf}
}
@Article{Hug2016a,
Title = {{A new view of the tree of life.}},
Author = {L. A. Hug and B. J. Baker and K. Anantharaman and C. T. Brown and A. J. Probst and C. J. Castelle and C. N. Butterfield and A. W. Hernsdorf and Y. Amano and K. Ise and Y. Suzuki and N. Dudek and D. A. Relman and K. M. Finstad and R. Amundson and B. C. Thomas and J. F. Banfield},
Journal = {Nat Microbiol},
Year = {2016},
Pages = {16048},
Volume = {1},
Abstract = {Fig. 2 and 3 contain two views on the tree},
Doi = {10.1038/nmicrobiol.2016.48},
File = {hug2016_new_view_tol_cand_phyla_rad.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24096423}
}
@Article{Hug2016,
Title = {{Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages.}},
Author = {L. A. Hug and B. C. Thomas and I. Sharon and C. T. Brown and R. Sharma and R. L. Hettich and M. J. Wilkins and K. H. Williams and A. Singh and J. F. Banfield},
Journal = {Environmental Microbiology},
Year = {2016},
Number = {1},
Pages = {159--173},
Volume = {18},
Abstract = {Dadabacteria (CSP 1-2) ~ Proteobacteria},
Doi = {10.1111/1462-2920.12930},
File = {hug2015_dadabacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26033198}
}
@Article{Hugenholtz2002,
Title = {{Exploring prokaryotic diversity in the genomic era}},
Author = {P. Hugenholtz},
Journal = {Genome Biol.},
Year = {2002},
Number = {2},
Pages = {1--8},
Volume = {3}
}
@Article{Hugenholtz1998,
Title = {{Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity}},
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@Article{Hugenholtz2004,
Title = {{Reclassification of \textit{Sphaerobacter thermophilus} from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description).}},
Author = {P. Hugenholtz and E. Stackebrandt},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2004},
Number = {6},
Pages = {2049--2051},
Volume = {54},
Abstract = {Anaerolineae, Dehalococcoidetes ~ Chloroflexi},
File = {hugenholtz2004.pdf}
}
@Article{Hugenholtz2001,
Title = {{Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives}},
Author = {P. Hugenholtz and G. W. Tyson and R. I. Webb and A. M. Wagner and L. L. Blackall},
Journal = {Appl. Environ. Microbiol.},
Year = {2001},
Number = {1},
Pages = {411--419},
Volume = {67},
Abstract = {TM7 -- third G+ lineage},
File = {hugenholtz2001_tm7.pdf}
}
@Article{Hughes1999,
Title = {{Phylogenetic relationships of the enigmatic hoatzin (\textit{Opisthocomus hoazin}) resolved using mitochondrial and nuclear gene sequences.}},
Author = {J. M. Hughes and A. J. Baker},
Journal = {Mol. Biol. Evol.},
Year = {1999},
Number = {9},
Pages = {1300--1307},
Volume = {16}
}
@Article{Hugler2007,
Title = {{Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage.}},
Author = {M. Hugler and H. Huber and S. J. Molyneaux and C. Vetriani and S. M. Sievert},
Journal = {Environ. Microbiol.},
Year = {2007},
Number = {1},
Pages = {81--92},
Volume = {9},
Abstract = {ATP citrate: Aquificae ~ e-proteobacteria},
File = {huegler2007_aquifex.pdf}
}
@Article{Hui2009,
Title = {{Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes}},
Author = {J. Hui and F. Raible and N. Korchagina and N. Dray and S. Samain and G. Magdelenat and C. Jubin and B. Segurens and G. Balavoine and D. Arendt and D. Ferrier},
Journal = {BMC Biol.},
Year = {2009},
Number = {1},
Pages = {43},
Volume = {7},
Abstract = {Closer to Deuterost than previously thought},
Doi = {10.1186/1741-7007-7-43},
File = {hiu2009_platynereis_parahox.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19627570}
}
@Article{Hui2008,
Title = {{Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster}},
Author = {J. H. L. Hui and P. W. H. Holland and D. E. K. Ferrier},
Journal = {Evol. Devel.},
Year = {2008},
Pages = {725--730},
Volume = {10},
Abstract = {Yes},
File = {hiu2008.pdf}
}
@Article{Hulpiau2008,
Title = {{Molecular evolution of the cadherin superfamily}},
Author = {P. Hulpiau and F. van Roy},
Journal = {The International Journal of Biochemistry \& Cell Biology},
Year = {2008},
Number = {2009},
Pages = {349--369},
Volume = {41},
Abstract = {Separate Protost. from Deuterost., show that plants have a different origin of multicellularity (do not have cadherins)},
Doi = {10.1016/j.biocel.2008.09.027},
File = {hulpiau2009.pdf}
}
@Article{Humber2007,
Title = {{Entomophthoromycota: A new phylum and reclassification for entomophthoroid fungi}},
Author = {R. A. Humber},
Journal = {Mycotaxon},
Year = {2007},
Pages = {477--492},
Volume = {120},
Abstract = {As in Gryganskyi et al., 2013},
Doi = {10.5248/120.477},
File = {humber2012_entomophthoromycota.pdf},
Url = {http://dx.doi.org/10.5248/120.477}
}
@Article{Hunt2017,
Title = {{Development of a lecithotrophic pilidium larva illustrates convergent evolution of trochophore-like morphology.}},
Author = {M. K. Hunt and S. A. Maslakova},
Journal = {Front. Zool.},
Year = {2017},
Pages = {7},
Volume = {14},
Abstract = {As stated},
Doi = {10.1186/s12983-017-0189-x},
File = {hunt2017_pilidium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/12639321}
}
@Article{Hustad2013,
Title = {{Generic circumscriptions in Geoglossomycetes}},
Author = {V. P. Hustad and A. N. Miller and B. T. M. Dentinger and P. F. Cannon},
Journal = {Persoonia},
Year = {2013},
Pages = {101--111},
Volume = {31},
Abstract = {As stated},
Doi = {10.3767/003158513X671235},
File = {hustad2013_geoglossomycetes.pdf},
Url = {www.ingentaconnect.com/content/nhn/pimj}
}
@Article{Huynen1999,
Title = {{Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes}},
Author = {M. Huynen and B. Snel and P. Bork},
Journal = {Science},
Year = {1999},
Number = {5444},
Pages = {1441},
Volume = {286}
}
@Article{Huys1993,
Title = {{The Tantulocaridan Life Cycle: The Circle Closed?}},
Author = {R. Huys and G. A. Boxshall and R. J. Lincoln},
Journal = {Journal of Crustacean Biology},
Year = {1993},
Number = {3},
Pages = {432--442},
Volume = {13},
Abstract = {Tantulocarida || Thecostraca},
File = {huys1993.pdf},
Url = {http://www.jstor.org/stable/1548786}
}
@Article{Hyde2017,
Title = {{The ranking of fungi: A tribute to David L. Hawksworth on his 70th birthday}},
Author = {K. D. Hyde and S. S. N. Maharachchikumbura and S. Hongsanan and M. C. Samarakoon and R. L{\"u}cking and D. Pem and D. Harishchandra and R. Jeewon and R.-L. Zhao and J.-C. Xu and J.-K. Liu and A. M. Al-Sadi and A. H. Bahkali and A. M. Elgorban},
Journal = {Fungal Diversity},
Year = {2017},
Abstract = {Sordariomycetes time ranking},
Doi = {10.1007/s13225-017-0383-3},
File = {hyde2017_ranking_fungi.pdf}
}
@Book{Hyman1940,
Title = {{The Invertebrates}},
Author = {L. H. Hyman},
Publisher = {McGraw-Hill},
Year = {1940--1967},
Address = {New York},
Volume = {1-6}
}
@Book{Hyman1940--1967,
Title = {{Invertebrates}},
Author = {L. H. Hyman},
Publisher = {McGraw-Hill},
Year = {1940--1967},
Address = {New York},
Volume = {I--VI},
Pages = {1--499}
}
@Article{Hyvonen1999,
Title = {{On Phylogeny of the Polytrichales}},
Author = {Jaakko Hyvonen and Terry A. Hedderson and Gary L. Smith Merrill and J. George Gibbings and Satu Koskinen},
Journal = {Bryologist},
Year = {1999},
Number = {4},
Pages = {489--504},
Volume = {101}
}
@Other{Raikova2016,
Title = {{The plastic nervous system of Nemertodermatida}},
Abstract = {As stated, ~ Xeno},
Author = {l. I. Raikova and I. Meyer-Wachsmuth and U. Jondelius},
Doi = {10.1007/s13127-015-0248-0},
File = {raikova2015_nemertodermatida_neur.pdf},
Journal = {Org Divers Evol},
Year = {2016}
}
@Article{IckertBond2016,
Title = {{The Gnetales: Recent insights on their morphology, reproductive biology, chromosome numbers, biogeography, and divergence times}},
Author = {S. M. Ickert-Bond and S. S. Renner},
Journal = {Journal of Systematics and Evolution},
Year = {2016},
Abstract = {Review},
Doi = {10.1111/jse.12190},
File = {ickert-bond2016_gnetales_review.pdf},
Url = {www.jse.ac.cn}
}
@Article{Idei2013,
Title = {{Sperm ultrastructure in the diatoms Melosira and Thalassiosira and the significance of the 9 + 0 configuration.}},
Author = {M. Idei and K. Osada and S. Sato and T. Nakayama and T. Nagumo and D. G. Mann},
Journal = {Protoplasma},
Year = {2013},
Number = {4},
Pages = {833--850},
Volume = {250},
Abstract = {Descriptive},
Doi = {10.1007/s00709-012-0465-8},
File = {idei2013_diatoms_9_plus_0.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23149627}
}
@Article{SmithIII1986,
Title = {{Is the Turbellaria polyphyletic?}},
Author = {J. P. S. Smith III and S. Teyler and R. M. Rieger},
Journal = {Hydrobiologia},
Year = {1986},
Pages = {13--21},
Volume = {132},
Abstract = {Yes},
File = {smith1986_turbellaria_polyphyletic.pdf}
}
@Article{Iino2009,
Title = {{Ignavibacterium album gen. Nov., Sp. Nov., A moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring, and proposal of Ignavibacteria classis nov. For a novel lineage at the periphery of the green sulfur bacteria}},
Author = {T. Iino and K. Mori and Y. Uchino and T. Nakagawa and S. Harayama and K. I. Suzuki},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {In press},
Abstract = {Bacteroidetes || Chlorobea || Ignavibacteria},
Doi = {10.1099/ijs.0.012484-0},
File = {iino2009_ignavibacterium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19671715}
}
@Article{Iino2013,
Title = {{Candidatus Methanogranum caenicola: A Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. Nov. And Methanomassiliicoccales ord. Nov., For a Methanogenic Lineage of the Class Thermoplasmata}},
Author = {T. Iino and H. Tamaki and S. Tamazawa and Y. Ueno and M. Ohkuma and K.-I. Suzuki and Y. Igarashi and S. Haruta},
Journal = {Microbes Environ.},
Year = {2013},
Abstract = {As stated},
Doi = {10.1264/jsme2.ME12189},
File = {iino2013_mathanomassiliicoccales_thermoplasmatae.pdf},
Url = {https://www.jstage.jst.go.jp/browse/jsme2}
}
@Article{IkedaOhtsubo2007,
Title = {{Phylogenetic diversity of ``Endomicrobia'' and their specific affiliation with termite gut flagellates}},
Author = {W. Ikeda-Ohtsubo and M. Desai and U. Stingl and A. Brune},
Journal = {Microbiology},
Year = {2007},
Pages = {3458--3465},
Volume = {153},
File = {ikeda-ohtsubo2007.pdf}
}
@Article{Im2012,
Title = {{Description of Fimbriimonas ginsengisoli gen. Nov., Sp. Nov. Within the Fimbriimonadia class nov., Of the phylum Armatimonadetes.}},
Author = {W.-T. Im and Z.-Y. Hu and K.-H. Kim and S.-K. Rhee and H. Meng and S.-T. Lee and Z.-X. Quan},
Journal = {Antonie Van Leeuwenhoek},
Year = {2012},
Number = {2},
Pages = {307--317},
Volume = {102},
Abstract = {Fimbriimonadia || Chthonomonadetes, Armatimonadida and unnamed groups},
Doi = {10.1007/s10482-012-9739-6},
File = {im2012_fimbriimonadida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22527625}
}
@Article{Imachi2020,
Title = {{Isolation of an archaeon at the prokaryote-eukaryote interface.}},
Author = {H. Imachi and M. K. Nobu and N. Nakahara and Y. Morono and M. Ogawara and Y. Takaki and Y. Takano and K. Uematsu and T. Ikuta and M. Ito and Y. Matsui and M. Miyazaki and K. Murata and Y. Saito and S. Sakai and C. Song and E. Tasumi and Y. Yamanaka and T. Yamaguchi and Y. Kamagata and H. Tamaki and K. Takai},
Journal = {Nature},
Year = {2020},
Abstract = {Lokiarchaeota: 'Candidatus Prometheoarchaeum syntrophicum'},
Doi = {10.1038/s41586-019-1916-6},
File = {imachi2020_prometheoarchaeum.djvu},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31942073}
}
@Article{Imanian2007,
Title = {{The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages}},
Author = {B. Imanian and P. J. Keeling},
Journal = {BMC Evol. Biol.},
Year = {2007},
Pages = {172},
Volume = {7},
Abstract = {Dinoflagellates with fucoxantin plastids from diatoms},
Doi = {10.1186/1471-2148-7-172},
File = {imanian2007.pdf}
}
@Article{Inagaki1997,
Title = {{Algae or Protozoa: phylogenetic position of Euglenophytes and Dinoflagellates as inferred from mitochondrial sequences}},
Author = {Y. Inagaki and Y. Hayashi-Ishimaru and M. Ehara and I. Igarashi and T. Ohama},
Journal = {J. Mol. Evol.},
Year = {1997},
Pages = {295--300},
Volume = {45}
}
@Article{Inagaki2009,
Title = {{Gene sampling can bias multi-gene phylogenetic inferences: The relationship between red algae and green plants as a case study}},
Author = {Y. Inagaki and Y. Nakajima and M. Sato and M. Sakaguchi and T. Hashimoto},
Journal = {Molecular Biology and Evolution},
Year = {In press},
Abstract = {The more genes the better},
File = {inagaki2009_archeplastida.pdf}
}
@Article{Ionescu2017,
Title = {{Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum.}},
Author = {D. Ionescu and M. Bizic-Ionescu and N. De Maio and H. Cypionka and H.-P. Grossart},
Journal = {Nat Commun},
Year = {2017},
Number = {1},
Pages = {455},
Volume = {8},
Abstract = {As stated},
Doi = {10.1038/s41467-017-00342-9},
File = {ionescu2017_achromatium_polyploid_bacterium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/16838295}
}
@Article{Irie2018,
Title = {{The phylum Vertebrata: A case for zoological recognition.}},
Author = {N. Irie and N. Satoh and S. Kuratani},
Journal = {Zoological Lett},
Year = {2018},
Pages = {32},
Volume = {4},
Abstract = {As stated => accept},
Doi = {10.1186/s40851-018-0114-y},
File = {irie2018_vertebrata_phylum.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30607258}
}
@Article{Irimia2007,
Title = {{Rare Coding Sequence Changes Are Consistent With Ecdysozoa, Not Coelomata}},
Author = {M. Irimia and I. Maeso and D. Penny and J. Garcia-Fernandez and S. W. Roy},
Journal = {Mol. Biol. and Evolution},
Year = {2007},
Number = {8},
Pages = {1604--1607},
Volume = {24},
Abstract = {Subj}
}
@Article{Irwin2019,
Title = {{Phylogenomics supports the monophyly of the Cercozoa.}},
Author = {N. A. T. Irwin and D. V. Tikhonenkov and E. Hehenberger and A. P. Mylnikov and F. Burki and P. J. Keeling},
Journal = {Mol. Phylogenet. Evol.},
Year = {2019},
Pages = {416--423},
Volume = {130},
Abstract = {Lapot (Tremula lineage representative) || Endomyxa},
Doi = {10.1016/j.ympev.2018.09.004},
File = {irwin2018_cercozoa_lapot_gusevi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30318266}
}
@Article{Ishida1998a,
Title = {The origin of chlorarachniophyte plastids, as inferred from phylogenetic comparisons of amino acid sequences of {EF}-{TU}},
Author = {K. Ishida and Y. Cao and M. Hasegawa and N. Okada and Y. Hara},
Journal = {J. Mol. Evol.},
Year = {1998},
Pages = {682--687},
Volume = {45}
}
@Article{Ishida2011,
Title = {{Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp}},
Author = {K.-i. Ishida and H. Endo and S. Koike},
Journal = {Phycological Research},
Year = {2011},
Pages = {120--122},
Volume = {59},
Abstract = {As stated},
Doi = {10.1111/j.1440-1835.2011.00608.x},
File = {ishida2011_partenskyella.pdf}
}
@Article{Ishida2002,
Title = {{Second- and third-hand chloroplasts in dinoflagellates: Phylogeny of oxygen-evolving enhancer 1 (PsbO) protein reveals replacement of a nuclear-encoded plastid gene by that of a haptophyte tertiary endosymbiont}},
Author = {K. Ishida and B. R. Green},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2002},
Pages = {9294--9299},
Volume = {99}
}
@Article{Ishida1998,
Title = {{Diversification of a Chimaeric Algal Group, the Chlorarachniophytes: Phylogeny of Nuclear and Nucleomorph Small-Subunit r{RNA} Genes}},
Author = {K. Ishida and B. R. Green and T. Cavalier-Smith},
Journal = {Mol. Biol. Evol.},
Year = {1998},
Number = {3},
Pages = {321--331.},
Volume = {16}
}
@Article{Ishida1996,
Title = {{Taxonomic srudies on the Chlorarachiniophyta}},
Author = {K. J. Ishida and T. Nakayama and Y. Kana},
Journal = {Phycol. Res.},
Year = {1996},
Number = {1},
Pages = {37--45},
Volume = {44}
}
@Article{Ishikawa2009,
Title = {{Distribution and phylogeny of the blue light receptors aureochromes in eukaryotes}},
Author = {M. Ishikawa and F. Takahashi and H. Nozaki and C. Nagasato and T. Motomura and H. Kataoka},
Journal = {Planta},
Year = {2009},
Number = {3},
Pages = {543--552},
Volume = {230},
Abstract = {Specific to photosynth. stramenopiles},
Doi = {10.1007/s00425-009-0967-6},
File = {ishikawa2009_aureochromes_stramenopiles.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19544070}
}
@Article{Ishitani2011,
Title = {{Multigene phylogenetic analyses including diverse radiolarian species support the "Retaria" hypothesis. The sister relationship of Radiolaria and Foraminifera}},
Author = {Y. Ishitani},
Journal = {Marine Micropaleontology},
Year = {2011},
Number = {1--2},
Pages = {32--42},
Volume = {81},
Abstract = {Foram || Acanth + Taxop || Spumell || Collod + Nassell},
Doi = {10.1016/j.marmicro.2011.06.007},
File = {ishitani2011_retaria.pdf},
ISSN = {0377-8398},
Url = {http://dx.doi.org/10.1016/j.marmicro.2011.06.007}
}
@Article{Ishitani2012,
Title = {{Evolution of Elongation Factor-Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences.}},
Author = {Y. Ishitani and R. Kamikawa and A. Yabuki and M. Tsuchiya and Y. Inagaki and K. Takishita},
Journal = {J. Eukaryot. Microbiol.},
Year = {2012},
Number = {4},
Pages = {367--373},
Volume = {59},
Abstract = {Endomyxa (Gromia) || Foram || Polycyst + Acantharea},
Doi = {10.1111/j.1550-7408.2012.00626.x},
File = {ishitani2012_efl_rhizaria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22672006}
}
@Article{Israelsson2008,
Title = {{\textit{Xenoturbella} (Deuterostomia) probably feeds on dissolved organic matter}},
Author = {O. Israelsson},
Journal = {Mar. Biol. Res.},
Year = {2008},
Number = {5},
Pages = {384--391},
Volume = {4},
Abstract = {As stated},
Doi = {10.1080/17451000802036085},
File = {israelsson2008.txt}
}
@InCollection{Issi1978,
Title = {The phylogeny and evolution of microsporidia},
Author = {I. V. Issi},
Booktitle = {Fauna i sistematika odnokletochnyh zhivotnyh},
Publisher = {Nauka},
Year = {1978},
Address = {Leningrad},
Note = {(In Russian)},
Pages = {30--43},
Abstract = {sistematika, Microsporidia}
}
@Article{Itoh2003,
Title = {{Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines}},
Author = {T. Itoh and K. Suzuki and P. C. Sanchez and T. Nakase},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2003},
Pages = {351 - 0198},
Volume = {53},
Abstract = {~ or || Desulfurococcales},
Doi = {10.1099/ijs.0.02580-0},
File = {itoh2003.pdf}
}
@InProceedings{Ivahnenko1987,
Title = {Permian parareplilies of USSR},
Author = {M. F. Ivahnenko},
Booktitle = {Trudy PIN},
Year = {1987},
Note = {(In Russian)},
Volume = {223}
}
@InCollection{Ivahnenko1981,
Title = {Some features of tetrapoda origin},
Author = {M. F. Ivahnenko},
Booktitle = {Questions of gerpetology},
Publisher = {Nauka},
Year = {1981},
Address = {Leningrad},
Note = {(In Russian)},
Pages = {58--59},
Abstract = {evoljucija, Tetrapoda}
}
@InCollection{Ivanov1991,
Title = {{The question about origin of Bilateria}},
Author = {A. V. Ivanov},
Booktitle = {Sovremennaja evoljucionnaja morfologija},
Publisher = {Nauka},
Year = {1991},
Address = {Kiev},
Note = {(In Russian)},
Pages = {191--194},
Abstract = {filogenija, Bilateria}
}
@Article{Ivanov1984,
Title = {{About macrosystem of animals}},
Author = {A. V. Ivanov},
Journal = {Vestnik AN SSSR},
Year = {1984},
Pages = {57--61},
Volume = {1984},
Abstract = {Phagocytellozoa, Enantiozoa, Eumetazoa: Radiata and Bilateria (Scolecida + Coelomata (Trochozoa, Tentaculata, Chaetognatha, Pogonophora, Deuterostomia))},
File = {ivanov1984.pdf}
}
@InCollection{Ivanov1979,
Title = {About some current goals of phylogenetic morphology of invertebrates},
Author = {A. V. Ivanov},
Booktitle = {The condition and perspectives of morphology development. The materials of all-union seminar},
Publisher = {Nauka},
Year = {1979},
Address = {Moscow},
Note = {(In Russian)},
Pages = {59--70},
Abstract = {sistematika, Metazoa}
}
@Article{Ivanov1976,
Title = {About relation between {P}rotostomia and {D}euterostomia and the classification of animals},
Author = {A. V. Ivanov},
Journal = {Zool. Zhurn.},
Year = {1976},
Note = {(In Russian)},
Number = {8},
Pages = {1125--1137},
Volume = {55},
Abstract = {sistematika, Animalia}
}
@Book{Ivanov1968,
Title = {The origin of multicellular animals},
Author = {A. V. Ivanov},
Publisher = {Nauka},
Year = {1968},
Address = {Leningrad},
Note = {(In Russian)},
Abstract = {evoljucija, Metazoa},
Keywords = {pr1}
}
@InCollection{Ivanov1963,
Title = {\textit{Neopilina} and its importance in the molluscan phylogeny},
Author = {A. V. Ivanov},
Booktitle = {Voprosy teoreticheskoj i prikladnoj malakologii},
Publisher = {Nauka},
Year = {1963},
Address = {Leningrad},
Note = {(In Russian)},
Pages = {164--173},
Abstract = {sistematika, Mollusca}
}
@Book{Ivanov1972,
Title = {Ciliary worms. Phylogenetic essays},
Author = {A. V. Ivanov and Ju. V. Mamkaev},
Publisher = {Nauka},
Year = {1972},
Address = {Leningrad},
Note = {(In Russian)},
Abstract = {sistematika, evoljucija, Turbellaria}
}
@Book{Ivanova1975,
Title = {The comparative embryology of invertebrates. In 6 volumes},
Author = {O. M. Ivanova-Kazas},
Publisher = {Nauka},
Year = {1975--1981},
Address = {Leningrad},
Note = {(In Russian)},
Abstract = {embriologija, morfologija, Animalia}
}
@Article{IvanovaKazas2015,
Title = {{Articulata and Ecdysozoa}},
Author = {O. M. Ivanova-Kazas},
Journal = {Russian Journal of Developmental Biology},
Year = {2015},
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Pages = {121--126},
Volume = {46},
Abstract = {Against Ecdysozoa},
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}
@Article{IvanovaKazas2008,
Title = {{Origin of Chordata and the "Upside-Down Theory"}},
Author = {O. M. Ivanova-Kazas},
Journal = {Mar. Biol.},
Year = {2008},
Number = {6},
Pages = {391--402},
Volume = {34},
Abstract = {Hemichordata + Chordata, against Ecdysozoa},
Doi = {10.1134/S1063074008060072},
File = {ivanova-kazas2008_chordata.pdf}
}
@Article{IvanovaKazas2007,
Title = {{On the problem of the origin of Pogonophora}},
Author = {O. M. Ivanova-Kazas},
Journal = {Biol. Morya},
Year = {2007},
Number = {5},
Pages = {387--391},
Volume = {33},
Abstract = {Closely related to Deuterostomia},
File = {ivanova-kazas2007.djvu}
}
@Book{Ivanova1995,
Title = {The evolutionary embryology of animals},
Author = {O. M. Ivanova-Kazas},
Publisher = {Nauka},
Year = {1995},
Address = {Saint-Petersburg},
Note = {(In Russian)},
Abstract = {embriologija, morfologija, Animalia}
}
@Article{Iverson2012,
Title = {{Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota.}},
Author = {V. Iverson and R. M. Morris and C. D. Frazar and C. T. Berthiaume and R. L. Morales and E. V. Armbrust},
Journal = {Science},
Year = {2012},
Number = {6068},
Pages = {587--590},
Volume = {335},
Abstract = {~ Thermoplasmata},
Doi = {10.1126/science.1212665},
File = {iverson2012_marine_group_2_eyryarcheota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22301318}
}
@Article{Iwasaki2007,
Title = {{Reconstruction of highly heterogeneous gene-content evolution across the three domains of life}},
Author = {W. Iwasaki and T. Takagi},
Journal = {Science},
Year = {2007},
Pages = {230--239},
Volume = {23},
Abstract = {Firmi:Clost+others, Actino+(Spiro,Plancto)+(Chlam,Bacteroid,Chlorobi)},
Doi = {10.1093/bioinformatics/btm165},
File = {iwasaki2007.pdf}
}
@Article{SiqueiraJr2005,
Title = {{Novel Bacterial Phylotypes in Endodontic Infections}},
Author = {J. F. Siqueira, Jr and I. N. Ras and C. D. Cunha and A. S. Rosado},
Journal = {J. Dent. Res.},
Year = {2005},
Number = {6},
Pages = {565--569},
Volume = {84},
Abstract = {Synergistes ~ Flexistipes > Deferribacteres},
File = {siqueira2005.pdf}
}
@Article{Jekely2015,
Title = {{The phylogenetic position of ctenophores and the origin(s) of nervous systems.}},
Author = {G. J{\'e}kely and J. Paps and C. Nielsen},
Journal = {Evodevo},
Year = {2015},
Pages = {1},
Volume = {6},
Abstract = {Shared ancestry of nervous systems},
Doi = {10.1186/2041-9139-6-1},
File = {jekely2014_ctenophores.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25905000}
}
@Article{Jaffe2020,
Title = {{The rise of diversity in metabolic platforms across the Candidate Phyla Radiation}},
Author = {A. L. Jaffe and C. J. Castelle and P. B. M. Carnevali and S. Gribaldo and J. F. Banfield},
Journal = {BMC Biology},
Year = {2020},
Abstract = {As stated},
Doi = {10.1186/s12915-020-00804-5},
File = {jaffe2020_metabol_cpr.pdf}
}
@Article{Jaglarz2014,
Title = {{The ovary structure and oogenesis in the basal crustaceans and hexapods. Possible phylogenetic significance}},
Author = {M. K. Jaglarz and J. Kubrakiewicz and S. M. Bilinski},
Journal = {Arthropod Struct Dev},
Year = {2014},
Abstract = {Similarities with Xenocarida (Ceph + Remipedia)},
Doi = {10.1016/j.asd.2014.05.003},
File = {jaglarz2014_ovarian_struct_xenocarida_hexapoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24858464}
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Title = {{Ultrastructural analysis of the ovary and oogenesis in Spinicaudata and Laevicaudata (Branchiopoda) and its phylogenetic implications.}},
Author = {M. K. Jaglarz and J. Kubrakiewicz and I. Jędrzejowska and B. Go{\l}dyn and S. M. Bili{\'n}ski},
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Year = {2014},
Number = {3},
Pages = {207--215},
Volume = {117},
Abstract = {morphological similarities with Notostraca as well as the basal hexapods Campodeina and Collembola},
Doi = {10.1016/j.zool.2013.12.002},
File = {jaglarz2014_brachiopod_embryol.pdf},
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@Article{Jain1999,
Title = {{Horizontal gene transfer among genomes: The compexity hypothesis}},
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@Article{James2012,
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@Article{Kadnikov2018a,
Title = {{Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer.}},
Author = {V. V. Kadnikov and A. V. Mardanov and A. V. Beletsky and A. L. Rakitin and Y. A. Frank and O. V. Karnachuk and N. V. Ravin},
Journal = {Syst. Appl. Microbiol.},
Year = {2018},
Abstract = {BRC1 ~ Nitrospirae, Acidobacteria},
Doi = {10.1016/j.syapm.2018.08.013},
File = {kadnikov2018_brc1_phylum.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30201528}
}
@Article{Kai2008,
Title = {{Aurearenophyceae classis nova, a New Class of Heterokontophyta Based on a New Marine Unicellular Alga \textit{Aurearena cruciata} gen. et sp. nov. Inhabiting Sandy Beaches}},
Author = {A. Kai and Y. Yoshii and T. Nakayama and I. Inouye},
Journal = {Protist},
Year = {2008},
Number = {3},
Pages = {435--457},
Volume = {159},
Abstract = {18S + rbcL: Dictyoch || Pelago || Diat + Bolid || Eust + Synchr + Synur + Chryso || Pingui, Raphido || PX clade: Chrysomero || Phaeo + Schizocl || Xantho s.str. || Phaeoth (or "TP clade") || Aurearen},
Doi = {10.1016/j.protis.2007.12.003},
File = {kai2008.pdf}
}
@Article{Kajander2006,
Title = {{Nanobacteria~--- propagating calcifying nanoparticles.}},
Author = {E. O. Kajander},
Journal = {Lett. Appl. Microbiol.},
Year = {2006},
Number = {6},
Pages = {549--552},
Volume = {42},
Abstract = {Nanobacteria, or CNP -- "third lineage of prokaryotes"?},
File = {kajander2006.pdf}
}
@Article{Kalina2005,
Title = {{New trends in the megasystems of Eukaryote (Review)}},
Author = {T. Kalina},
Journal = {Czech Phycology},
Year = {2005},
Pages = {37--42},
Volume = {5},
Abstract = {Review},
File = {kalina2005.pdf}
}
@Article{Kamikawa2010a,
Title = {{Rooting for the root of elongation factor-like protein phylogeny}},
Author = {R. Kamikawa and M. Sakaguchi and T. Matsumoto and T. Hashimoto and Y. Inagaki},
Journal = {Mol. Phylogenet. Evol.},
Year = {2010},
Number = {3},
Pages = {1082 - 1088},
Volume = {56},
Abstract = {Tangled tree},
Doi = {10.1016/j.ympev.2010.04.040},
File = {F:/ref/os/1/kamikawa2010_efl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20450979}
}
@Article{Kamikawa2009,
Title = {{Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes.}},
Author = {R. Kamikawa and G. F. Sanchez-Perez and Y. Sako and A. J. Roger and Y. Inagaki},
Journal = {Mol. Phylogenet. Evol.},
Year = {2009},
Number = {2},
Pages = {565 - 570},
Volume = {53},
Abstract = {Malawi ~ Naegleria; all panplantae except Crypto have a support},
Doi = {10.1016/j.ympev.2009.06.016},
File = {kamikawa2009_mat_euk.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19577655}
}
@Article{Kamikawa2016,
Title = {{Group II Intron-Mediated Trans-Splicing in the Gene-Rich Mitochondrial Genome of an Enigmatic Eukaryote, Diphylleia rotans.}},
Author = {R. Kamikawa and T. Shiratori and K.-I. Ishida and H. Miyashita and A. J. Roger},
Journal = {Genome Biol Evol},
Year = {2016},
Number = {2},
Pages = {458--466},
Volume = {8},
Abstract = {~ Malawimonas, some similarities with Chloroplastida},
Doi = {10.1093/gbe/evw011},
File = {kamikawa2016_diphylleia_mt_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23335123}
}
@Article{Kamikawa2015,
Title = {{Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum.}},
Author = {R. Kamikawa and G. Tanifuji and M. Kawachi and H. Miyashita and T. Hashimoto and Y. Inagaki},
Journal = {Genome Biol Evol},
Year = {2015},
Number = {4},
Pages = {1133--1140},
Volume = {7},
Abstract = {From Pedinomonas},
Doi = {10.1093/gbe/evv060},
File = {kamikawa2015_leptodinium_pedinomonas.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19074760}
}
@Article{Kamikawa2010b,
Title = {{Cercozoa comprises both EF-1a-containing and EFL-containing members}},
Author = {R. Kamikawa and A. Yabuki and T. Nakayama and K.-i. Ishida and T. Hashimoto and Y. Inagaki},
Journal = {European Journal of Protistology},
Year = {2010},
Abstract = {cercozoan EF-1a genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1a genes},
Doi = {10.1016/j.ejop.2010.08.002},
File = {kamikawa2010_cercozoa_ef-1.pdf},
ISSN = {0932-4739},
Url = {http://dx.doi.org/10.1016/j.ejop.2010.08.002}
}
@Article{Kamke2014,
Title = {{The candidate phylum Poribacteria by single-cell genomics: New insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features.}},
Author = {J. Kamke and C. Rinke and P. Schwientek and K. Mavromatis and N. Ivanova and A. Sczyrba and T. Woyke and U. Hentschel},
Journal = {PLoS ONE},
Year = {2014},
Number = {1},
Pages = {e87353},
Volume = {9},
Abstract = {Outside of PVC; may be close to Hydrogenedentes, Aerophobetes, Elusimicrobia and Atribacteria (OP9)},
Doi = {10.1371/journal.pone.0087353},
File = {kamke2014_poribacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23842652}
}
@Article{Kamneva2012,
Title = {{Analysis of genome content evolution in PVC bacterial super-phylum: Assessment of candidate genes associated with cellular organization and life-style}},
Author = {O. K. Kamneva and S. J. Knight and D. A. Liberles and N. L. Ward},
Journal = {Genome Biology and Evolution},
Year = {2012},
Abstract = {Plancto || Lenti || Verru || Chla},
Doi = {10.1093/gbe/evs113},
File = {kamneva2012_pvc_genome_content.pdf},
Url = {http://creativecommons.org/licenses/by-nc/3.0/),}
}
@Article{Kan2021,
Title = {{Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome}},
Author = {S.-L. Kan and T.-T. Shen and J.-H. Ran and X.-Q. Wang},
Journal = {BMC Biology},
Year = {2021},
Abstract = {Pinopsida, Gnetopsida, Cupressopsida ("Conifer II")},
Doi = {10.1186/s12915-021-01096-z},
File = {kan2021_gnecup_mt_genes.pdf}
}
@Article{Kang2017,
Title = {{Between a pod and a hard test: The deep evolution of amoebae}},
Author = {S. Kang and A. K. Tice and F. W. Spiegel and J. D. Silberman and T. P{\'a}nek and I. {\v{C}}epi{\v{c}}ka and M. Kostka and A. Kosakyan and D. M. Alc{\^a}ntara and A. J. Roger and L. L. Shadwick and A. Smirnov and A. Kudryavstev and D. J. G. Lahr and M. W. Brown},
Journal = {Molecular Biology and Evolution},
Year = {2017},
Abstract = {Discosea + Tevosa: [Tubulinea + Evosea: [Cutosea + Archamoeb., Eumyc., Variosea]]},
Doi = {10.1007/978-3-642-38487-5_12.},
File = {kang2017_amoebozoa.pdf},
ISBN = {978-3-642-38487-5}
}
@Article{Kapli2021,
Title = {{Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha}},
Author = {P. Kapli and M. J. Telford},
Journal = {Science},
Year = {2021},
Abstract = {Porifera first and Xenambulacralia},
File = {kapli2020_ctenoph_first_and_nephrozoa_error_prone.pdf}
}
@Article{Karlin2000,
Title = {{Heat shock protein 60 sequence comparisions: Duplications, lateral transfer, and mitochondrial evolution}},
Author = {S. Karlin and L. Brocchieri},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2000},
Number = {21},
Pages = {11348--11353},
Volume = {97}
}
@Article{Karlin1999,
Title = {{A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes}},
Author = {S. Karlin and L. Brocchieri and J. Mrrzek and A. M. Campbell and A. M. Spormann},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1999},
Number = {16},
Pages = {9190--9195},
Volume = {96}
}
@Article{Karol2010,
Title = {{Complete plastome sequences of Equisetum arvense and Isoetes flaccida: Implications for phylogeny and plastid genome evolution of early land plant lineages}},
Author = {K. G. Karol and K. Arumuganathan and J. L. Boore and A. M. Duffy and K. D. E. Everett and J. D. Hall and S. K. Hansen and J. V. Kuehl and D. F. Mandoli and B. D. Mishler and R. G. Olmstead and K. S. Renzaglia and P. G. Wolf},
Journal = {BMC Evolutionary Biology},
Year = {2010},
Pages = {321},
Volume = {10},
Abstract = {...we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae},
Doi = {10.1186/1471-2148-10-321},
File = {karol2010_land_plants.pdf},
Url = {http://www.biomedcentral.com/1471-2148/10/321}
}
@Manual{Karpov1992,
Title = {Ultrastructure and classification of mastigiphores: Thesises of dissertation},
Address = {Saint-Petersburg},
Author = {A. Karpov},
Note = {(In Russian)},
Year = {1992},
Abstract = {sistematika, morfologija, Protista},
Pages = {36},
School = {Saint-Petersburg University}
}
@Book{Karpov1990,
Title = {The classification of protists},
Author = {A. Karpov},
Publisher = {Omsk Pedagogocal University},
Year = {1990},
Address = {Omsk, Saint-Petersburg},
Note = {(In Russian)}
}
@Conference{Karpov1989a,
Title = {The short summary of eukaryote classification},
Author = {A. Karpov},
Booktitle = {Ecological morphology and freshwater protists: thesises of presentations to the 2nd All-Union symposia of protozoologists. September 12--15, 1989},
Year = {1989},
Address = {Jaroslavl},
Note = {(In Russian)},
Pages = {28},
Abstract = {sistematika, Protista},
Annote = {xerox}
}
@Article{Karpov1994,
Title = {Electron microscope investigarion of the flagellar apparate of sponge Ephydratia fluviatilis hoanocyte},
Author = {A. Karpov and M. Efremova},
Journal = {Tsitologiya},
Year = {1994},
Note = {(In Russian)},
Number = {5},
Pages = {403--407},
Volume = {36},
Abstract = {morfologija, citologija, Spongia},
Annote = {Hoanocity blizhe k Chytridiomycetes, Infusoria; ne ochen pohozhi na Choanoflagellata}
}
@InCollection{Karpov2000,
Title = {{The classification of protists and problems of megataxonomy}},
Author = {S. A. Karpov},
Booktitle = {{Protists}},
Publisher = {Nauka},
Year = {2000},
Address = {Saint-Petersburg},
Editor = {A. F. Alimov},
Pages = {127--137}
}
@Article{Karpov2008,
Title = {{The flagellar apparatus structure of {Apusomonas proboscidea} and apusomonad relationships}},
Author = {S. A. Karpov},
Journal = {Protistology},
Year = {2008},
Number = {2/3},
Pages = {146--155},
Volume = {5},
Abstract = {The most similar groups in this respect are cryptomonads and myxogastrids; Multicilia and excavates have fewer common features}
}
@Book{Karpov2005,
Title = {{The system of protists: history and modernity}},
Author = {S. A. Karpov},
Publisher = {TESSA},
Year = {2005},
Address = {Sankt-Petersburg},
Note = {(In Russian)},
Pages = {1--72}
}
@Book{Karpov2000b,
Title = {{The system of protists}},
Author = {S. A. Karpov},
Publisher = {Izdatelstvo OmGPU},
Year = {2000},
Address = {Sankt-Petersburg, Omsk},
Edition = {3},
Note = {(In Russian)},
Volume = {1--4},
Pages = {1--215}
}
@Article{Karpov2014b,
Title = {{Gromochytrium mamkaevae gen. \& Sp. Nov. And two new orders: Gromochytriales and Mesochytriales (Chytridiomycetes).}},
Author = {S. A. Karpov and A. A. Kobseva and M. A. Mamkaeva and K. A. Mamkaeva and K. V. Mikhailov and G. S. Mirzaeva and V. V. Aleoshin},
Journal = {Persoonia},
Year = {2014},
Pages = {115--126},
Volume = {32},
Abstract = {Neocalli + Monobl + Chytr},
Doi = {10.3767/003158514X680234},
File = {karpov2014_gromochytrium_chytridiomycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25264386}
}
@Article{Karpov2018,
Title = {{The Chytrid-like Parasites of Algae Amoeboradix gromovi gen. et sp. nov. and Sanchytrium tribonematis Belong to a New Fungal Lineage.}},
Author = {S. A. Karpov and P. L{\'o}pez-Garc{\'i}a and M. A. Mamkaeva and V. I. Klimov and A. E. Vishnyakov and V. S. Tcvetkova and D. Moreira},
Journal = {Protist},
Year = {2018},
Number = {1},
Pages = {122 - 140},
Volume = {169},
Abstract = {Close to Glomerul + Dikarya!, after Mucor.},
Doi = {10.1016/j.protis.2017.11.002},
File = {karpov2017_amoeboradix_new_fungal_group.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29477669}
}
@Article{Karpov2010,
Title = {{Phylogenetic position of the genus Mesochytrium (Chytridiomycota) based on zoospore ultrastructure and sequences from the 18S and 28S rRNA gene}},
Author = {S. A. Karpov and P. M. Letcher and M. A. Mamkaeva and K. A. Mamkaeva},
Journal = {Nova Hedwigia},
Year = {2010},
Number = {1--2},
Pages = {81--94},
Volume = {90},
Abstract = {Caulochytrium -- unplaced in Chytr.},
Doi = {10.1127/0029-5035/2010/0090-0081},
File = {karpov2010_mesochytrium.pdf}
}
@Article{Karpov1989,
Title = {{Phagocytosis and endocytosis in the colorless flagellate {Thaumatomonas lauterborni}}},
Author = {S. A. Karpov and E. P. Makarenkova},
Journal = {Tsitologiya},
Year = {1989},
Number = {3},
Pages = {347--349},
Volume = {31}
}
@Article{Karpov2014a,
Title = {{Morphology, phylogeny, and ecology of the aphelids (Aphelidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia.}},
Author = {S. A. Karpov and M. A. Mamkaeva and V. V. Aleoshin and E. Nassonova and O. Lilje and F. H. Gleason},
Journal = {Front Microbiol},
Year = {2014},
Pages = {112},
Volume = {5},
Abstract = {Opisthosporidia = Microsporidia + Rozellomycota/Cryptomycota + Aphelida},
Doi = {10.3389/fmicb.2014.00112},
File = {karpov2014_aphelidea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24734027}
}
@Article{Karpov2014,
Title = {{Molecular Phylogeny and Ultrastructure of Aphelidium aff. Melosirae (Aphelida, Opisthosporidia)}},
Author = {S. A. Karpov and M. A. Mamkaeva and K. Benzerara and D. Moreira and P. Lopez-Garci{\'a}},
Journal = {Protist},
Year = {2014},
Abstract = {Nothing changed in Aphelida},
Doi = {10.1016/j.protis.2014.05.003},
File = {karpov2014_aphelidium.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2014.05.003}
}
@Article{Karpov2012,
Title = {{Obligately Phagotrophic Aphelids Turned out to Branch with the Earliest-diverging Fungi}},
Author = {S. A. Karpov and K. V. Mikhailov and G. S. Mirzaeva and I. M. Mirabdullaev},
Journal = {Protist},
Year = {2012},
Abstract = {Amoeboaphelidium ~ Rozella},
Doi = {10.1016/j.protis.2012.08},
File = {karpov2012_aphelids.djvu},
Url = {http://dx.doi.org/10.1016/j.protis.2012.08}
}
@Article{Karpov2001,
Title = {{Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences}},
Author = {S. A. Karpov and M. L. Sogin and J. D. Silberman},
Journal = {Protistology},
Year = {2001},
Number = {1},
Pages = {34--47},
Volume = {2},
Abstract = {Discocelis ~ Bicosoec.}
}
@Article{Karpov2016,
Title = {{Morphological and Genetic Diversity of Opisthosporidia: New Aphelid Paraphelidium tribonemae Gen. Et Sp. Nov.}},
Author = {S. A. Karpov and V. S. Tcvetkova and M. A. Mamkaeva and G. Torruella and H. Timpano and D. Moreira and K. S. Mamanazarova and P. L{\'o}pez-Garc{\'i}a},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2016},
Abstract = {As stated},
Doi = {10.1111/jeu.12352-4854},
File = {karpov2016_opisthosporidia_paraphelidium.pdf}
}
@Article{Karpov2019,
Title = {{The Ultrastructure of Sanchytrium tribonematis (Sanchytriaceae, Fungi incertae sedis) Confirms its Close Relationship to Amoeboradix}},
Author = {S. A. Karpov and A. E. Vishnyakov and D. Moreira and P. L{\'o}pez-Garc{\'i}a},
Journal = {Journal of Eukartyotic Microbiology},
Year = {2019},
Abstract = {As stated},
Doi = {10.1111/jeu.12740},
File = {karpov2019_sanchytrium_morph.pdf}
}
@Article{Karpov1986,
Title = {{Ultrastructure and taxonomic position of {Apusomonas proboscidea} Alexeieff}},
Author = {S. A. Karpov and B. F. Zhukov},
Journal = {Arch. Protistenkd.},
Year = {1986},
Pages = {13--26},
Volume = {131}
}
@Article{Kasatkina1997,
Title = {Chaetodonta~~--- new superphylum of animals and its placement in the animal classification},
Author = {A. P. Kasatkina and G. I. Burko},
Journal = {Doklady Akademii Nauk},
Year = {1997},
Note = {(In Russian)},
Number = {6},
Pages = {843--845},
Volume = {356},
Abstract = {sistematika, Chaetognatha}
}
@Article{Katayama1995,
Title = {{Phylogenetic position of the dicyemid mesozoa inferred from 18S rDNA sequences.}},
Author = {T. Katayama and H. Wada and H. Furuya and N. Satoh and M. Yamamoto},
Journal = {Biol. Bull.},
Year = {1995},
Number = {2},
Pages = {81--90},
Volume = {189}
}
@Article{Katayama1993,
Title = {{Phylogenetic position of Acoel turbellarians inferred from partial 18S rDNA sequences.}},
Author = {T. Katayama and M. Yamamoto and H. Wada and N. Satoh},
Journal = {Zool. Sci.},
Year = {1993},
Number = {3},
Pages = {529--536},
Volume = {10}
}
@Article{Kato1988,
Title = {{The phylogenetic relationship of Ophioglossaceae}},
Author = {M. Kato},
Journal = {Taxon},
Year = {1988},
Number = {2},
Pages = {381--386},
Volume = {367}
}
@Article{Kato2018,
Title = {{Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle.}},
Author = {S. Kato and S. Sakai and M. Hirai and E. Tasumi and M. Nishizawa and K. Suzuki and K. Takai},
Journal = {Microbes Environ.},
Year = {2018},
Number = {1},
Pages = {107--110},
Volume = {33},
Abstract = {GAL15 ~ Fervidibacter, Armatimonadetes},
Doi = {10.1264/jsme2.ME17165},
File = {kato2018_gal15.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22303444}
}
@Article{Kato2009,
Title = {{Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough}},
Author = {S. Kato and K. Yanagawa and M. Sunamura and Y. Takano and J. I. Ishibashi and T. Kakegawa and M. Utsumi and T. Yamanaka and T. Toki and T. Noguchi and K. Kobayashi and A. Moroi and H. Kimura and Y. Kawarabayasi and K. Marumo and T. Urabe and A. Yamagishi},
Journal = {Environ. Microbiol.},
Year = {In press},
Abstract = {Epsilonoproteobactera || Delta || Zeta || Magnetococc + Alpha || Beta + Gamma},
Doi = {10.1111/j.1462-2920.2009.02031.x},
File = {kato2009_zeta.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19691504}
}
@Article{Katz2012b,
Title = {{Origin and Diversification of Eukaryotes}},
Author = {L. A. Katz},
Journal = {Annu. Rev. Microbiol.},
Year = {2012},
Abstract = {Review},
Doi = {10.1146/annurev-micro-090110-102808},
File = {katz2012_orig_dive_euk_review.pdf},
Url = {www.annualreviews.org}
}
@Article{Katz2011a,
Title = {{Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life}},
Author = {L. A. Katz},
Journal = {Journal of Phycology},
Year = {2011},
Pages = {3},
Volume = {47},
Abstract = {Several major groups are both stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ???Chromalveolata??? is rejected},
File = {katz_psa_abstracts_2011.pdf}
}
@Article{Katz2011b,
Title = {{Subulatomonas tetraspora nov. Gen. Nov. Sp. Is a Member of a Previously Unrecognized Major Clade of Eukaryotes}},
Author = {L. A. Katz and J. Grant and L. W. Parfrey and A. Gant and C. J. O'Kelly and O. R. Anderson and R. E. Molestina and T. Nerad},
Journal = {Protist},
Year = {2011},
Abstract = {Ancy || Apuso || Breviata + Subulatomonas; five supergroups: SBAA, Opi, Amoeb, Exca, SAR},
Doi = {10.1016/j.protis.2011.05.002},
File = {katz2011_subulatomonas.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2011.05.002}
}
@Article{Katz2015,
Title = {{Taxon-rich phylogenomic analyses resolve the eukaryotic tree of life and reveal the power of subsampling by sites.}},
Author = {L. A. Katz and J. R. Grant},
Journal = {Syst. Biol.},
Year = {2015},
Number = {3},
Pages = {406--415},
Volume = {64},
Abstract = {Cryptista || Archeplastida},
Doi = {10.1093/sysbio/syu126},
File = {katz2014_euk.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25540455}
}
@Article{Katz2012a,
Title = {{Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life}},
Author = {L. A. Katz and J. R. Grant and L. W. Parfrey and J. G. Burleigh},
Journal = {Systematic Biology},
Year = {2012},
Abstract = {Opisthok vs. Amoeb + Exc || "Plants" incl. green, Hapto, Stram, Alveol},
File = {katz2012_euk_tol.pdf},
Url = {http://sysbio.oxfordjournals.org/}
}
@Article{Kauff2011,
Title = {{Phylogeny of Cyanobacteria: An Overview}},
Author = {F. Kauff},
Journal = {Progress in Botany},
Year = {2011},
Pages = {209--224},
Volume = {72},
Abstract = {Gloeobacter sister},
Doi = {10.1007/978-3-642-13145-5_8},
File = {kauff2010_cyanobact.pdf}
}
@Article{Kawachi2002,
Title = {{The Pinguiophyceae classis nova, a new class of photosynthetic stramenopiles whose members produce large amounts of omega-3 fatty acids}},
Author = {M. Kawachi and I. Inouye and D. Honda and C. J. O'Kelly and J. C. Bailey and R. R. Bidigare and R. A. Andersen},
Journal = {Phycol. Res.},
Year = {2002},
Number = {1},
Pages = {31--47},
Volume = {50},
Abstract = {Close to Raphidophyceae},
Doi = {10.1046/j.1440-1835.2002.00260.x}
}
@Article{Kawai2007,
Title = {{Molecular phylogeny of \textit{Discosporangium mesarthrocarpum} (Phaeophyceae) with a reinstatement of the order Discosporangiales}},
Author = {H. Kawai and T. Hanyuda and S. G. A. Draisma and D. G. Muller},
Journal = {J. Phycol.},
Year = {2007},
Number = {2007},
Pages = {186--194},
Volume = {43},
Abstract = {Discosporangium + Choristocarpus || all other Phaeophyceae},
Doi = {10.1111/j.1529-8817.2006.00308.x},
File = {kawai2006.pdf}
}
@Article{Kawai2015,
Title = {{Molecular phylogeny of two unusual brown algae, Phaeostrophion irregulare and Platysiphon glacialis, proposal of the Stschapoviales ord. Nov. And Platysiphonaceae fam. Nov., And a re-examination of divergence times for brown algal orders.}},
Author = {H. Kawai and T. Hanyuda and S. G. A. Draisma and R. T. Wilce and R. A. Andersen},
Journal = {J. Phycol.},
Year = {2015},
Number = {5},
Pages = {918--928},
Volume = {51},
Abstract = {Schizocladia, then Discosporangiales first},
Doi = {10.1111/jpy.12332},
File = {kawai2016_brown_algae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27037597}
}
@Article{Kawai2015a,
Title = {{Molecular phylogeny of two unusual brown algae, Phaeostrophion irregulare and Platysiphon verticillatus, proposal of the Stschapoviales ord. Nov. And Platysiphonaceae fam. Nov., And a re-examination of divergence times for brown algal orders}},
Author = {H. Kawai and T. Hanyuda and S. G. A. Draisma and R. T. Wilce and R. A. Andersen},
Journal = {Journal of Phycology},
Year = {2015},
Abstract = {Schizocladiophyceae || Discosporangiales || Ischigeales etc.},
Doi = {10.1111/jpy.12332-14-093},
File = {kawai2015_brown_algae.pdf},
Url = {http://tree.bio.ed.ac.uk/software/tracer/}
}
@Article{Kawaia2003,
Title = {{\textit{Schizocladia ischiensis}: A New Filamentous Marine Chromophyte Belonging to a New Class, Schizocladiophyceae}},
Author = {H. Kawai and S. Maeba and H. Sasaki and K. Okuda and E. C. Henry},
Journal = {Protist},
Year = {2003},
Pages = {211--228},
Volume = {154},
Abstract = {Schizocladia || Phaeophy; next Tetrasporopsis || Xanto || rest Phaeothamn},
File = {kawai2003.pdf}
}
@Article{Kawaichi2013,
Title = {{Ardenticatena maritima gen. Nov., Sp. Nov., A ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov.}},
Author = {S. Kawaichi and N. Ito and R. Kamikawa and T. Sugawara and T. Yoshida and Y. Sako},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2013},
Number = {Pt--8},
Pages = {2992--3002},
Volume = {63},
Abstract = {~ Anaerolineae/Caldilineae},
Doi = {10.1099/ijs.0.046532-0},
File = {kawaichi2013_ardenticatenia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23378114}
}
@Article{Kayal2012,
Title = {{Evolution of linear mitochondrial genomes in medusozoan cnidarians.}},
Author = {E. Kayal and B. Bentlage and A. G. Collins and M. Kayal and S. Pirro and D. V. Lavrov},
Journal = {Genome Biol Evol},
Year = {2012},
Number = {1},
Pages = {1--12},
Volume = {4},
Abstract = {As stated},
Doi = {10.1093/gbe/evr123},
File = {kayal2011_medusozoa_linear_mt.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22113796}
}
@Article{Kayal2007,
Title = {{The mitochondrial genome of \textit{Hydra oligactis} (Cnidaria, Hydrozoa) sheds new light on animal mtDNA evolution and cnidarian phylogeny}},
Author = {E. Kayal and D. V. Lavrov},
Journal = {Gene},
Year = {2007},
Number = {7},
Pages = {1--31},
Volume = {1119},
Abstract = {Anthozoa may be paraphyletic},
File = {kayal2007.pdf}
}
@Article{Kayal2013,
Title = {{Cnidarian phylogenetic relationships as revealed by mitogenomics.}},
Author = {E. Kayal and B. Roure and H. Philippe and A. G. Collins and D. V. Lavrov},
Journal = {BMC Evol. Biol.},
Year = {2013},
Pages = {5},
Volume = {13},
Abstract = {Hexacorallia || Octocorallia || Coronatae (Linuche) + Staurozoa + Cubozoa || Hydrozoa || Discomedusae (Scyphozoa p.p.)},
Doi = {10.1186/1471-2148-13-5},
File = {kayal2013_cnidaria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/16754865}
}
@Article{Kaygorodova2010,
Title = {{Molecular Phylogeny and Systematics of Oligochaeta: Pro et Contra}},
Author = {I. A. Kaygorodova},
Journal = {Moscow University Biological Sciences Bulletin},
Year = {2010},
Number = {4},
Pages = {164--166},
Volume = {65},
Abstract = {Small review; subclasses Megadrili and Microdrili},
Doi = {10.3103/S0096392510040115},
File = {kaygorodova2010_oligochaeta.pdf}
}
@Article{Keeling2010,
Title = {{The endosymbiotic origin, diversification and fate of plastids}},
Author = {P. J. Keeling},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2010},
Number = {1541},
Pages = {729 - 748},
Volume = {365},
Abstract = {Review},
Doi = {10.1098/rstb.2009.0103},
File = {keeling2010_plastids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20124341}
}
@Article{Keeling2007,
Title = {{Deep Questions in the Tree of Life}},
Author = {P. J. Keeling},
Journal = {Science},
Year = {2007},
Pages = {1875},
Volume = {317},
File = {keeling2007.pdf}
}
@Article{Keeling2001,
Title = {{Foraminifera and Cercozoa Are Related in Actin Phylogeny: Two Orphans Find a Home?}},
Author = {Patrick J. Keeling},
Journal = {Mol. Biol. Evol.},
Year = {2001},
Pages = {1551--1557},
Volume = {18}
}
@Article{Keeling2007b,
Title = {{Organelle Evolution: What's in a Name?}},
Author = {P. J. Keeling and J. M. Archibald},
Journal = {J. Neurosci.},
Year = {2007},
Number = {8},
Pages = {R345--R347},
Volume = {18},
Abstract = {Paulinella have thing intermediate between symbiont and organelle},
Doi = {10.1016/j.cub.2008.02.059},
File = {keeling2008.pdf}
}
@Article{Keeling1999a,
Title = {{The Secondary Endosymbiont of the Cryptomonad \textit{Guillardia theta} Contains Alpha-, Beta-, and Gamma-Tubulin Genes}},
Author = {P. J. Keeling and J. A. Deane and C. Hink-Schauer and S. E. Douglas and U.-G. Maier and G. I. Mcfadden},
Journal = {Mol. Biol. Evol.},
Year = {1999},
Number = {9},
Pages = {1308--1313},
Volume = {16}
}
@Article{Keeling1999,
Title = {{The Phylogenetic Position of Alpha- and Beta-Tubulins from the \textit{Chlorarachnion} Host and \textit{Cercomonas} (Cercozoa)}},
Author = {Patrick J. Keeling and James A. Deane and Geoffrey I. McFadden},
Journal = {J. Euk. Microbiol.},
Year = {1999},
Number = {5},
Pages = {561--570},
Volume = {45}
}
@Article{Keeling1997,
Title = {{Evidence that eukaryotic triosephosphate isomerase is of alpha-proteobacterial origin}},
Author = {P. J. Keeling and W. F. Doolittle},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1997},
Number = {4},
Pages = {1270--1275},
Volume = {94}
}
@Article{Keeling2000,
Title = {{Evidence from Beta-Tubulin Phylogeny that Microsporidia Evolved from Within the Fungi}},
Author = {P. J. Keeling and M. A. Luker and J. D. Palmer},
Journal = {Mol. Biol. Evol.},
Year = {2000},
Number = {1},
Pages = {23--31},
Volume = {17}
}
@Article{Keeling1998,
Title = {{Origins of microsporidia}},
Author = {P. J. Keeling and G. I. McFadden},
Journal = {Trends Microbiol.},
Year = {1998},
Number = {1},
Pages = {19--23},
Volume = {6}
}
@Article{Kelch1998,
Title = {Phylogeny of Podocarpaceae: comparison of evidence from morphology and 18{S} r{DNA}},
Author = {D. G. Kelch},
Journal = {Amer. J. Bot.},
Year = {1998},
Pages = {986},
Volume = {85}
}
@Article{Kelly2011,
Title = {{Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes}},
Author = {S. Kelly and B. Wickstead and K. Gull},
Journal = {Proc. R. Soc. B},
Year = {2011},
Pages = {1009--1018},
Volume = {278},
Abstract = {As stated},
Doi = {10.1098/rspb.2010.1427},
File = {kelly2011_archeal_origin.pdf},
Url = {http://rspb.royalsocietypublishing.org/content/suppl/2010/09/22/rspb.2010.1427.DC1.h}
}
@Article{Kelly2010,
Title = {{Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.}},
Author = {S. Kelly and B. Wickstead and K. Gull},
Journal = {Proceedings. Biological sciences / The Royal Society},
Year = {2010},
Abstract = {As stated; Thaum separate, Kora ~ Cren},
Doi = {10.1098/rspb.2010.1427},
File = {kelly2010_archaea_euk.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20880885}
}
@Article{Kenrick2018,
Title = {{Changing expressions: A hypothesis for the origin of the vascular plant life cycle.}},
Author = {P. Kenrick},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2018},
Number = {1739},
Volume = {373},
Abstract = {Expansion of gene expression (branching, rhizoids, horiz + vert system) from gametophyte into sporophyte},
Doi = {10.1098/rstb.2017.0149},
File = {kenrick2018_orig_vasc_pl_life_cycle.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24117890}
}
@Article{Kenrick1997,
Title = {{The origin and early evolution of plants on land}},
Author = {P. Kenrick and P. R. Crane},
Journal = {Nature},
Year = {1997},
Number = {6646},
Pages = {33--40},
Volume = {389}
}
@Article{Kent2001,
Title = {{Recent Advances in Our Knowledge of the Myxozoa}},
Author = {M. L. Kent and K. B. Andree and J. L. Bartholomew and M. El-Matbouli and S. S. Desser and R. H. Devlin and S. W. Feist and R. P. Hedrick and R. W. Hoffmann and J. Khattra and S. L. Hallett and R. J. Lester and M. Longshaw and O. Palenzeula and M. E. Siddall ME and C. Xiao},
Journal = {J. Euk. Microbiol.},
Year = {2001},
Pages = {395--413},
Volume = {48}
}
@Article{Kerbl2015,
Title = {{Detailed reconstruction of the nervous and muscular system of Lobatocerebridae with an evaluation of its annelid affinity.}},
Author = {A. Kerbl and N. Bekkouche and W. Sterrer and K. Worsaae},
Journal = {BMC Evol. Biol.},
Year = {2015},
Pages = {277},
Volume = {15},
Abstract = {Does not contradict with annelid affinity but no direct support either},
Doi = {10.1186/s12862-015-0531-x},
File = {kerbl2015_lobatocerebrum.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22457790}
}
@Article{Kerbl2016,
Title = {{Comparison of neuromuscular development in two dinophilid species (Annelida) suggests progenetic origin of Dinophilus gyrociliatus}},
Author = {A. Kerbl and E. G. Fofanova and T. D. Mayorova and E. E. Voronezhskaya and K. Worsaae},
Journal = {Front. Zool.},
Year = {2016},
Pages = {49},
Volume = {13},
Abstract = {As stated},
Doi = {10.1186/s12983-016-0181-x},
File = {kerbl2016_dinophilus_progenesis.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23144898}
}
@Article{Kerp2018,
Title = {{Organs and tissues of Rhynie chert plants.}},
Author = {H. Kerp},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2018},
Number = {1739},
Volume = {373},
Abstract = {Review},
Doi = {10.1098/rstb.2016.0495},
File = {kerp2017_organs_tissues_rhynie_chart_plants_review.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17820048}
}
@Article{Khodami2017,
Title = {{Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda).}},
Author = {S. Khodami and J. V. McArthur and L. Blanco-Bercial and P. M. Arbizu},
Journal = {Sci Rep},
Year = {2017},
Number = {1},
Pages = {9164},
Volume = {7},
Abstract = {As stated},
Doi = {10.1038/s41598-017-06656-4},
File = {khodami2017_copepoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20975721}
}
@Article{Khonsari2009,
Title = {{Agnathan brain anatomy and craniate phylogeny}},
Author = {R. H. Khonsari and B. Li and P. Vernier and R. G. Northcutt and P. Janvier},
Journal = {Acta Zoologica},
Year = {2009},
Pages = {52--68},
Volume = {90},
Abstract = {supports cyclostome paraphyly},
Doi = {10.1111/j.1463-6395.2008.00388.x},
File = {khonsari2009_agnatha_brain.pdf}
}
@Article{Ki2010,
Title = {{Nuclear 28S rDNA phylogeny supports the basal placement of Noctiluca scintillans (Dinophyceae; Noctilucales) in dinoflagellates}},
Author = {J.-S. Ki},
Journal = {Eur. J. Protistol.},
Year = {2010},
Number = {2},
Pages = {111--120},
Volume = {46},
Abstract = {Near Oxyrrhis},
Doi = {10.1016/j.ejop.2009.11.001},
File = {ki2010_noctiluca.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20347580}
}
@InProceedings{Kieneke2009,
Title = {{Evolution of the reproductive system of Gastrotricha}},
Author = {A. Kieneke and W. H. Ahlrichs and P. M. M. Arbizu},
Booktitle = {{Systematics 2009. Leiden, August 11-14. Abstracts}},
Year = {2009},
Pages = {11 - 14},
Abstract = {Some characters might indicate synapomorphies of a group Platyzoa comprising at least Plathelminthes, Gnathifera and Gastrotricha},
File = {kieneke2009_gastrotricha.txt}
}
@Conference{Kiethega2008,
Title = {{Unprecedented mitochondrial genomes throughout diplonemids}},
Author = {G. N. Kiethega and S. Teijeiro and J. Roy and G. Burger},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
File = {kiethega2008.txt}
}
@Article{Kim1996,
Title = {{Phylogenetic relationships of Annelids, Molluscs, and Arthropods evidenced from molecules and morphology}},
Author = {C. B. Kim and S. Y. Moon and S. R. Gelder and W. Kim},
Journal = {J. Mol. Evol.},
Year = {1996},
Pages = {207--215},
Volume = {43}
}
@Article{Kim2008a,
Title = {{EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata}},
Author = {E. Kim and L. E. Graham},
Journal = {PLoS ONE},
Year = {2008},
Number = {7},
Pages = {e2621},
Volume = {3},
Abstract = {6 proteins: (Malawi || Jacob || Heterol) || Eugleno || ( Crypto || Kata || Hapto) || Rhodo ||Chloro; Rhizo + Chromalv (+ Trimastix?), Amoeb + Opisto, Cyanophora unplaced, Metamonada unclear},
Doi = {10.1371/journal.pone.0002621},
File = {kim2008.pdf}
}
@Article{Kim2010,
Title = {{Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life}},
Author = {E. Kim and J. W. Harrison and S. Sudek and M. D. M. Jones and H. M. Wilcox and T. A. Richards and A. Z. Worden and J. M. Archibald},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2010},
Volume = {22},
Abstract = {"rappenomonads": rDNA group OM270, third class of Hapto?, not biliphytes},
Doi = {10.1073/pnas.1013337108},
File = {kim2010_rappenomonads.pdf},
Url = {www.pnas.org/cgi/doi/10.1073/pnas.1013337108}
}
@Article{Kim2015,
Title = {{A contemplation on the secondary origin of green algal and plant plastids}},
Author = {E. Kim and S. Maruyama},
Journal = {Acta Societatis Botanicorum Poloniae},
Year = {2015},
Number = {4},
Pages = {331--336},
Volume = {83},
Abstract = {As stated},
Doi = {10.5586/asbp.2014.040},
File = {kim2014_green_plastids_could_be_secondary.pdf},
Url = {http://chloroplast.ocean.washington.edu)}
}
@Article{Kim2006,
Title = {{Evolutionary relationships of apusomonads inferred from taxon-rich analyses of six nuclear-encoded genes}},
Author = {E. Kim and A. G. B. Simpson and L. E. Graham},
Journal = {Mol. Biol. Evol.},
Year = {2006},
Pages = {608--262},
Volume = {18},
Abstract = {Bikonta || Amoeb || Apuso || Opist; Hapt+Crypt || Glauc+Chlor || Rhiza || Exca || Chromalv},
File = {kim2006.pdf}
}
@Article{Kim2016,
Title = {{Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms}},
Author = {E. Kim and B. Sprung and S. Duhamel and C. Filardi and M. K. Shin},
Journal = {Journal of Eukaryotic Microbiolohy},
Year = {2016},
Abstract = {As stated; many are near Sulcozoa/Cryptista},
File = {kim2016_environmental_protists.pdf}
}
@Article{Kim2006b,
Title = {{Phylogenetic position of the green flagellate \textit{Mesostigma viride} based on a-tubulin and b-tubulin gene sequences}},
Author = {E. Kim and L. W. Wilcox and M. W. Fawley and L. E. Graham},
Journal = {Int. J. Plant Sci.},
Year = {2006},
Number = {4},
Pages = {873--883},
Volume = {167},
Abstract = {Pras I,II || Pras III (Nephro) || Chloro; Meso || Charo},
File = {kim2006b.pdf}
}
@Conference{Kim2008b,
Title = {{Episymbioses involving three new genera of heterotrophic Stramenopiles flagellates: Apoikia lindahli nov. comb. (Chrysophyceae), Filos agilis gen. et sp. nov. (Bicosoecida), and Nanos amicus gen. et sp. nov. (Bicosoecida)}},
Author = {E. Kim and N. Yubuki and B. Leander and L. E. Graham},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {In SSU rRNA phylogenies, F. agilis and N. amicus were closely related to the bicosoecids Adriamonas, Siluania, Paramonas, and Nerada},
File = {kim2008.txt}
}
@Article{Kim2009,
Title = {{Ultrastructure and 18S rDNA Phylogeny of Apoikia lindahlii comb. Nov. (Chrysophyceae) and its Epibiontic Protists, Filos agilis gen. Et sp. Nov. (Bicosoecida) and Nanos amicus gen. Et sp. Nov. (Bicosoecida).}},
Author = {E. Kim and N. Yubuki and B. S. Leander and L. E. Graham},
Journal = {Protist},
Year = {2009},
Abstract = {Labyr || Opaloz || Oo || Chromo},
Doi = {10.1016/j.protis.2009.09.003},
File = {kim2009_apoikia_nanos_filos.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20022300}
}
@Article{Kim2018,
Title = {{Evolution of six novel ORFs in the plastome of Mankyua chejuense and phylogeny of eusporangiate ferns.}},
Author = {H. T. Kim and K.-J. Kim},
Journal = {Sci Rep},
Year = {2018},
Number = {1},
Pages = {16466},
Volume = {8},
Abstract = {Basal to Ophioglossaceae},
Doi = {10.1038/s41598-018-34825-6},
File = {kim2018_mankyua.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30405200}
}
@Article{Kim2012,
Title = {{The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.}},
Author = {K. M. Kim and G. Caetano-Anolles},
Journal = {BMC evolutionary biology},
Year = {2012},
Number = {1},
Pages = {13},
Volume = {12},
Abstract = {(Euk + Bact) Ar},
Doi = {10.1186/1471-2148-12-13},
File = {kin2012_superkingdoms.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22284070}
}
@Article{Kim2014,
Title = {{A tree of cellular life inferred from a genomic census of molecular functions.}},
Author = {K. M. Kim and A. Nasir and K. Hwang and G. Caetano-Anoll{\'e}s},
Journal = {J. Mol. Evol.},
Year = {2014},
Number = {5--6},
Pages = {240--262},
Volume = {79},
Abstract = {Almost no support for Bacteria groups},
Doi = {10.1007/s00239-014-9637-9},
File = {kim2014_tol_functionome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25128982}
}
@Conference{Yamazaki2006,
Title = {{Polyphyletic origin of land plants: Bryophytes are fungi with chloroplasts}},
Author = {T. Kim and H. N. Yamazaki},
Booktitle = {{Botany 2006}},
Year = {2006},
Abstract = {Histone 3 of mosses is from fungi}
}
@Article{Kindaichi2016,
Title = {{Phylogenetic diversity and ecophysiology of Candidate phylum Saccharibacteria in activated sludge.}},
Author = {T. Kindaichi and S. Yamaoka and R. Uehara and N. Ozaki and A. Ohashi and M. Albertsen and P. H. Nielsen and J. L. Nielsen},
Journal = {FEMS Microbiology Ecology},
Year = {2016},
Number = {6},
Pages = {fiw078},
Volume = {92},
Abstract = {Several subdivisions},
Doi = {10.1093/femsec/fiw078},
File = {kindaichi2016_saccharibacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27090759}
}
@Article{King2008,
Title = {{The genome of the choanoflagellate \textit{Monosiga brevicollis} and the origin of metazoans}},
Author = {N. King and M. J. Westbrook and S. L. Young and A. Kuo and M. Abedin and J. Chapman and S. Fairclough and U. Hellsten and Y. Isogai and I. Letunic and M. Marr and D. Pincus and N. Putnam and A. Rokas and K. J. Wright and R. Zuzow and W. Dirks and M. Good and D. Goodstein and D. Lemons and W. Li and J. B. Lyons and A. Morris and S. Nichols and D. J. Richter and A. Salamov and J. G. I. Sequencing and P. Bork and W. A. Lim and G. Manning and W. T. Miller and W. McGinnis and H. Shapiro and R. Tjian and I. V. Grigoriev and D. Rokhsar},
Journal = {Nature},
Year = {2008},
Pages = {583--588},
Volume = {451},
Abstract = {Sister group to Metazoa, has many genes "beforehand"},
Doi = {10.1038/nature06617},
File = {king2008.pdf}
}
@Article{Kirkpatrick2006,
Title = {{Diversity and Distribution of Planctomycetes and Related Bacteria in the Suboxic Zone of the Black Sea}},
Author = {J. Kirkpatrick and B. Oakley and C. Fuchsman and S. Srinivasan and J. T. Staley and J. W. Murray},
Journal = {Appl. Environ. Microbiol.},
Year = {2006},
Number = {4},
Pages = {3079--3083},
Volume = {72},
Abstract = {OD1, then OP3, then WS3 close to Lenti-Verru-Chla-Planct},
File = {kirkpatrick2006_planct.pdf}
}
@Article{Kirzhner2005,
Title = {{Large-scale genome clustering across life based on a linguistic approach}},
Author = {V. Kirzhner and A. Bolshoy and Z. Volkovich and A. Korol and E. Nevo},
Journal = {BioSystems},
Year = {2005},
Number = {3},
Pages = {208--222},
Volume = {81},
Abstract = {Oligo frequencies unite some Archaea with Bacteria and some Archaea with Eukar.},
File = {kirzhner2005.pdf}
}
@Article{Kirzhner2007,
Title = {{Different Clustering of Genomes Across Life Using the A-T-C-G and Degenerate R-Y Alphabets: Early and Late Signaling on Genome Evolution?}},
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Year = {2020},
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Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {Phylogenetic analyses suggest that all Carpediemonas-like isolates, including C. membranifera and D. brevis, form at least 5 distinct lineages. These branch paraphyletically at the base of the diplomonads-retortamonads, although resolution is weak.},
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Pages = {33},
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Abstract = {Against Doolittle},
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File = {koonin2008.pdf},
Keywords = {pr1}
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@Article{Kotikova2008,
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Year = {2008},
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Doi = {10.1098/rspb.2009.1884},
File = {kottke2009_attractiellomycetes.pdf},
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@Article{Kozubal2013,
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Abstract = {Copromyxa in Hartmanellidae},
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File = {lahr2013_tubulinea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23499265}
}
@Article{Lake2009b,
Title = {{Evidence for an early prokaryotic endosymbiosis}},
Author = {J. A. Lake},
Journal = {Nature},
Year = {2009},
Number = {7258},
Pages = {967--971},
Volume = {460},
Abstract = {Clostridia + Actinobacteria gave Double-mambrane bacteria},
Doi = {10.1038/nature08183},
File = {lake2009_early_prok_endosymb.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19693078}
}
@Article{Lake2006,
Title = {{Rooting the Tree of Life using Non-ubiquitous Genes}},
Author = {J. A. Lake and C. W. Herbold and M. C. Rivera and J. A. Servin and R. G. Skophammer},
Journal = {Mol. Biol. Evol.},
Year = {2006},
Pages = {1--18},
Volume = {2},
Abstract = {Root is not within G-},
File = {lake2006.pdf}
}
@Article{Lake2008,
Title = {{Evidence for a new root of the tree of life.}},
Author = {J. A. Lake and J. A. Servin and C. W. Herbold and R. G. Skophammer},
Journal = {Syst. Biol.},
Year = {2008},
Number = {6},
Pages = {835--843},
Volume = {57},
Abstract = {Actino + Posi vs. Firmi + Archeb (Bacteria paraphyletic -- sic!)},
Doi = {10.1080/10635150802555933},
File = {lake2008.pdf},
Keywords = {pr1}
}
@Article{Lake2009,
Title = {{Genome beginnings: Rooting the tree of life}},
Author = {J. A. Lake and R. G. Skophammer and C. W. Herbold and J. A. Servin},
Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2009},
Number = {1527},
Pages = {2177--2185},
Volume = {364},
Abstract = {Actin + Negibact vs. Firm + Archaea},
Doi = {10.1098/rstb.2009.0035},
File = {skophammer2009_tol_root.pdf}
}
@InProceedings{Lam2009,
Title = {{Phylogenetic placement of the parasitic and mycoheterotrophic conifer Parasitaxus usta and molecular evolution of its plastid genome}},
Author = {V. Lam and Y. Chang and H. Rai and T. J. Brodribb and T. S. Feild and S. Mathews and S. W. Graham},
Booktitle = {{Botany and Mycology 2009. Snowbird, Utah, July 25-29. Abstracts}},
Year = {2009},
Abstract = {strong support for a sister-group relationship between Parasitaxus and two monotypic genera [of Podocarpaceae] found outside New Caledonia},
File = {lam2009_parasitaxus.txt}
}
@Article{Land1977,
Title = {{The morphology of Lamellibranchia (Annelids, Vestimentifera)}},
Author = {J. van der Land and A. Norrevang},
Journal = {K. Dan. Vidensk. Selsk. Biol. Skr.},
Year = {1977},
Pages = {1--102},
Volume = {21}
}
@Article{Lane2009,
Title = {{Reply to Bodyl, Stiller and Mackiewicz: ``Chromalveolate plastids: direct descent or multiple endosymbioses?''}},
Author = {C. E. Lane and J. M. Archibald},
Journal = {Trends Ecol. Evol.},
Year = {2009},
Number = {3},
Pages = {121-122},
Volume = {24},
Abstract = {Against tertiary},
Doi = {10.1016/j.tree.2008.11.002},
File = {lane2009_to_bodyl.pdf},
ISSN = {0169-5347},
Url = {http://dx.doi.org/10.1016/j.tree.2008.11.002}
}
@Article{Lane2008,
Title = {{The eukaryotic tree of life: endosymbiosis takes its TOL}},
Author = {C. E. Lane and J. M. Archibald},
Journal = {Trends Ecol. Evol.},
Year = {2008},
Number = {5},
Pages = {268--275},
Volume = {23},
Abstract = {Two hypotheses: (a) 4 Bikonta groups (Pl, Exc, Rhiz, Chroa) and (b) Pl, Exc, (Hapt+Cry) || Rhiz || Chroa p.p.},
Doi = {10.1016/j.tree.2008.02.004},
File = {lane2008.pdf}
}
@Article{Lang1997,
Title = {{An ancestral mitochondrial DNA resembling a eubacterial genome in miniature.}},
Author = {B. F. Lang and G. Burger and C. J. O'Kelly and R. Cedergren and G. B. Golding and C. Lemieux and D. Sankoff and M. Turmel and M. W. Gray},
Journal = {Nature},
Year = {1997},
Number = {6632},
Pages = {493--497},
Volume = {387}
}
@Article{Lang1999,
Title = {{A Comparative Genomics Approach to the Evolution of Eukaryotes and their Mitochondria}},
Author = {B. F. Lang and E. Seif and M. W. Gray and C. J. O'Kelly and G. Burger},
Journal = {J. Euk. Microbiol.},
Year = {1999},
Number = {4},
Pages = {320--326},
Volume = {46}
}
@Article{Lang2013,
Title = {{Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices}},
Author = {J. M. Lang and A. E. Darling and J. A. Eisen},
Journal = {PLOS One},
Year = {2013},
Number = {4},
Pages = {e62510},
Volume = {8},
Abstract = {Low support for most interphyla nodes},
Doi = {10.1371/journal.},
File = {lang2013_prokar_genomes_supertree.djvu},
Url = {www.moore.org)}
}
@Article{Lanterbecq2008,
Title = {{Locomotion and fine structure of parapodia in Myzostoma cirriferum (Myzostomida)}},
Author = {D. Lanterbecq and C. Bleidorn and S. Michel and I. Eeckhaut},
Journal = {Zoomorphology},
Year = {2008},
Pages = {59--68},
Volume = {127},
Abstract = {Annelid chaetae},
Doi = {10.1007/s00435-007-0052-2},
File = {anterbecq2008.pdf}
}
@Article{Lanterbecq2009,
Title = {{Bodyplan diversification in crinoid-associated myzostomes (Myzostomida, Protostomia)}},
Author = {D. Lanterbecq and G. W. Rouse and I. Eeckhaut},
Journal = {Invertebrate Biology},
Year = {2009},
Number = {3},
Pages = {283--301},
Volume = {128},
Abstract = {Myzostomid phylogeny},
Doi = {10.1111/j.1744-7410.2009.00172.x},
File = {lanterbecq2009_myzost_body_plan.pdf}
}
@Article{Lara2011,
Title = {{SSU rRNA reveals major trends in oomycete evolution}},
Author = {E. Lara and L. Belbahri},
Journal = {Fungal Diversity},
Year = {2011},
Abstract = {Similar to previous reports},
Doi = {10.1007/s13225-011-0098-9},
File = {lara2011_oomycetes.pdf}
}
@Article{Lara2006,
Title = {{Andalucia (n. gen.)--the Deepest Branch Within Jakobids (Jakobida; Excavata), Based on Morphological and Molecular Study of a New Flagellate from Soil}},
Author = {E. Lara and A. Chatzinotas and A. G. B. Simpson},
Journal = {J. Euk. Microbiol.},
Year = {2006},
Pages = {112--120},
Volume = {53},
Abstract = {Andalucia || other Jacob. || Heterol || Eugle},
File = {lara2006.pdf}
}
@Article{Lara2009,
Title = {{The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi}},
Author = {E. Lara and D. Moreira and P. Lopez-Garcia},
Journal = {Protist},
Year = {In press},
Abstract = {SSU: "Rozellida" || Blastocl || Chytr, Zygo || Glomerulo || others},
Doi = {10.1016/j.protis.2009.06.005},
File = {lara2009_rosella.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19674933}
}
@InBook{Larsson2014,
Title = {{The Primitive Microsporidia}},
Author = {J. I. R. Larsson},
Year = {2014},
Abstract = {Metchnikovellida and others},
Booktitle = {{Microsporidia: Pathogens of Opportunity, First Edition}},
File = {larsson2014_primitive_microsporidia.pdf},
ISBN = {9781118395226},
Journal = {Nature}
}
@MastersThesis{Larsson2003,
Title = {{Early Development of Nemertoderma westbladi}},
Author = {K. Larsson},
School = {Uppsala Universitet},
Year = {2003},
File = {larsson2003.pdf},
Pages = {1--13}
}
@Article{Larsson2008,
Title = {{Phylogeny of Catenulida and support for Platyhelminthes}},
Author = {K. Larsson and U. Jondelius},
Journal = {Organisms, Diversity \& Evolution},
Year = {2008},
Pages = {378--387},
Volume = {8},
Abstract = {Catenul || Macrost || others},
Doi = {10.1016/j.ode.2008.09.002},
File = {larsson2008.pdf},
Url = {www.elsevier.de/ode}
}
@InProceedings{Larsson2009,
Title = {{Building the fungal tree of life: Recent achievements and future challenges}},
Author = {K.-H. Larsson},
Booktitle = {{Systematics 2009. Leiden, August 11-14. Abstracts}},
Year = {2009},
Abstract = {Olpidium ~ Basidiobolus},
File = {larsson2009_fungal_tol.txt}
}
@Article{Lartillot2008,
Title = {{Improvement of molecular phylogenetic inference and the phylogeny of Bilateria}},
Author = {N. Lartillot and H. Philippe},
Journal = {Phil. Trans. R. Soc. B},
Year = {2008},
Number = {1496},
Pages = {1463--1472},
Volume = {363},
Abstract = {Deuterostomia para?; (Anne+Platy) || Moll (but sampling is scarse)},
Doi = {10.1098/rstb.2007.2236},
File = {lartillot2008.pdf}
}
@Article{LasekNesselquist2013,
Title = {{The effects of model choice and mitigating bias on the ribosomal tree of life.}},
Author = {E. Lasek-Nesselquist and J. P. Gogarten},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Number = {1},
Pages = {17--38},
Volume = {69},
Abstract = {two-domain topology for the tree of life, where Eukarya emerges from within Archaea as sister to a Korarchaeota/Thaumarchaeota (KT) or Crenarchaeota/KT clade for all models under all or at least one of the strategies employed},
Doi = {10.1016/j.ympev.2013.05.006},
File = {lasek_nesselquist2013_tol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23707703}
}
@Article{Lau2009,
Title = {{Babesia bovis: A comprehensive phylogenetic analysis of plastid-encoded genes supports green algal origin of apicoplasts}},
Author = {A. O. T. Lau and T. F. McElwain and K. A. Brayton and D. P. Knowles and E. H. Roalson},
Journal = {Experimental Parasitology},
Year = {2009},
Number = {3},
Pages = {236--243},
Volume = {123},
Abstract = {Close to Helicosporidium, not to red algae},
Doi = {10.1016/j.exppara.2009.07.007},
File = {lau2009_apicoplast_origin.pdf},
ISSN = {0014-4894},
Url = {http://dx.doi.org/10.1016/j.exppara.2009.07.007}
}
@Article{Laumer2015,
Title = {{Spiralian phylogeny informs the evolution of microscopic lineages.}},
Author = {C. E. Laumer and N. Bekkouche and A. Kerbl and F. Goetz and R. C. Neves and M. V. S{\o}rensen and R. M. Kristensen and A. Hejnol and C. W. Dunn and G. Giribet and K. Worsaae},
Journal = {Curr. Biol.},
Year = {2015},
Number = {15},
Pages = {2000--2006},
Volume = {25},
Abstract = {402 orthologs: Gnathost || Microgn || Rotif, Gastrotr + Plathelm, Cyclioph?, Moll, Nemert, Brach + Phor + Ectopr and Entopr., Annelida (deeply) incl. Diurodrilus and Lobatocerebrum},
Doi = {10.1016/j.cub.2015.06.068},
File = {laumer2015_spiralian_evol_micrognath_diurodrilus_lobatocerebr.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26325138}
}
@Article{Laumer2019,
Title = {{Revisiting metazoan phylogeny with genomic sampling of all phyla.}},
Author = {C. E. Laumer and R. Fern{\'a}ndez and S. Lemer and D. Combosch and K. M. Kocot and A. Riesgo and S. C. S. Andrade and W. Sterrer and M. V. S{\o}rensen and G. Giribet},
Journal = {Proceedings. Biological sciences},
Year = {2019},
Number = {1906},
Pages = {20190831},
Volume = {286},
Abstract = {Lophotrochozoa see Bleindorn, 2019; Ctenophora mostly first},
Doi = {10.1098/rspb.2019.0831},
File = {laumer2019_genomic_metazoa_with_corr.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31690235}
}
@Article{Laumer2014,
Title = {{Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes}},
Author = {C. E. Laumer and G. Giribet},
Journal = {Biological Journal of the Linnean Society},
Year = {2014},
Pages = {570--588},
Volume = {111},
Abstract = {Catenulida basal},
File = {laumer2011_plathelminthes.pdf}
}
@Article{Laumer2018,
Title = {{Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias}},
Author = {C. E. Laumer and H. Gruber-Vodicka and M. G. Hadfield and V. B. Pearse and A. Riesgo and J. C. Marioni and G. Giribet},
Journal = {eLife},
Year = {2018},
Pages = {e36278},
Volume = {7},
Abstract = {Ctenofora, Porifera || Bilateria || Placozoa + Cnidaria},
Doi = {10.5061/dryad.6cm1166},
File = {laumer2018_placozoa_cnidaria_clade.pdf},
Url = {https://sourceforge.net/projects/bbmap/)}
}
@Article{Laumer2015a,
Title = {{Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation}},
Author = {C. E. Laumer and A. Hejnol and G. Giribet},
Journal = {eLIFE},
Year = {2015},
Pages = {e05503},
Volume = {4},
Abstract = {Catenulida sister},
Doi = {10.7554/eLife.05503.001},
File = {laumer2015_platyhelminthes.pdf}
}
@Article{LaurinLemay2012,
Title = {{Origin of land plants revisited in the light of sequence contamination and missing data.}},
Author = {S. Laurin-Lemay and H. Brinkmann and H. Philippe},
Journal = {Curr. Biol.},
Year = {2012},
Number = {15},
Pages = {R593--4},
Volume = {22},
Abstract = {Zygnematales and Coleochaetales},
Doi = {10.1016/j.cub.2012.06.013},
File = {laurin-lemay2012_orig_land_plants.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22877776}
}
@Article{Lavrov2004,
Title = {{Phylogenetic position of the Pentastomida and (pan)crustacean relationships}},
Author = {D. V. Lavrov and W. M. Brown and J. L. Boore},
Journal = {Proc. R. Soc. B},
Year = {2004},
Pages = {537--544},
Volume = {271},
Abstract = {Pentastomida close to Branchiura, Cirripedia ans Cephalocarida (full mitoch genome)},
File = {lavrov2004.pdf}
}
@Article{Lavrov2008,
Title = {{Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data}},
Author = {D. V. Lavrov and X. Wang and M. Kelly},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Pages = {111--124},
Volume = {49},
Abstract = {Placozoa || Bilateria + Hexactinell + Cnidaria + Demospongia) [Homoscl. and Calcar. absent]},
Doi = {doi:10.1016/j.ympev.2008.05.014},
File = {lavrov2008.pdf}
}
@InBook{Lawrence2016,
Title = {{Using tRNA class informative features to determine the phylogenetic placement of Gnetophyta.}},
Author = {T. J. Lawrence and D. Ardell},
Year = {2016},
Abstract = {Gnetifer supported (sister to conifers)},
Booktitle = {{Botany 2016. Savannah, Georgia, July 30--August 3, 2016}}
}
@Article{Lawrey2009,
Title = {{High concentration of basidiolichens in a single family of agaricoid mushrooms (Basidiomycota: Agaricales: Hygrophoraceae)}},
Author = {J. D. Lawrey and R. L{\"u}cking and H. J. M. Sipman and J. L. Chaves and S. A. Redhead and F. Bungartz and M. Sikaroodi and P. M. Gillevet},
Journal = {Mycol. Res.},
Year = {In press},
Abstract = {As stated},
Doi = {10.1016/j.mycres.2009.07.016},
File = {lawrey2009_basidiolichens.pdf}
}
@Article{Lax2018,
Title = {{Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes.}},
Author = {G. Lax and Y. Eglit and L. Eme and E. M. Bertrand and A. J. Roger and A. G. B. Simpson},
Journal = {Nature},
Year = {2018},
Abstract = {Malawi || CRuMs (Mantamonas, Diphyll., Rigifilia) || Amoeboz + Obazoa; Discoba; Hemimast || Cryptista || Archaeplastida: Picozoa + Rhodophyta (!!), Glauco + Chloro; Centrohel + Hapt || TSAR},
Doi = {10.1038/s41586-018-0708-8},
File = {lax2018_hemimastigophora.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30429611}
}
@Article{Layden2010,
Title = {{Expression and phylogenetic analysis of the zic gene family in the evolution and development of metazoans}},
Author = {M. J. Layden and N. P. Meyer and K. Pang and E. C. Seaver and M. Q. Martindale},
Journal = {EvoDevo},
Year = {2010},
Pages = {12},
Volume = {1},
Abstract = {Porif, Cteno || Plac || Bil + Cnid},
Doi = {10.1186/2041-9139-1-12},
File = {layden2010_zic_parahoxozoa.pdf},
Url = {http://www.evodevojournal.com/content/1/1/12}
}
@Article{Leadbeater2008,
Title = {{Choanoflagellate evolution: the morphological perspective}},
Author = {B. S. C. Leadbeater},
Journal = {Protistology},
Year = {2008},
Number = {4},
Pages = {256--267},
Volume = {5},
File = {leadbeater2008.pdf}
}
@Article{Leander2008,
Title = {{Marine gregarines: evolutionary prelude to the apicomplexan radiation?}},
Author = {B. S. Leander},
Journal = {Trends Parasitol.},
Year = {2008},
Number = {2},
Pages = {60--67},
Volume = {24},
Abstract = {Myozoa: Dino(incl. Perkins., Synd.) || Colpodell (incl. Voromon.) || Cocc+Piropl, Rhytidocystis, Cryptosporidium (or in Greg), Gregarines; Greg.: Selenidium-like || Lecudina-like (5 branches)},
Doi = {10.1016/j.pt.2007.11.005},
File = {leander2008.pdf}
}
@Article{Leander2008b,
Title = {{A Hierarchical View of Convergent Evolution in Microbial Eukaryotes}},
Author = {B. S. Leander},
Journal = {J. Euk. Microbiol.},
Year = {2008},
Number = {2},
Pages = {59--68},
Volume = {55},
Abstract = {Staphanopogon > Eugl. + Heterolob.},
Doi = {10.1111/j.1550-7408.2008.00308.x},
File = {leander2008.pdf}
}
@Article{Leander2004,
Title = {{Early evolutionary history of dinoflagellates and apicomplexans (alveolata) as inferred from HSP90 and actin phylogenies}},
Author = {B. S. Leander and P. J. Keeling},
Journal = {J. Phycol.},
Year = {2004},
Pages = {341--350},
Volume = {40},
Abstract = {Cryptosporidium ~ Gregarines},
File = {leander2004a.pdf}
}
@Article{Leander2006,
Title = {{Cellular Identity of a Novel Small Subunit rDNA Sequence Clade of Apicomplexans: Description of the Marine Parasite Rhytidocystis polygordiae n. sp. (Host: Polygordius sp., Polychaeta)}},
Author = {B. S. Leander and P. A. Ramey},
Journal = {J. Euk. Microbiol.},
Year = {2006},
Pages = {1--12},
Volume = {53},
Abstract = {Dino+Perkin || Colpodell || Grega incl. Cryprosporidium, Selenidium, Rhytidocystis vs. Coccidi + Piroplasm},
File = {leander2006.pdf}
}
@Article{Leander2001,
Title = {{The Labyrinthulomycota is comprised of three distinct lineages}},
Author = {Celeste A. Leander},
Journal = {Mycologia},
Year = {2001},
Pages = {459--464},
Volume = {93}
}
@Article{Leblond2009,
Title = {{Mono- and digalactosyldiacylglycerol composition of dinoflagellates. II. Lepidodinium chlorophorum, Karenia brevis, and Kryptoperidinium foliaceum, three dinoflagellates with aberrant plastids}},
Author = {J. D. Leblond and A. D. Lasiter},
Journal = {European Journal of Phycology},
Year = {2009},
Number = {2},
Pages = {199--205},
Volume = {44},
Doi = {10.1080/09670260802524611},
File = {leblond2009_aberrant_dinoflag.txt}
}
@Article{Lecroq2009,
Title = {{A new genus of xenophyophores (Foraminifera) from Japan Trench: Morphological description, molecular phylogeny and elemental analysis}},
Author = {B. Lecroq and A. J. Gooday and M. Tsuchiya and J. Pawlowski},
Journal = {Zool. Journ. Linn. Soc.},
Year = {2009},
Pages = {455--464},
Volume = {156},
Abstract = {Close to Textulariida},
File = {lecroq2009_xenophyoph.pdf}
}
@Article{Lee2011,
Title = {{A functional phylogenomic view of the seed plants.}},
Author = {E. K. Lee and A. Cibrian-Jaramillo and S.-O. Kolokotronis and M. S. Katari and A. Stamatakis and M. Ott and J. C. Chiu and D. P. Little and D. W. Stevenson and W. R. McCombie and R. A. Martienssen and G. Coruzzi and R. Desalle},
Journal = {PLoS Genet.},
Year = {2011},
Number = {12},
Pages = {e1002411},
Volume = {7},
Abstract = {Gnetales sister to all gymnosperms},
Doi = {10.1371/journal.pgen.1002411},
File = {lee2011_seed_plants.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22194700}
}
@Article{Lee2009b,
Title = {{The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus}},
Author = {J. Lee and J. P. Young},
Journal = {New Phytol.},
Year = {In press},
Abstract = {Chytr || Blastocl || "Zygo" incl. Giomus},
Doi = {10.1111/j.1469-8137.2009.02834.x},
File = {lee2009_glomus_mt.pdf}
}
@Article{Lee2013,
Title = {{Phylogenetic delineation of the novel phylum Armatimonadetes (former candidate division OP10) and definition of two novel candidate divisions.}},
Author = {K. C. Y. Lee and C. W. Herbold and P. F. Dunfield and X. C. Morgan and I. R. McDonald and M. B. Stott},
Journal = {Appl. Environ. Microbiol.},
Year = {2013},
Number = {7},
Pages = {2484--2487},
Volume = {79},
Abstract = {Armatimonadia, Chthonomonadetes, Fimbriimonadia and 7 others + WS1 and FBP independent},
Doi = {10.1128/AEM.03333-12},
File = {lee2013_armatimonadetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23377935}
}
@Article{Lee2010,
Title = {{Chthonomonas calidirosea gen. Nov., Sp. Nov., An aerobic, pigmented, thermophilic microorganism of a novel bacterial class, Chthonomonadetes classis. Nov., Of the newly described phylum Armatimonadetes originally designated candidate division OP10}},
Author = {K. C.-Y. Lee and P. F. Dunfield and X. C. Morgan and M. A. Crowe and K. M. Houghton and M. Vyssotski and J. L. J. Ryan and K. Lagutin and I. R. McDonald and M. B. Stott},
Journal = {IJSEM},
Year = {2010},
Abstract = {Armatimonadetes; WS7 close?},
Doi = {10.1099/ijs.0.027235-0},
File = {lee2010_chthonomonas.pdf}
}
@Article{Lee2009c,
Title = {{The cell cycle of the planctomycete Gemmata obscuriglobus with respect to cell compartmentalization.}},
Author = {K.-C. Lee and R. I. Webb and J. A. Fuerst},
Journal = {BMC Cell Biol.},
Year = {2009},
Pages = {4},
Volume = {10},
Abstract = {Cell compartments: double nuclear membrane!},
Doi = {10.1186/1471-2121-10-4},
File = {lee2010_gemmata_cell_compartments.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/12824468}
}
@Article{Lee2009a,
Title = {{Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes}},
Author = {K.-C. Lee and R. I. Webb and P. H. Janssen and P. Sangwan and T. Romeo and J. T. Staley and J. A. Fuerst},
Journal = {BMC Microbiology},
Year = {2009},
Pages = {5},
Volume = {9},
Abstract = {PVC strongly supported},
Doi = {10.1186/1471-2180-9-5},
File = {lee2009.pdf}
}
@Article{Lee1999,
Title = {{Molecular Clock Calibrations and Metazoan Divergence Dates}},
Author = {M. S. Y. Lee},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {385--391},
Volume = {49}
}
@Book{Lee2008,
Title = {{Phycology}},
Author = {R. E. Lee},
Publisher = {Cambridge University Press},
Year = {2008},
Address = {Cambridge},
Edition = {3},
ISBN = {9780521864084},
Pages = {1--401}
}
@Article{Lee1991,
Title = {{Feeding apparatus of the colourless flagellata \textit{Katablepharis} (Cryptophyceae)}},
Author = {R. E. Lee and P. Kurgens and A. P. Mylnikov},
Journal = {J. Phycol.},
Year = {1991},
Pages = {725--733},
Volume = {27}
}
@Article{Lee2008b,
Title = {{Microsporidia Evolved from Ancestral Sexual Fungi}},
Author = {S. C. Lee and N. Corradi and E. J. Byrnes III and S. Torres-Martinez and F. S. Dietrich and P. J. Keeling and J. Heitman},
Journal = {Curr. Biol.},
Year = {2008},
Number = {21},
Pages = {1675--1679},
Volume = {18},
Abstract = {~ Mucorales},
Doi = {10.1016/j.cub.2008.09.030},
File = {lee2008.pdf}
}
@Article{Lee2014,
Title = {{Morphological and Molecular Characterisation of a New Species of Stephanopogon, Stephanopogon pattersoni n. sp.}},
Author = {W. J. Lee and K. Miller and A. G. B. Simpson},
Year = {2014},
Abstract = {As stated; Percolomonas || Stephanopogon},
Doi = {10.1111/jeu.12124-4477},
File = {lee2014_stephanopogon_pattersonii.pdf}
}
@Article{Lee2016,
Title = {{Placement of the unclassified Cyranomonas australis Lee 2002 within a novel clade of Cercozoa.}},
Author = {W. J. Lee and J. S. Park},
Journal = {Eur. J. Protistol.},
Year = {2016},
Pages = {60 - 66},
Volume = {56},
Abstract = {Chlorarachn + Metromonas, Metopion separate},
Doi = {10.1016/j.ejop.2016.06.004},
File = {lee2016_cyranomonas_cercozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27541187}
}
@Article{Lee2014a,
Title = {{Morphological and Molecular Characterisation of Notosolenus urceolatus Larsen and Patterson 1990, a Member of an Understudied Deepbranching Euglenid Group (Petalomonads)}},
Author = {W. J. Lee and A. G. B. Simpson},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2014},
Abstract = {Symbiontids || Ploeotiids || Petalomonads (incl. Notosolenus)},
Doi = {10.1111/jeu.12126-4520},
File = {lee2014_petalomonads.pdf}
}
@Article{Legg2011,
Title = {{Lobopodian phylogeny reanalysed}},
Author = {D. A. Legg},
Journal = {Nature},
Year = {2011},
Number = {7359},
Pages = {526--530},
Volume = {476},
Abstract = {Diania is just a lobopod},
Doi = {10.1038/nature10267},
File = {legg2011_lobopoda.pdf},
ISSN = {0028-0836}
}
@Article{Lehmacher2014,
Title = {{Immunohistochemical and ultrastructural analysis of the muscular and nervous systems in the interstitial polychaete Polygordius appendiculatus (Annelida)}},
Author = {C. Lehmacher and D. Fiege},
Journal = {Zoomorphology},
Year = {2014},
Pages = {21--41},
Volume = {133},
Abstract = {Could be basal},
Doi = {10.1007/s00435-013-0203-6},
File = {lehmacher2014_polygordius.djvu}
}
@Article{Lehmacher2013,
Title = {{Immunohistochemical and ultrastructural analysis of the muscular and nervous systems in the interstitial polychaete Polygordius appendiculatus (Annelida)}},
Author = {C. Lehmacher and D. Fiege and G. Purschke},
Journal = {Zoomorphology},
Year = {2013},
Pages = {1--21},
Abstract = {Very likely, a basiepithelial and non-ganglionic organization of the ventral nerve cord as well as an orthogonal nervous system represent plesiomorphic characters. The same applies for the predominance of longitudinal muscle fibers.},
Doi = {10.1007/s00435-013-0203-6},
File = {lehmacher2013_polygordius.pdf}
}
@Article{Lehmann2013,
Title = {{Near intron pairs and the metazoan tree.}},
Author = {J. Lehmann and P. F. Stadler and V. Krauss},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Number = {3},
Pages = {811--823},
Volume = {66},
Abstract = {Bilateria + Ctenophora (questionable)},
Doi = {10.1016/j.ympev.2012.11.012},
File = {lehmann2013_introns_metazoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23201572}
}
@Article{Lehmann2018,
Title = {{Also looking like Limulus? - retinula axons and visual neuropils of Amblypygi (whip spiders)}},
Author = {T. Lehmann and R. R. Melzer},
Journal = {Front. Zool.},
Year = {2018},
Pages = {52},
Volume = {15},
Abstract = {Close evolutionary relationships between Xiphosura, Scorpiones, and Amblypygi},
Doi = {10.1186/s12983-018-0293-6},
File = {lehmann2018_amblypygi_xiphosura_scorpiones.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30574172}
}
@Article{Lehrke2008,
Title = {{On the Phylogeny of Echiura}},
Author = {J. Lehrke and T. Bartolomaeus},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {Echiura are most likely the sister taxon of the Capitellida and thus a subordinate taxon within the Annelida},
Doi = {10.1002/jmor.10683},
File = {lehrke2008.txt}
}
@Article{Lehtonen2011,
Title = {{Towards Resolving the Complete Fern Tree of Life}},
Author = {S. Lehtonen},
Journal = {PLoS ONE},
Year = {2011},
Number = {10},
Pages = {e24851},
Volume = {6},
Abstract = {Psil + Ophi || Maratt || Eq || others},
Doi = {10.1371/journal.pone.0024851},
File = {lehtonen2011_fern_tol.pdf},
Url = {www.plosone.org}
}
@Article{Lei2007,
Title = {{Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology}},
Author = {G. Lei and Q. Ji and S. JianDong and H. BaiLin},
Journal = {Journal Sci. China Ser. C: Life Sci.s},
Year = {2007},
Number = {5},
Pages = {587--599},
Volume = {50},
Abstract = {Spiro (excl. Leptosp) + Chlamyd, Dein/Th + Aquific + Chloroflexi, Mollucites || Archaea},
File = {gao2007.pdf}
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@Article{Leipe1999,
Title = {{Did DNA replication evolve twice independently?}},
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Journal = {Nucl. Acids Res.},
Year = {1999},
Number = {17},
Pages = {3389--3401},
Volume = {27}
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@Article{Leipe1996,
Title = {{16S-like rDNA sequences from \textit{Developayella elegans}, \textit{Labyrinthuloides hailotidis}, and \textit{Proteromonas lacertae} confirm that the stramenopiles are a primarily heterotrophic group}},
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Year = {1996},
Pages = {449--458},
Volume = {32}
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@Article{Leliaert2011,
Title = {{New discoveries at the base of the green plant phylogeny}},
Author = {F. Leliaert and H. Verbruggen and F. W. Zechman},
Journal = {Bioessays},
Year = {2011},
Abstract = {Chlorodendrophy, Picosystis clade, Mammielloph + Pyraminomod, Pycnococc, Nephroselmidophy, Prasinococc, Palmophyllales},
Doi = {10.1002/bies.201100035},
File = {leliaert2011_chlorophyta.pdf},
Url = {www.bioessays-journal.com}
}
@Article{Lemieux2014,
Title = {{Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae.}},
Author = {C. Lemieux and C. Otis and M. Turmel},
Journal = {BMC Evol. Biol.},
Year = {2014},
Pages = {211},
Volume = {14},
Abstract = {Pedino + Chlorellales (not strong) || core Trebouxiophyceae (incl. Geminella, Prasiola clades)},
Doi = {10.1186/s12862-014-0211-2},
File = {lemieux2014_trebouxiophyceae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10827456}
}
@Article{Lemieux2014a,
Title = {{Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species.}},
Author = {C. Lemieux and C. Otis and M. Turmel},
Journal = {BMC Genomics},
Year = {2014},
Pages = {857},
Volume = {15},
Abstract = {VI (Prasinococcus, Prasinoderma) || I + II (Pyraminomonas, Ostreociccus, Micromonas) || III (Nephroselmis) || V (Pycnococcus) || VII (Picosystis) || Pedino etc. (Oltmannsiellipsis in Ulv., Tetraselmis absent)},
Doi = {10.1186/1471-2164-15-857},
File = {lemieux2014_prasinophytes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/16236178}
}
@Article{Lemieux2007,
Title = {{A clade uniting the green algae \textit{Mesostigma viride} and \textit{Chlorokybus atmophyticus} represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies}},
Author = {C. Lemieux and C. Otis and M. Turmel},
Journal = {BMC Biology},
Year = {2007},
Number = {2},
Pages = {1--17},
Volume = {5},
Abstract = {Conjugatophyceae is separate class},
File = {lemieux2007.pdf}
}
@Article{Lemieux2000,
Title = {{Ancestral chloroplast genome in \textit{Mesostigma viride} reveals an earthy branch of green plant evolution}},
Author = {C. Lemieux and C. Otis and M. Turmel},
Journal = {Nature},
Year = {2000},
Pages = {649--652},
Volume = {403}
}
@Article{Leonard2012,
Title = {{Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life}},
Author = {G. Leonard and T. A. Richards},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2012},
Abstract = {Leotiomycetes ~ Sordariomycetes},
Doi = {10.1073/pnas.1210909110},
File = {leonard2012_fungi_gene_fusions.pdf},
Url = {www.pnas.org/cgi/doi/10.1073/pnas.1210909110}
}
@Article{Leontyev2019,
Title = {{Towards a phylogenetic classification of the Myxomycetes}},
Author = {D. V. Leontyev},
Journal = {Phytotaxa},
Year = {2019},
Number = {3},
Pages = {209--238},
Volume = {399},
Abstract = {Ceratiomyx, Myxomyc: Lucisporomycetidae and Columellomycetidae},
Doi = {10.11646/phytotaxa.399.3.5},
File = {leontyev2019_phylog_classif_myxomyc.pdf}
}
@Article{Leslie2018,
Title = {{An overview of extant conifer evolution from the perspective of the fossil record.}},
Author = {A. B. Leslie and J. Beaulieu and G. Holman and C. S. Campbell and W. Mei and L. R. Raubeson and S. Mathews},
Journal = {Am. J. Bot.},
Year = {2018},
Number = {9},
Pages = {1531--1544},
Volume = {105},
Doi = {10.1002/ajb2.1143},
File = {leslie2018_conifer_evol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30157290}
}
@Article{Letcher2018,
Title = {{Morphology, Ultrastructure, and Molecular Phylogeny of Rozella multimorpha, a New Species in Cryptomycota.}},
Author = {P. M. Letcher and J. E. Longcore and T. Y. James and D. S. Leite and D. R. Simmons and M. J. Powell},
Journal = {J. Eukaryot. Microbiol.},
Year = {2018},
Number = {2},
Pages = {180 - 190},
Volume = {65},
Abstract = {As stated},
Doi = {10.1111/jeu.12452},
File = {letcher2018_rozella_multimorpha.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28749611}
}
@Article{Letcher2013,
Title = {{Characterization of Amoeboaphelidium protococcarum, an algal parasite new to the cryptomycota isolated from an outdoor algal pond used for the production of biofuel.}},
Author = {P. M. Letcher and S. Lopez and R. Schmieder and P. A. Lee and C. Behnke and M. J. Powell and R. C. McBride},
Journal = {PLoS ONE},
Year = {2013},
Number = {2},
Pages = {e56232},
Volume = {8},
Abstract = {Rozella || Amoeboaphelidium + Cryptomycota || Microsporidia},
Doi = {10.1371/journal.pone.0056232},
File = {letcher2013_ameboaphelidium_cryptomycota_microsporidia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23437098}
}
@Article{Letcher2018a,
Title = {{A taxonomic summary and revision of Rozella (Cryptomycota)}},
Author = {P. M. Letcher and M. J. Powell},
Journal = {IMA FUNGUS},
Year = {2018},
Number = {2},
Pages = {383--399},
Volume = {9},
Doi = {10.5598/imafungus.2018.09.02.09},
File = {letcher2018_rozella_revision.pdf}
}
@Article{Letcher2008,
Title = {{Rhizophlyctidales--a new order in Chytridiomycota}},
Author = {P. M. Letcher and M. J. Powell and D. J. S. Barr and P. F. Churchill and W. S. Wakefield and K. T. Picard},
Journal = {Mycol. Res.},
Year = {2008},
Number = {9},
Pages = {1031--1048},
Volume = {112},
Abstract = {Sister to Spizellomycetales},
Doi = {10.1016/j.mycres.2008.03.007},
File = {letcher2008.pdf}
}
@Article{Letcher2015,
Title = {{A new isolate of Amoeboaphelidium protococcarum, and Amoeboaphelidium occidentale, a new species in phylum Aphelida (Opisthosporidia).}},
Author = {P. M. Letcher and M. J. Powell and S. Lopez and P. A. Lee and R. C. McBride},
Journal = {Mycologia},
Year = {2015},
Abstract = {Opisthosporidia: Aphelida || Cryptomycota || Paramicrosporidia || Nucleophaga || Microsporidia},
Doi = {10.3852/14-064},
File = {letcher2015_aphelida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25661716}
}
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Title = {{The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes.}},
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Journal = {Genome Biol Evol},
Year = {2017},
Number = {10},
Pages = {2635 - 2639},
Volume = {9},
Abstract = {[Rhizome is network of genes]},
Doi = {10.1093/gbe/evx208},
File = {levasseur2017_lokiarchaeota_mosaic_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29048529}
}
@Article{Levi1996,
Title = {{La classification des Porifera Grant, 1836 en 1996}},
Author = {C. Levi},
Journal = {Bull. Soc. Zool. Fr.},
Year = {1996},
Number = {122},
Pages = {255--259},
Volume = {97}
}
@Article{Levine1980,
Title = {{A new revised classification of Protozoa. The comittee of systematics and evolution of the society of Protozoologists}},
Author = {N. P. Levine and J. O. Corliss and F. E. G. Cox and Others},
Journal = {J. Protozool.},
Year = {1980},
Number = {1},
Pages = {37--58},
Volume = {27}
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@Article{Lewin2002,
Title = {{Prochlorophyta~--- a matter of class distinctions}},
Author = {R. A. Lewin},
Journal = {Photosynth. Res.},
Year = {2002},
Pages = {59--61},
Volume = {73},
Abstract = {Not a taxon},
File = {lewin2002.pdf}
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@Article{Lewis2004,
Title = {{Green algae and the origin of land plants}},
Author = {L. A. Lewis and R. M. Mccourt},
Journal = {Amer. J. Bot.},
Year = {2004},
Number = {10},
Pages = {1535--1556},
Volume = {91},
Abstract = {Support for Chlorodendrophyceae, paraphyly of Prasino, too many classes of Charo},
File = {lewis2004.pdf}
}
@Article{Lewis1997,
Title = {Phylogenetic Relationships of the Liverworts (Hepaticae), a Basal Embryophyte Lineage, Inferred from Nucleotide Sequence Data of the Chloroplast Gene rbc{L}},
Author = {L. A. Lewis and B. D. Misher and R. Vilgalys},
Journal = {Mol. Phyl. Evol.},
Year = {1997},
Number = {3},
Pages = {377--393},
Volume = {7}
}
@Article{Leys2003,
Title = {{The Significance of Syncytial Tissues for the Position of the Hexactinellida in the Metazoa}},
Author = {S. P. Leys},
Journal = {Integr. Comp. Biol.},
Year = {2003},
Pages = {19--27},
Volume = {43},
Abstract = {Hexact are unique; have plant-like cell contacts},
File = {leys2003.pdf}
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@Article{Leys2006,
Title = {{Embryogenesis in the glass sponge Oopsacas minuta: Formation of syncytia by fusion of blastomeres}},
Author = {S. P. Leys and E. Cheung and N. Boury-Esnaulty},
Journal = {Integr. Comp. Biol.},
Year = {2006},
Number = {2},
Pages = {104--117},
Volume = {46},
Abstract = {Hexactinell ~ Demosp},
File = {leys2006.pdf}
}
@Article{Li2009,
Title = {{Classification of life by the mechanism of genome size evolution}},
Author = {D. J. Li and S. Zhang},
Journal = {Mod. Phys. Lett. B},
Year = {2009},
Number = {30},
Pages = {3563 - 3580},
Volume = {30},
Abstract = {Crap?},
File = {li2009_classif_life_genome_size.pdf}
}
@Article{Li2020,
Title = {{The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants}},
Author = {L. Li and S. Wang and H. Wang and S. K. Sahu and B. Marin and H. Li and Y. Xu and H. Liang and Z. Li and S. Cheng and T. Reder and Z. {\c C}ebi and S. Wittek and M. Petersen and B. Melkonian and H. Du and H. Yang and J. Wang and G. K.-S. Wong and X. Xu and X. Liu and Y. Van de Peer and M. Melkonian and H. Liu},
Journal = {Nature Ecology \& Evolution},
Year = {2020},
Abstract = {Prasinodermophyta (Prasinodermophyceae and Palmophyllophyceae incl. Prasinococcus, Palmophyllum, Verdigellas) || Chlorophyta (Pyram + Mamiell || Nephros | Chloropic || Pedino || Treboux | Chlorodendr || Chlor + Ulv)) + Streptophyta},
Doi = {10.1038/s41559-020-1221-7},
File = {li2020_prasinodermophyta.pdf}
}
@Article{Li2022,
Title = {{The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea}},
Author = {M. Li and Y. Liu},
Journal = {mLife},
Year = {2022},
Abstract = {Njordarchaeota in between Asgard and Kora},
Doi = {10.1002/mlf2.12020},
File = {liu2022_korarchaeota_njordarchaeota.pdf}
}
@Article{Li2022a,
Title = {{Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1}},
Author = {Q. Li and Y. Zhou and R. Lu and P. Zheng and Y. Wang},
Journal = {PeerJ},
Year = {2022},
Number = {7795},
Volume = {578},
Abstract = {~ Marinimicrobia},
Doi = {10.7717/peerj.13241},
File = {li2022_ksb1_fcb.djvu}
}
@Article{Li2021a,
Title = {{Large phylogenomic datasets reveal deep relationships and trait evolution in chlorophyte green algae}},
Author = {X. Li and Z. Hou and C. Xu and X. Shi and L. Yang and L. A. Lewis and B. Zhong},
Journal = {Genome Biology and Evolution},
Year = {2021},
Abstract = {Chllorodendrophyceae might be outside of Pedinophyceae},
Doi = {10.1093/gbe/evab101/6265471},
File = {li2021_chlorophyta.pdf}
}
@Article{Li2021,
Title = {{Rooting the animal tree of life}},
Author = {Y. Li and X.-X. Shen and B. Evans and C. W. Dunn and A. Rokas},
Journal = {Mol. Biol. Evol.},
Year = {2021},
Abstract = {Ctenophora sister :)},
Doi = {10.1093/molbev/msab170/6294409},
File = {li2021_ctenophora_sister_metaanalysis.pdf}
}
@Article{Li2021b,
Title = {{A genome-scale phylogeny of the kingdom Fungi}},
Author = {Y. Li and J. L. Steenwyk and Y. Chang and C. T. Hittinger and X.-X. Shen and A. Rokas},
Journal = {Current Biology},
Year = {2021},
Abstract = {Zygomycete classes unstable},
Doi = {10.1016/j.cub.2021.01.074},
File = {yuanning2021_genome_phylog_fungi.pdf},
ISSN = {0960-9822}
}
@Article{Liang2013,
Title = {{1290 Nuclear Genes from a Genome-wide Survey Support Lungfishes as the Sister Group of Tetrapods.}},
Author = {D. Liang and X. X. Shen and P. Zhang},
Journal = {Mol. Biol. Evol.},
Year = {2013},
Abstract = {Latimeria || Protopterus || Tetrapoda},
Doi = {10.1093/molbev/mst072},
File = {liang2013_lungfishes_sister_tetrapods.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23589454}
}
@Article{Liaud2000,
Title = {{Compartment-Specific Isoforms of TPI and GAPDH are Imported into Diatom Mitochondria as a Fusion Protein: Evidence in Favor of a Mitochondrial Origin of the Eukaryotic Glycolytic Pathway}},
Author = {M.-F. Liaud and C. Lichtl and K. Apt and W. Martin and R. Cerff},
Journal = {Mol. Biol. Evol.},
Year = {2000},
Number = {2},
Pages = {213--223},
Volume = {17}
}
@InCollection{Lichtneckert2006,
Title = {{Origin and Evolution of the First Nervous System}},
Author = {R. Lichtneckert and H. Reichert},
Booktitle = {{Evolution of Nervous Systems}},
Publisher = {Academic Press},
Year = {2006},
Editor = {J. H. Kaas},
Pages = {289--315},
Volume = {1--2},
Abstract = {Trichoplax might have remains of nervous system (antibodies for some proteins)},
ISBN = {0123925606}
}
@Article{Lichtwardt1973,
Title = {{The Trichomycetes: What Are Their Relationships?}},
Author = {R. W. Lichtwardt},
Journal = {Mycologia},
Year = {1973},
Number = {1},
Pages = {1--20},
Volume = {65}
}
@Article{Lieb2008,
Title = {{Hemocyanin in mollusks~--- a molecular survey and new data on hemocyanin genes in Solenogastres and Caudofoveata}},
Author = {B. Lieb and C. Todt},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {1},
Pages = {382--385},
Volume = {49},
Abstract = {Solenogastres lack hemocyanin; exact position of Caudofov. hemoc. unclear},
Doi = {10.1016/j.ympev.2008.06.005},
File = {lieb2008.pdf}
}
@Article{Liebau2005,
Title = {{A revised classification of the higher taxa of the Ostracoda (Crustacea)}},
Author = {A. Liebau},
Journal = {Hydrobiologia},
Year = {2005},
Pages = {115--137},
Volume = {538},
Abstract = {Superorders Podocopomorpha and Myodocopomorpha},
Doi = {10.1007/s10750-004-4943-7},
File = {liebau2005_ostracoda.pdf}
}
@Article{Liebeskind2015,
Title = {{Convergence of ion channel genome content in early animal evolution.}},
Author = {B. J. Liebeskind and D. M. Hillis and H. H. Zakon},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2015},
Number = {8},
Pages = {E846--51},
Volume = {112},
Abstract = {As stated},
Doi = {10.1073/pnas.1501195112},
File = {liebeskind2015_neur_channels_gen_converg.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24050174}
}
@Article{Lienau2010,
Title = {{The megamatrix tree of life: Using genomescale horizontal gene transfer and sequence evolution data as information about the vertical history of life}},
Author = {E. K. Lienau and R. DeSalle and M. Allard and E. W. Brown and D. Swofford and J. A. Rosenfeld and I. N. Sarkar and P. J. Planet},
Journal = {Cladistics},
Year = {2010},
Pages = {1--11},
Volume = {26},
Abstract = {Actino ~ Cyano ~ Spiroch},
Doi = {10.1111/j.1096-0031.2010.00337.x},
File = {lienau2010_tol.pdf}
}
@Article{LiFang2010,
Title = {{Protocruzia, a highly ambiguous ciliate (Protozoa; Ciliophora): Very likely an ancestral form for Heterotrichea, Colpodea or Spirotrichea? With reevaluation of its evolutionary position based on multigene analyses}},
Author = {L. I. LiFang and S. Thorsten and S. M. Kyoon and A.-R. K. A. S and A.-K. B. A and S. O. N. G. WeiBo},
Journal = {Life Sci.},
Year = {2010},
Number = {1},
Pages = {131--138},
Volume = {53},
Abstract = {Separate class, sometimes close to Heterotrich},
Doi = {10.1007/s11427-010-0012-9},
File = {li2010_protocruziidea.pdf}
}
@Article{Ligrone2011,
Title = {{Morphology versus molecules in moss phylogeny: New insights (or controversies) from placental and vascular anatomy in Oedipodium griffithianum}},
Author = {R. Ligrone and J. G. Duckett},
Journal = {Plant Syst. Evol.},
Year = {2011},
Abstract = {results do not support molecular phylogenies resolving Oedipodium as the sister group to polytrichopsid mosses or to all peristomate mosses, but are compatible with a sister relationship to a clade encompassing Tetraphis, Buxbaumia and arthrodontous mosses},
Doi = {10.1007/s00606-011-0496-1},
File = {ligrone2011_oedipodium.pdf}
}
@Article{Ligrone2012,
Title = {{Major transitions in the evolution of early land plants: A bryological perspective}},
Author = {R. Ligrone and J. G. Duckett and K. S. Renzaglia},
Journal = {Annals of Botany},
Year = {2012},
Abstract = {Ancestral poikilo axial (!) gametophyte bearing simple unisporangiate sporophytes || Stomatophytes incl. mosses and hornw. || Polysporangiophytes},
Doi = {10.1093/aob/mcs017},
File = {ligrone2012_mosses_evol.pdf},
Url = {www.aob.oxfordjournals.org}
}
@Article{Lilaud1997,
Title = {{Evolutionary orygin of cryptomonad microalgae: two novel chloropkast/cytosol-specific {GAPDH} genes as potential markers of ancewstral endosymbiont and host cell components}},
Author = {M. Lilaud and U. Brandt and M. Scherzinger and R. Cerff},
Journal = {J. Mol. Evol.},
Year = {1997},
Number = {1},
Pages = {28--37},
Volume = {44}
}
@Article{Lim2006,
Title = {{The Complete Mitochondrial Genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): Non-Monophylies of Maxillopoda and Crustacea}},
Author = {J. T. Lim and U. W. Hwang},
Journal = {Mol. Cells},
Year = {2006},
Number = {3},
Pages = {314--322},
Volume = {22},
Abstract = {Ostracoda+Branchiura+Penta sep. from Remi+Cirr || Chel+Myr; Cephal || Collem || Branchiop || Hexa || Malaco},
File = {lim2006.pdf}
}
@Article{Lin2010,
Title = {{Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies}},
Author = {C.-P. Lin and J.-P. Huang and C.-S. Wu and C.-Y. Hsu and S.-M. Chaw},
Journal = {Genome Biol Evol},
Year = {2010},
Pages = {504 - 517},
Volume = {2},
Abstract = {New classification},
Doi = {10.1093/gbe/evq036},
File = {lin2010_pinaceae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20651328}
}
@Article{Lin2012,
Title = {{Distribution patterns and phylogeny of marine stramenopiles (MAST) in the North Pacific Ocean.}},
Author = {Y.-C. Lin and T. Campbell and C.-C. Chung and G.-C. Gong and K.-P. Chiang and A. Z. Worden},
Journal = {Applied and environmental microbiology},
Year = {2012},
Abstract = {9 || Bicos || 6 + Labyr || 8, 11, 7, 4 || 12, 3 incl. Solenicola || 2 || Oo etc. || 1 || Bolido, Bacill || Dictyoch || others},
Doi = {10.1128/AEM.06952-11},
File = {lin2012_mast.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22344659}
}
@Article{Lindberg2009,
Title = {{Monoplacophorans and the Origin and Relationships of Mollusks}},
Author = {D. R. Lindberg},
Journal = {Evo. Edu. Outreach},
Year = {In press},
Abstract = {Review},
Doi = {10.1007/s12052-009-0125-4},
File = {lindberg2009_monoplac.pdf}
}
@Article{Linton1999,
Title = {{A Molecular Study of Euglenoid Phylogeny using Small Subunit rDNA}},
Author = {E. W. Linton and D. Hittner and C. Lewandowski and T. Auld and R. E. Triemer},
Journal = {J. Euk. Microbiol.},
Year = {1999},
Number = {2},
Pages = {217--223},
Volume = {46}
}
@Article{Lipscomb1982,
Title = {{Stephanopogon, a Phylogenetically Important ``Ciliate'', Shown by Ultrastructural Studies to Be a Flagellate}},
Author = {D. L. Lipscomb and J. O. Corliss},
Journal = {Science},
Year = {1982},
Number = {4530},
Pages = {303--304},
Volume = {215}
}
@Article{Lipscomb1998,
Title = {{Support, ribosomal sequences and phylogeny of the eukaryotes}},
Author = {D. L. Lipscomb and J. S. Farris and M. Kallersjo and A. Tehler},
Journal = {Cladistics},
Year = {1998},
Pages = {303--338},
Volume = {14}
}
@Article{Litaker1999,
Title = {{The phylogenetic relationship of \textit{Pfiesteria piscicida}, cryptoperidiniopsoid sp., \textit{Amyloodinoum ocellatum} and a pfiesteria-like dinoflagellate to other dinoflagellates and apicomplexans}},
Author = {R. W. Litaker and Patricia A. and A. Colorni and M. G. Levy and E. J. Noga},
Journal = {J. Phycol.},
Year = {1999},
Number = {6},
Pages = {1379--1389},
Volume = {35}
}
@InCollection{Littlewood2005,
Title = {{The Evolution of Parasitism in Flatworms}},
Author = {D. T. J. Littlewood},
Booktitle = {{Parasitic Flatworms: Mol. Biol., Biochemistry, Immunology and Physiology}},
Publisher = {CABI},
Year = {2005},
Address = {Wallingford, UK},
Editor = {A. G. Maule and N. J. Marks},
Pages = {1--36},
File = {littlewood_in_maule2005_paras_flatworms.pdf}
}
@Article{Littlewood1999a,
Title = {{Phylogeny of the Platyhelminthes and the evolution of parasitism}},
Author = {D. T. J. Littlewood and K. Rohde and R. A. Bray and E. A. Herniou},
Journal = {Mol. Phyl. Evol.},
Year = {1999},
Number = {1--2},
Pages = {257--287},
Volume = {68},
Doi = {10.1111/j.1095-8312.1999.tb01169.x}
}
@Article{Littlewood1999,
Title = {{The interrelationships of all major groups of Platyhelminthes: phylogenetic evidence from morphology and molecules}},
Author = {D. T. T. Littlewood and K. Rohde and K. A. Clough},
Journal = {Biol. J. Linn. Soc.},
Year = {1999},
Number = {1},
Pages = {75--114},
Volume = {66}
}
@Article{Liu1999,
Title = {{Phylogenetic assessment of molecular and morphological data for Eutherian mammals}},
Author = {Fu-Guo Robert Liu and Michael M. Miyamoto},
Journal = {Syst. Biol.},
Year = {1999},
Number = {1},
Pages = {54--64},
Volume = {48}
}
@Article{Liu2010,
Title = {{A time line of the environmental genetics of the haptophytes}},
Author = {H. Liu and S. Aris-Brosou and I. Probert and C. de Vargas},
Journal = {Mol. Biol. Evol.},
Year = {2010},
Number = {1},
Pages = {161 - 176},
Volume = {27},
Abstract = {Pavlovales sister},
Doi = {10.1093/molbev/msp222},
File = {liu2009_haptophytes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19762334}
}
@Article{Liu2011,
Title = {{An armoured Cambrian lobopodian from China with arthropod-like appendages}},
Author = {J. Liu and M. Steiner and J. A. Dunlop and H. Keupp and D. Shu and Q. Ou and J. Han and Z. Zhang and X. Zhang},
Journal = {Nature},
Year = {2011},
Pages = {526-530},
Volume = {470},
Abstract = {As stated},
Doi = {10.1038/nature09704},
File = {liu2011_diania_cactiformis.pdf},
ISSN = {0028-0836}
}
@Article{Liu2018,
Title = {{Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages.}},
Author = {X. Liu and M. Li and C. J. Castelle and A. J. Probst and Z. Zhou and J. Pan and Y. Liu and J. F. Banfield and J.-D. Gu},
Journal = {Microbiome},
Year = {2018},
Number = {1},
Pages = {102},
Volume = {6},
Doi = {10.1186/s40168-018-0488-2},
File = {liu2018_woesearchaeota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19897353}
}
@Article{Liu2015,
Title = {{Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses}},
Author = {X.-Z. Liu and Q.-M. Wang and B. Theelen and M. Groenewald and F.-Y. Bai and T. Boekhout},
Journal = {STUDIES IN MYCOLOGY},
Year = {2015},
Abstract = {As stated},
Doi = {10.1016/j.simyco.2015.08.001.},
File = {liu2015_tremellomycetes.pdf},
ISBN = {978-3-87429-425-6},
Url = {www.studiesinmycology.org}
}
@Article{Liu2014,
Title = {{Mitochondrial phylogenomics of early land plants: Mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias.}},
Author = {Y. Liu and C. J. Cox and W. Wang and B. Goffinet},
Journal = {Syst. Biol.},
Year = {2014},
Number = {6},
Pages = {862--878},
Volume = {63},
Abstract = {Hepaticae might not be sister},
Doi = {10.1093/sysbio/syu049},
File = {liu2014_mt_genomes_early_land_plants.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25070972}
}
@Article{Liu2008,
Title = {{Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts}},
Author = {Y. Liu and J. W. Leigh and H. Brinkmann and M. T. Cushion and N. Rodriguez-Ezpeleta and H. Philippe and B. F. Lang},
Journal = {Mol. Biol. Evol.},
Year = {2009},
Number = {1},
Pages = {27--34},
Volume = {26},
Abstract = {As stated (but Neolecta has not been analyzed)},
Doi = {10.1093/molbev/msn221},
File = {liu2008.pdf}
}
@Article{Liu2021,
Title = {{Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes}},
Author = {Y. Liu and K. S. Makarova and W.-C. Huang and Y. I. Wolf and A. Nikolskaya and X. Zhang and M. Cai and C.-J. Zhang and W. Xu and Z. Luo and L. Cheng and E. V. Koonin and M. Li},
Journal = {Nature},
Year = {2021},
Abstract = {(1) Wukongarchaeota [Wukongarchaeum] || (2) Former Heimdallarchaeota clade: (Hodarchaeota [Hodarchaeum] || Gerdarchaeota || Kariarchaeota [Kariarchaeum] + Heimdallarchaeota) || (3) Borrarchaeota [Borrarchaeum] || (Helarchaeota + Lokiarchaeota || Baldrarchaeota + Odinarchaeota || Thorarchaeota + Hermodarchaeota [Hermodarchaeum])},
Doi = {10.1101/2020.10.19.343400;},
File = {liu2021_asgard_archaea.pdf}
}
@Article{Liu2009,
Title = {{Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support}},
Author = {Y. Liu and E. T. Steenkamp and H. Brinkmann and L. Forget and H. Philippe and B. F. Lang},
Journal = {BMC Evol. Biol.},
Year = {2009},
Pages = {272},
Volume = {9},
Abstract = {(Malawimonadozoa ||| Excavata + Panplantae), Amoebozoa, Holozoa + Holomycota (Nuclearia || others (but Rozella absent))},
Doi = {10.1186/1471-2148-9-272},
File = {liu2009_phylogenomic_fungi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19939264}
}
@Article{Liu2006,
Title = {{Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes}},
Author = {Y. J. Liu and M. C. Hodson and B. D. Hall},
Journal = {BMC Evol. Biol.},
Year = {2006},
Pages = {1--13},
Volume = {2006},
Abstract = {No Olpi, Rozell; Zygo monophyl. and incl. Glomus (!)},
File = {liu2006.pdf}
}
@Article{Liu1999a,
Title = {{Phylogenetic Relationships Among Ascomycetes: Evidence from an RNA Polymerse II Subunit}},
Author = {Y. J. Liu and S. Whelen and B. D. HallD. Of Botany and U. Of Washington},
Journal = {Mol. Biol. Evol.},
Year = {1999},
Number = {12},
Pages = {1799--1808},
Volume = {16}
}
@Article{Livanov1970,
Title = {About origin of Metazoa},
Author = {N. A. Livanov},
Journal = {Zool. Zhurn.},
Year = {1970},
Note = {(In Russian)},
Number = {4},
Pages = {15},
Volume = {49},
Abstract = {evoljucija, Metazoa}
}
@Article{Livanov1963,
Title = {Foronids, bryozoans and brachiopods},
Author = {N. A. Livanov},
Journal = {Trudy Kazanskogo Universiteta},
Year = {1963},
Note = {(In Russian)},
Number = {11},
Pages = {55--81},
Volume = {66},
Abstract = {sistematika, Tentaculata}
}
@Article{Lloyd2018,
Title = {{Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes.}},
Author = {K. G. Lloyd and A. D. Steen and J. Ladau and J. Yin and L. Crosby},
Journal = {mSystems},
Year = {2018},
Number = {5},
Volume = {3},
Doi = {10.1128/mSystems.00055-18},
File = {lloyd2018_uncultivable_bact_dominate.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10543821}
}
@Article{Loesel2010,
Title = {{The mushroom bodies~--- prominent brain centres of arthropods and annelids with enigmatic evolutionary origin}},
Author = {R. Loesel and C. M. Heuer},
Journal = {Acta Zoologica},
Year = {2010},
Pages = {29--34},
Volume = {91},
Abstract = {Cannot resolve if it is a synapomorphy of Articulata},
Doi = {10.1111/j.1463-6395.2009.00422.x},
File = {loesel2010_mushroom_bodies.pdf}
}
@Article{Logares2007,
Title = {{Extensive dinoflagellate phylogenies indicate infrequent marine~---freshwater transitions}},
Author = {R. Logares and K. Shalchian-Tabrizi and A. Boltovskoy and K. Rengefors},
Journal = {Mol. Phyl. Evol.},
Year = {2007},
Pages = {887--903},
Volume = {45},
Abstract = {SSU: Perkins || Syndi || Noctil || others (incl. Symbiod.)},
Doi = {10.1016/j.ympev.2007.08.005},
File = {logares2007.pdf}
}
@Article{Lohr2010,
Title = {{A Daphnia Parasite (Caullerya mesnili) Constitutes a New Member of the Ichthyosporea, a Group of Protists near the Animal-Fungi Divergence.}},
Author = {J. N. Lohr and C. Laforsch and H. Koerner and J. Wolinska},
Journal = {The Journal of eukaryotic microbiology},
Year = {2010},
Abstract = {Ichthyophonida},
Doi = {10.1111/j.1550-7408.2010.00479.x},
File = {lohr2010_caullerya.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20456000}
}
@Article{Long2020,
Title = {{Descent of Bacteria and Eukarya From an Archaeal Root of Life}},
Author = {X. Long and H. Xue and J. T.-F. Wong},
Journal = {Evolutionary Bioinformatics},
Year = {2020},
Abstract = {As stated},
Doi = {10.1177/1176934320908267},
File = {long2020_bacteria_eukarya_from_archaea.pdf}
}
@Article{Longet2004,
Title = {{Multigene Evidence for Close Evolutionary Relations between Gromia and Foraminifera}},
Author = {D. Longet and F. Burki and J. Flakowski and C. Berney and S. Polet and J. Fahrni and J. Pawlowski},
Journal = {Acta Protozool.},
Year = {2004},
Pages = {303--311},
Volume = {43},
Abstract = {Gromia || Foramin or (Gromia || Haplo || Forami) || Plasmodioph},
File = {longet2004.pdf}
}
@Article{Lonhienne2010,
Title = {{Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus.}},
Author = {T. G. A. Lonhienne and E. Sagulenko and R. I. Webb and K.-C. Lee and J. Franke and D. P. Devos and A. Nouwens and B. J. Carroll and J. A. Fuerst},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2010},
Number = {29},
Pages = {12883--12888},
Volume = {107},
Abstract = {As stated},
Doi = {10.1073/pnas.1001085107},
File = {lonhienne2010_gemmata_endocytosis.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20624972}
}
@Article{Lopez1999a,
Title = {{The Root of the Tree of Life in the Light of the Covarion Model}},
Author = {P. Lopez and P. Forterre and H. Philippe},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {496--508},
Volume = {49}
}
@Article{LopezGarcia2004,
Title = {{Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers}},
Author = {P. Lopez-Garcia and C. Brochier and D. Moreira and F. Rodriguez-Valera},
Journal = {Environ. Microbiol.},
Year = {2004},
Number = {1},
Pages = {19--34},
Volume = {6}
}
@Article{Lopez-Garcia2002,
Title = {{Toward the monophyly of Haeckel's Radiolaria: 18S rRNA enviromental data support the sisterhood ofg Polycystinea and Radiolaria}},
Author = {P. Lopez-Garcia and F. Rodriges-Valera and D. Moreira},
Journal = {Mol. Biol. Evol.},
Year = {2002},
Pages = {118--121},
Volume = {19}
}
@Article{Lotman2000,
Title = {{Morphological Observations on the Life Cycle of \textit{Dermocystidium cyprini} Eervinka and Lom}},
Author = {K. Lotman and M. Pekkarinen and J. Kasesalu},
Journal = {Acta Protozool.},
Year = {2000},
Pages = {125--134},
Volume = {39}
}
@Article{Lovisetto2011,
Title = {{Molecular analyses of MADS-box genes trace back to Gymnosperms the invention of fleshy fruits}},
Author = {A. Lovisetto and F. Guzzo and A. Tadiello and K. Toffali and A. Favretto and G. Casadoro},
Journal = {Molecular Biology and Evolution},
Year = {2011},
Abstract = {This finding indicates that the main molecular networks operating in the development of fleshy fruits have independently appeared in distantly related Gymnosperm taxa},
File = {lovisetto2011_gymn_fleshy.pdf}
}
@Article{Lowe2008,
Title = {{Molecular genetic insights into deuterostome evolution from the direct-developing hemichordate \textit{Saccoglossus kowalevskii}}},
Author = {C. J. Lowe},
Journal = {Phil. Trans. R. Soc. B},
Year = {2008},
Number = {1496},
Pages = {1569--1578},
Volume = {363},
Abstract = {Inversion of Chordata body plan supported},
Doi = {10.1098/rstb.2007.2247},
File = {lowe2008.pdf}
}
@Article{LozanoFernandez2019,
Title = {{Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling.}},
Author = {J. Lozano-Fernandez and M. Giacomelli and J. F. Fleming and A. Chen and J. Vinther and P. F. Thomsen and H. Glenner and F. Palero and D. A. Legg and T. M. Iliffe and D. Pisani and J. Olesen},
Journal = {Genome biology and evolution},
Year = {2019},
Number = {8},
Pages = {2055 - 2070},
Volume = {11},
Abstract = {Robust Oligostraca incl. Ostracoda; others like in current synat},
Doi = {10.1093/gbe/evz097},
File = {lozano-fernandez_2019_pancrustacea.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31270537}
}
@Article{Lu2015,
Title = {{Chloroplast phylogenomics resolves key relationships in ferns}},
Author = {J.-M. Lu and N. Zhang and X.-Y. Du and J. Wen and D.-Z. Li},
Journal = {Journal of Systematics and Evolution},
Year = {2015},
Abstract = {Equisetum || Oph + Psil || Maratt || other ferns},
Doi = {10.1111/jse.12180},
File = {lu1025_cp_phylogenomics_ferns.pdf},
Url = {www.jse.ac.cn}
}
@Article{Lu2017,
Title = {{The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution.}},
Author = {T.-M. Lu and M. Kanda and N. Satoh and H. Furuya},
Journal = {Zoological Lett},
Year = {2017},
Pages = {6},
Volume = {3},
Abstract = {(Orth + Dicy) || Gastrotricha !! || Plath ; Gnatho || Microgn + Synderm},
Doi = {10.1186/s40851-017-0068-5},
File = {lu2017_mesozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10548100}
}
@Article{Lu2014,
Title = {{Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes.}},
Author = {Y. Lu and J.-H. Ran and D.-M. Guo and Z.-Y. Yang and X.-Q. Wang},
Journal = {PLoS ONE},
Year = {2014},
Number = {9},
Pages = {e107679},
Volume = {9},
Abstract = {Cycads basal; Gnetales unresolved},
Doi = {10.1371/journal.pone.0107679},
File = {lu2014_gymnosperms.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20601411}
}
@Article{Luan2005,
Title = {{The Phylogenetic Positions of Three Basal-Hexapod Groups (Protura, Diplura, and Collembola) Based on Ribosomal RNA Gene Sequences}},
Author = {Y.-x. Luan and J. M. Mallatt and R.-d. Xie and Y.-m. Yang and W.-y. Yin},
Journal = {Mol. Biol. Evol.},
Year = {2005},
Number = {7},
Pages = {1579--1592},
Volume = {22},
Abstract = {(Collembola (Protura+Diplura)) || other Hexa},
File = {luan2005.pdf}
}
@Article{Ludwig2006,
Title = {{Occurrence of hydrogenases in cyanobacteria and anoxygenic photosynthetic bacteria: implications for the phylogenetic origin of cyanobacterial and algal hydrogenases.}},
Author = {M. Ludwig and R. Schulz-Friedrich and J. Appel},
Journal = {J. Mol. Evol.},
Year = {2006},
Number = {6},
Pages = {758--768},
Volume = {63},
Abstract = {Cyano ~ Chloroflexi},
File = {ludwig2006.pdf}
}
@Unpublished{Ludwig2008b,
Title = {{Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes}},
Author = {W. Ludwig and J. Euzeby and W. B. Whitman},
Note = {http://bergeys.org/outlines.html},
Year = {2008},
Abstract = {Planctomycetes>Planctomycea, Chlamydiae, Spirochaetes>Spirochaetes, Fibrobacteres>Fibrobacteria, Acidobacteria, Bacteroidetes>Bacteroidia-Flavobacteria-Sphingobacteria-Cytophagia, Fusobacteria, Verrucomicrobia>Verrucomicrobiae-Opitutae-Spartobacteria, Dictyoglomi>Dictyoglomia, Gemmatimonadetes, Lentisphaerae>Lentisphaeria},
File = {ludwig2008_bergeys_vol_4_outline.pdf},
Url = {http://bergeys.org/outlines.html},
Volume = {4}
}
@InCollection{Ludwig2001,
Title = {{Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systematics}},
Author = {W. Ludwig and H.-P. Klenk},
Booktitle = {Bergey's Manual of Systematic Bacteriology},
Publisher = {Springer-Verlag},
Year = {2001},
Address = {Berlin},
Editor = {D. R. Boone and R. W. C. Eds},
Pages = {49--65}
}
@Unpublished{Ludwig2008a,
Title = {{Revised Road Map to the Phylum Firmicutes}},
Author = {W. Ludwig and K.-H. Schleifer and W. B. Whitman},
Note = {http://bergeys.org/outlines.html},
Year = {2008},
Abstract = {Bacilli, Clostridia (incl. Sulfobacillus-Thermaerobacter and Symbiobacterium i.s., Halanaerobiales, Thermoanaerobacterales), Erysipelotrichi},
File = {ludwig2008_bergeys_vol_3_outline.pdf},
Url = {http://bergeys.org/outlines.html}
}
@Article{Luecking2009,
Title = {{Fungi evolved right on track}},
Author = {R. Luecking and S. Huhndorf and D. H. Pfister and E. R. Plata and H. T. Lumbsch},
Journal = {Mycologia},
Year = {In press},
Abstract = {Origin time ~ land plants},
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Volume = {269},
Abstract = {Ctenophora is a sister group to the clade of Cnidaria1Bilateria. Primary bilaterians are supposed to be complicated organisms having coelom, segmentation, and primordial limbs},
Doi = {10.1002/jmor.10683},
File = {malakhov2008a.txt}
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Year = {2008},
Number = {12},
Pages = {1456--1500},
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Abstract = {The ventral intestinal groove of enteropneusts is the true homologue of the ``chorda dorsalis.''},
Doi = {10.1002/jmor.10683},
File = {malakhov2008c.txt}
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Year = {2008},
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Pages = {1456--1500},
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Abstract = {brachiopods and phoronids can be regarded as true metameric organisms. It is likely that bryozoans lost the metamery as a result of miniaturiza- tion},
Doi = {10.1002/jmor.10683},
File = {malakhov2008b.txt}
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Volume = {80},
Abstract = {(Lophophorata + Trochozoa), Deuterostomia, Ecdysozoa},
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File = {malakhov2010_bilateria.pdf}
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Volume = {30},
Abstract = {From Cnidaria},
File = {malakhov2004.djvu}
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Address = {Kiev},
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Year = {2019},
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Pages = {303--316},
Volume = {50},
Abstract = {Ctenophora first},
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Title = {{Evolutionary relationships of eukaryotes inferred with the largest subunit of RNA polymerase II}},
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Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {Initial results from Bayesian analysis support the placement of the Apusozoa (Amastigamonas and Ancyromonas) as a sister to Opisthokonts, other results are unclear},
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Year = {2008},
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Year = {In press},
Abstract = {Porif || Cten || Plac || Cnid || Acoel || Deuter (Tunic. separated) || Lophotr (mix!, Rotif basal, Symbion + Barentsia) + Ecdys (Sagitta + Peripatus?!, Hexap + Branch)},
Doi = {10.1016/j.ympev.2009.09.028},
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Year = {2012},
Number = {3},
Pages = {603--617},
Volume = {64},
Abstract = {Slightly messy. Porif + Cten || Platyz + Cnid || Myxozoa || Bilateria; Symbion + Entoprocta; Scalidophora; Mystacocarida ~ basal crust.},
Doi = {10.1016/j.ympev.2012.05.016},
File = {mallatt2012_rrna_animalia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22641172}
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@Article{Mallatt2006,
Title = {{Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch}},
Author = {J. Mallatt and G. Giribet},
Journal = {Mol. Phyl. Evol.},
Year = {2006},
Number = {2006},
Pages = {772--794},
Volume = {40},
Abstract = {Scalidophora+Nematoidea || Tardigrada + Onychophora || Chelic (inc. Xi)+Pycn||Myriap; Ostr+Branchu+Pent || Cirr+Malac || Branchiopoda || Hexapoda},
File = {mallatt2006.pdf}
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@Article{Mallatt2013,
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Year = {2013},
Abstract = {Pikaia, not Amphioxus, specialized},
Doi = {10.1002/jez.b.22500},
File = {mallatt2013_pikaia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23606659}
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@Article{Mallatt2007,
Title = {{Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star}},
Author = {J. Mallatt and C. J. Winchell},
Journal = {Mol. Phyl. Evol.},
Year = {2007},
Pages = {1005--1022},
Volume = {43},
Abstract = {Chondrichthyes+Actinoprerygia || Tetrapoda+Dipnoi, Latimeria unstable; Tunicata sister to all Deuter},
File = {mallatt2007.pdf}
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@Article{Mallatt2002,
Title = {{Testing the New Animal Phylogeny: First Use of Combined Large-Subunit and Small-Subunit rRNA Gene Sequences to Classify the Protostomes}},
Author = {Jon Mallatt and Christopher J. Winchell},
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Year = {2002},
Pages = {289--301},
Volume = {19}
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@Article{Mallatt2004,
Title = {{Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin}},
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Year = {2004},
Pages = {178--191},
Volume = {31},
Abstract = {Priap || Nematoida || Tard.+Onych. || Pycn+Chel+Myriap || Pancrust., incl. Hexapoda},
File = {mallatt2004.pdf}
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File = {mamkaev2008.txt}
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@Article{Manuel2003,
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Year = {2009},
Abstract = {Nothing special},
Doi = {10.1111/j.1462-2920.2009.02023.x},
File = {marande2009_euk_div_envir.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19678831}
}
@Article{MarcetHouben2009,
Title = {{The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome}},
Author = {M. Marcet-Houben and T. Gabaldon},
Journal = {PLoS ONE},
Year = {2009},
Number = {2},
Pages = {e4357},
Volume = {4},
Abstract = {"Normal" tree},
Doi = {10.1371/journal.pone.0004357},
File = {marcet-houben2009_fungal_tol.pdf}
}
@Article{Marchandin2010,
Title = {{Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin.}},
Author = {H. Marchandin and A. Damay and L. Roudi{\`e}re and C. Teyssier and I. Zorgniotti and H. Dechaud and H. Jean-Pierre and E. Jumas-Bilak},
Journal = {Res. Microbiol.},
Year = {2010},
Abstract = {As stated},
Doi = {10.1016/j.resmic.2009.12.008},
File = {marchandin2010_synergistites.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20079831}
}
@Article{Marchandin2009,
Title = {{Negativicoccus succinicivorans gen. Nov., Sp. Nov., Isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. Nov, and Acidaminococcaceae fam. Nov. In the bacterial phylum Firmicutes}},
Author = {H. Marchandin and C. Teyssier and J. Campos and H. Jean-Pierre and F. Roger and B. Gay and J. P. Carlier and E. Jumas-Bilak},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {In press},
Abstract = {Thermolitho || Clostr + Symbiobact || Negativicutes (incl. Selenomonas) || Bacilli + Erysipelotrichi },
Doi = {10.1099/ijs.0.013102-0},
File = {marchandin2009_negativicoccus.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19667386}
}
@Article{Marcy2007,
Title = {{Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth}},
Author = {Y. Marcy and C. Ouverney and E. M. Bik and T. Losekann and N. Ivanova and H. G. Martin and E. Szeto and D. Platt and P. Hugenholtz and D. A. Relman and S. R. Quake},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2007},
Number = {29},
Pages = {11889--11894},
Volume = {104},
Abstract = {TM7 on 16S ~ Chlorof and OP11 (sic!), BLAST show maximal hits with Bacilli/Clostridia/Fusobacteria; genes and microscopy show Gram-positiveness},
Doi = {10.1073/pnas.0704662104},
File = {marcy2007_tm7.pdf}
}
@Article{Mares2013,
Title = {{The Primitive Thylakoid-Less Cyanobacterium Gloeobacter Is a Common Rock-Dwelling Organism.}},
Author = {J. Mare{\v{s}} and P. Hrouzek and R. Kaňa and S. Ventura and O. Struneck{\'y} and J. Kom{\'a}rek},
Journal = {PLoS ONE},
Year = {2013},
Number = {6},
Pages = {e66323},
Volume = {8},
Abstract = {Gloeobacter violaceus = Aphanothece caldariorum},
Doi = {10.1371/journal.pone.0066323},
File = {mares2013_gloeobacter_is_aphanothece.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23823729}
}
@Article{Margulis1996,
Title = {{Archaeal-eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life}},
Author = {L. Margulis},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1996},
Number = {3},
Pages = {1071--1076},
Volume = {93}
}
@Book{Margelis1983,
Title = {The role of symbiosis in cell evolution},
Author = {L. Margulis},
Publisher = {Mir},
Year = {1983},
Address = {Moscow},
Note = {(In Russian)},
Abstract = {evoljucija, sistematika, obschaja sistematika, Protista, Bacteria},
Pages = {352}
}
@Book{Margulis1998,
Title = {{Five Kingdoms: an illustrated guide to the Phyla of life on earth}},
Author = {L. Margulis and K. V. Schwartz},
Publisher = {Freeman},
Year = {1998},
Address = {New York},
Edition = {3},
ISBN = {0-7167-3027-8},
Pages = {520}
}
@Article{Margulis1978,
Title = {{Protist classification and the kingdoms of organisms}},
Author = {L. Margulis and R. H. Whittaker},
Journal = {BioSystems},
Year = {1978},
Number = {1},
Pages = {3--18},
Volume = {10}
}
@Article{Marin2011,
Title = {{Nested in the Chlorellales or Independent Class? Phylogeny and Classification of the Pedinophyceae (Viridiplantae) Revealed by Molecular Phylogenetic Analyses of Complete Nuclear and Plastid-encoded rRNA Operons.}},
Author = {B. Marin},
Journal = {Protist},
Year = {2011},
Abstract = {Pyramimonadales + Mamiellophyceae || Prasinod + Prasinococc || Nephroselm || Pycnococcus etc. || Picosystis || Pedinophyceae incl. Marsupiomonas, Pedinomonas, Chlorochytridion, Resultamonas || Chlorodendrophyceae incl. Tetraselmis, Scherffelia || Treb || Chlor || Ulv},
Doi = {10.1016/j.protis.2011.11.004},
File = {marin2011_pedinophyceae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22192529}
}
@Article{Marin2009,
Title = {{Molecular Phylogeny and Classification of the Mamiellophyceae class. Nov. (Chlorophyta) based on Sequence Comparisons of the Nuclear- and Plastid-encoded rRNA Operons.}},
Author = {B. Marin and M. Melkonian},
Journal = {Protist},
Year = {2009},
Abstract = {3 basal: I/Pyraminomonadales, II/Mamiel, VI/Prasinococc-Prasinoderma; 3 intermediate III/Nephroselmidoph, V/Pycnococcac-Pseudoscourfieldia, VII/Picocystis; and IV/Chlorodendrophyceae},
Doi = {10.1016/j.protis.2009.10.002},
File = {marin2009_mamiellophyceae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20005168}
}
@Article{Marin1999,
Title = {{Mesostigmatophyceae, a New Class of Streptophyte Green Algae Revealed by SSU rRNA Sequence Comparison}},
Author = {B. Marin and M. Melkonian},
Journal = {Protist},
Year = {1999},
Pages = {399--417},
Volume = {150}
}
@Article{Marin2007,
Title = {{The ancestor of the \textit{Paulinella chromatophore} obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like gamma-proteobacterium}},
Author = {B. Marin and E. C. Nowack and G. Glockner and M. Melkonian},
Journal = {BMC Evol. Biol.},
Year = {2007},
Number = {85},
Pages = {1--24},
Volume = {2007},
Abstract = {Paulinella chromatophores belomg to alpha-cyanobacteria (Chroobacteria) whereas others belong to Hormogoneae},
File = {marin2007.pdf}
}
@Article{Marin2005,
Title = {{A Plastid in the Making: Evidence for a Second Primary Endosymbiosis}},
Author = {B. Marin and E. C. M. Nowack and M. Melkonian},
Journal = {Protist},
Year = {2005},
Pages = {425--432},
Volume = {156},
Abstract = {Paulinella have cyanelle-like symbiont},
File = {marin2005.pdf}
}
@Article{Hanson2016,
Title = {{The timetree of prokaryotes: New insights into their evolution and speciation}},
Author = {J. Marin and F.U. Battistuzzi and A.C. Brown and S.B. Hedges},
Journal = {Mol. Biol. Evol.},
Year = {2016},
Abstract = {Arch first (4200), then Thermot, Fuso, Aquific, then (3000) Hydrobacteria, then (2900) Terrabacteria},
File = {marin2016_prok_timetree.pdf}
}
@Article{Mariotti2016,
Title = {{Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.}},
Author = {M. Mariotti and A. V. Lobanov and B. Manta and D. Santesmasses and A. Bofill and R. Guig{\'o} and T. Gabald{\'o}n and V. N. Gladyshev},
Journal = {Mol. Biol. Evol.},
Year = {2016},
Number = {9},
Pages = {2441 - 2453},
Volume = {33},
Abstract = {As stated},
Doi = {10.1093/molbev/msw122},
File = {mariotti2016_lokiarchaeota_selenocysteine.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27413050}
}
@InProceedings{Markevich1993,
Title = {The evolution of rotifers and a ptoblem of their pacement in the Metazoa classification},
Author = {G. I. Markevich},
Booktitle = {Institut biologii vnutrennih vod; Trudy},
Year = {1993},
Note = {(In Russian)},
Pages = {3--52},
Volume = {68 (71)},
Abstract = {sistematika, Rotifera, Animalia},
Annote = {Blizki k Monogenea (est modificirovannye v schetinki cerkalnye krjuchja)}
}
@Article{Marletaz2019,
Title = {{A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans.}},
Author = {F. Marl{\'e}taz and K. T. C. A. Peijnenburg and T. Goto and N. Satoh and D. S. Rokhsar},
Journal = {Curr. Biol.},
Year = {2019},
Number = {2},
Pages = {312 - 318 - e3},
Volume = {29},
Abstract = {Gnatifera: Gnathost. || Chaetognatha || Rotif + Micrognath; Mollusca + Entoprocta; Gastr + Tentaculata; then Annel, Platyh, Nemert => Chaetogn close to Platyzoa},
Doi = {10.1016/j.cub.2018.11.042},
File = {marletaz2019_chetognatha_gnatifera.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30639106}
}
@Article{Marletaz2008,
Title = {{Chaetognath transcriptome reveals ancestral and unique features among bilaterians}},
Author = {F. Marletaz and A. Gilles and X. Caubit and Y. Perez and C. Dossat and S. Samain and G. Gyapay and P. Wincker and Y. L. Parco},
Journal = {Genome Biol.},
Year = {2008},
Pages = {R94},
Volume = {9},
Abstract = {Chaeto || Lopho + Ecdyso},
Doi = {10.1186/gb-2008-9-6-r94},
File = {marletaz2008.pdf}
}
@Article{Marletaz2008b,
Title = {{Careful with understudied phyla: the case of chaetognath}},
Author = {F. Marletaz and P. Y. Le},
Journal = {BMC Evol. Biol.},
Year = {2008},
Number = {1},
Pages = {251},
Volume = {8},
Abstract = {Chaetognatha robustly supported as sister to Ecdys + Lophotr},
Doi = {10.1186/1471-2148-8-251},
File = {marletaz2008.pdf}
}
@Article{Marotta2008,
Title = {{Combined-data phylogenetics and character evolution of Clitellata (Annelida) using 18S rDNA and morphology}},
Author = {R. Marotta and M. Ferraguti and C. Erseus and L. M. Gustavsson},
Journal = {Zoological Journal of the Linnean Society},
Year = {2008},
Pages = {1--26},
Volume = {154},
Abstract = {Hirudinea > other Oligo},
File = {marotta2008.pdf}
}
@Article{Marshall2017,
Title = {{The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins.}},
Author = {I. P. G. Marshall and P. Starnawski and C. Cupit and E. F. C{\'a}ceres and T. J. G. Ettema and A. Schramm and K. U. Kjeldsen},
Journal = {Environ Microbiol Rep},
Year = {2017},
Abstract = {FCB Group: Fibrobacteres, Elusimicrobium, Cloacimonas, Gemmatimonadetes | Calditrichaeota | Bacteroidetes etc.},
Doi = {10.1111/1758-2229.12544},
File = {marshall2017_calditrichaeota_ecol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28488795}
}
@Article{Marshall2010,
Title = {{Facing Unknowns: Living Cultures (Pirum gemmata gen. Nov., Sp. Nov., And Abeoforma whisleri, gen. Nov., Sp. Nov.) From Invertebrate Digestive Tracts Represent an Undescribed Clade within the Unicellular Opisthokont Lineage Ichthyosporea (Mesomycetozoea).}},
Author = {W. L. Marshall and M. L. Berbee},
Journal = {Protist},
Year = {2010},
Abstract = {New Ichthyophonida; Capsasp sister to Mesomyc; Nuclearia suster to Fungi, Corallochy to Choanofl; Ministeria to animals},
Doi = {10.1016/j.protis.2010.06.002},
File = {marshall2010_ichthyosporea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20708961}
}
@Conference{Marshall2008b,
Title = {{Secret sex in cryptic species: Population level analysis of Ichthyosporeans (Mesomycetozoa, Opisthokonta)}},
Author = {W. L. Marshall and M. L. Berbee},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
File = {marshall2008.txt}
}
@Article{Marshall2008a,
Title = {{Multiple Isolations of a Culturable, Motile Ichthyosporean (Mesomycetozoa, Opisthokonta), \textit{Creolimax fragrantissima} n. gen., n. sp., from Marine Invertebrate Digestive Tracts}},
Author = {W. L. Marshall and G. Celio and D. J. McLaughlin and M. L. Berbee},
Journal = {Protist},
Year = {2008},
Number = {3},
Pages = {415--433},
Volume = {159},
Abstract = {Ichthyosporea: Ichthyophonida + Dermocystida},
Doi = {10.1016/j.protis.2008.03.003},
File = {marshall2008.pdf}
}
@Article{MartinDuran2015,
Title = {{The study of Priapulus caudatus reveals conserved molecular patterning underlying different gut morphogenesis in the Ecdysozoa.}},
Author = {J. M. Mart{\'i}n-Dur{\'a}n and A. Hejnol},
Journal = {BMC Biol.},
Year = {2015},
Number = {1},
Pages = {29},
Volume = {13},
Abstract = {midgut formed by a single endodermal population of vegetal cells, a ventral mouth, and the blastoporal origin of the anus are ancestral features in the Ecdysozoa},
Doi = {10.1186/s12915-015-0139-z},
File = {martin-duran2015_priapulus_ecdysozoa.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10711574}
}
@Article{MartinDuran2018,
Title = {{Convergent evolution of bilaterian nerve cords.}},
Author = {J. M. Mart{\'i}n-Dur{\'a}n and K. Pang and A. B{\o}rve and H. S. L{\^e} and A. Furu and J. T. Cannon and U. Jondelius and A. Hejnol},
Journal = {Nature},
Year = {2018},
Number = {7686},
Pages = {45 - 50},
Volume = {553},
Abstract = {... Our findings restrict the use of molecular patterns to explain nervous system evolution, and suggest that the similarities in dorsoventral patterning and trunk neuroanatomies evolved independently in Bilateria ...},
Doi = {10.1038/nature25030},
File = {martin-duran2017_evol_bilat_nerv_cord.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20017953}
}
@Article{Martel2008,
Title = {{Purported nanobacteria in human blood as calcium carbonate nanoparticles}},
Author = {J. Martel and J. D.-E. Young},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {14},
Pages = {5549--5554},
Volume = {105},
Abstract = {No nanobacteria},
File = {martel2008_no_nanobacteria.pdf},
Url = {www.pnas.org}
}
@Article{Martens2007,
Title = {{Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species}},
Author = {C. Martens and K. Vandepoele and Y. Van de Peer},
Journal = {Proc. Natl. Acad. Sci. USAs},
Year = {2007},
Number = {9},
Pages = {3427--3432},
Volume = {105},
Abstract = {As stated},
File = {martens2008.pdf}
}
@Article{Martijn2013,
Title = {{From archaeon to eukaryote: The evolutionary dark ages of the eukaryotic cell.}},
Author = {J. Martijn and T. J. G. Ettema},
Journal = {Biochem. Soc. Trans.},
Year = {2013},
Number = {1},
Pages = {451--457},
Volume = {41},
Abstract = {From archaeon to eukaryotic cell: PhAT (phagocytosing archaeon theory)},
Doi = {10.1042/BST20120292},
File = {martijn2013_leca.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23356327}
}
@Article{Martijn2020,
Title = {{Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition}},
Author = {J. Martijn and M. E. Sch{\"o}n and A. E. Lind and J. V. A. Spang and T. J. G. Ettema and T. A. Williams},
Journal = {Nature Communications},
Year = {2020},
Abstract = {Marine Group IV archaea (Hikarchaeia),
the closest known relatives of Haloarchaea...},
Doi = {10.1038/s41467-020-19200-2},
File = {martijn2020_hikarcheia_halob.pdf},
ISSN = {2041-1723}
}
@Article{Martin2001,
Title = {{An Updated Classification of the Recent Crustacea}},
Author = {J. W. Martin and G. E. Davis},
Journal = {Natural History Museum of Los Angeles County Science Series},
Year = {2001},
Pages = {1--123},
Volume = {39},
Abstract = {Brachiopoda, Remipedia, Cephalocarida, Maxillopoda (Thecostraca, Cirripedia, Tantulocarida, Brachiura, Pentastomida, Mystacocarida, Copepoda), Ostracoda, Malacostraca},
File = {martin2001.pdf}
}
@Article{Martin2000,
Title = {{Rapidly Evolving Lineages Impede the Resolution of Phylogenetic Relationships among Clitellata (Annelida)}},
Author = {P. Martin and I. Kaygorodova and D. Y. Sherbakov and E. Verheyen},
Journal = {Mol. Phyl. Evol.},
Year = {2000},
Number = {3},
Pages = {355--368},
Volume = {15}
}
@Article{Martin2006,
Title = {{A positive definition of prokaryotes}},
Author = {W. Martin and E. V. Koonin},
Journal = {Nature},
Year = {2006},
Pages = {868},
Volume = {441},
Abstract = {As stated},
File = {martin2006.pdf},
Keywords = {pr1}
}
@Article{MartinCereceda2009,
Title = {{Morphology, Ultrastructure, and Small Subunit rDNA Phylogeny of the Marine Heterotrophic Flagellate Goniomonas aff. Amphinema}},
Author = {M. Martin-Cereceda and E. C. Roberts and E. C. Wootton and E. Bonaccorso and P. Dyal and A. Guinea and D. Rogers and C. J. Wright and G. Novarino},
Journal = {The Journal of eukaryotic microbiology},
Year = {2009},
Abstract = {Second branch of cryptom.},
Doi = {10.1111/j.1550-7408.2009.00449.x},
File = {martin-cereceda2009_goniomonas.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20015186}
}
@Article{Martinez2019,
Title = {{Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. Nov., Ca. Cryosericaceae fam. Nov., Comprising the four species Cryosericum septentrionale gen. Nov. Sp. Nov., Ca. C. Hinesii sp. Nov., Ca. C. Odellii sp. Nov., Ca. C. Terrychapinii sp. Nov.}},
Author = {M. A. Martinez and B. J. Woodcroft and J. C. I. Espinoza and A. A. Zayed and C. M. Singleton and J. A. Boyd and Y.-F. Li and S. Purvine and H. Maughan and S. B. Hodgkins and D. Anderson and M. Sederholm and B. Temperton and B. Bolduc and S. R. Saleska and G. W. Tyson and V. I. Rich and S. R. Saleska and G. W. Tyson and V. I. Rich},
Journal = {Syst. Appl. Microbiol.},
Year = {2019},
Number = {1},
Pages = {54 - 66},
Volume = {42},
Abstract = {SMC Caldiserica = Cryosericota => incl.},
Doi = {10.1016/j.syapm.2018.12.003},
File = {martinez2019_cryosericota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30616913}
}
@Article{Martynov2013,
Title = {{Evolutionary history of Metazoa, ancestral status of the Bilateria clonal reproduction, and semicolonial origin of the Mollusca}},
Author = {A. V. Martynov},
Journal = {Zhurnal Obschei Biologii},
Year = {2013},
Pages = {201--240},
Abstract = {Colonial origin of Bilateria},
File = {martynov2013_evol_istor_mnogokl_moll.txt}
}
@Article{Maruyama2009,
Title = {{Cyanobacterial contribution to the genomes of the plastid-lacking protists}},
Author = {S. Maruyama and M. Matsuzaki and K. Misawa and H. Nozaki},
Journal = {BMC Evol. Biol.},
Year = {2009},
Number = {1},
Pages = {197},
Volume = {9},
Abstract = {Multiple contribution to bikonts (ancient endosymb.?)},
Doi = {10.1186/1471-2148-9-197},
File = {maruyama2009_cyanob_genes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19664294}
}
@Conference{Maruyama2008b,
Title = {{Cyanobacterial contribution to plastid lacking protist genome}},
Author = {S. Maruyama and M. Matsuzaki and K. Misawa and H. Nozaki},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Volume = {12},
Abstract = {bikonts, or Plantae sensu lato ("Super" Plant Kingdom)},
File = {maruyama2008.txt}
}
@Article{Maruyama2008a,
Title = {{Origins of a cyanobacterial 6-phosphogluconate dehydrogenase in plastid-lacking eukaryotes}},
Author = {S. Maruyama and K. Misawa and M. Iseki and M. Watanabe and H. Nozaki},
Journal = {BMC Evol. Biol.},
Year = {2008},
Number = {151},
Pages = {1--30},
Volume = {8},
Abstract = {Excavata + Rhod. || Chromalveol. + Glauco + Chloroph. -- the most parsimonous scenario},
Doi = {10.1186/1471-2148-8-151},
File = {maryama2008.pdf}
}
@Article{Maruyama2011,
Title = {{Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids}},
Author = {S. Maruyama and T. Suzaki and A. P. M. Weber and J. M. Archibald and H. Nozaki},
Journal = {BMC Evolutionary Biology},
Year = {2011},
Pages = {105},
Volume = {11},
Abstract = {From red algae},
Doi = {10.1186/1471-2148-11-105},
File = {maruyama2011_euglenoid_hgt.pdf},
Url = {http://www.biomedcentral.com/1471-2148/11/105}
}
@Article{Mashanov2009,
Title = {{The central nervous system of sea cucumbers (Echinodermata: Holothuroidea) shows positive immunostaining for a chordate glial secretion.}},
Author = {V. S. Mashanov and O. R. Zueva and T. Heinzeller and B. Aschauer and W. W. Naumann and J. M. Grondona and M. Cifuentes and J. E. Garcia-Arraras},
Journal = {Front. Zool.},
Year = {2009},
Number = {1},
Pages = {11},
Volume = {6},
Doi = {10.1186/1742-9994-6-11},
File = {mashanov2009_holot_chord.txt}
}
@Article{Maslakova2008,
Title = {{Larval Diversity and Evolution in Nemerteans (Phylum Nemertea)}},
Author = {S. Maslakova},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {Palaeone- mertean planuliform larvae, for example, turned out to be modified tro- chophores with a hidden prototroch},
Doi = {10.1002/jmor.10683},
File = {maslakova2008.txt}
}
@Article{Maslov1999,
Title = {{Phylogenetic Affinities of Diplonema within the Euglenozoa as Inferred from the SSU rRNA Gene and Partial COI Protein Sequences}},
Author = {D. A. Maslov and S. Yasuhira and L. Simpson},
Journal = {Protist},
Year = {1999},
Number = {1},
Pages = {33--42},
Volume = {150}
}
@Article{Massana2014,
Title = {{Exploring the uncultured microeukaryote majority in the oceans: Reevaluation of ribogroups within stramenopiles}},
Author = {R. Massana},
Journal = {Mar. Biol.},
Year = {2014},
Number = {4},
Pages = {854--866},
Volume = {8},
Abstract = {Olisthodiscus could be far from Rahidophyceae; most of MASTs are Sagenista},
Doi = {10.1038/ismej.2013.204},
File = {massana2014_masts.pdf},
ISSN = {1751-7362}
}
@Article{Massana2004,
Title = {{Phylogenetic and Ecological Analysis of Novel Marine Stramenopiles}},
Author = {R. Massana and J. Castresana and V. Balague and L. Guillou and K. Romari and A. Groisillier and K. Valentin and C. Pedros-Alio},
Journal = {Appl. Environ. Microbiol.},
Year = {2004},
Number = {6},
Pages = {3528--3534},
Volume = {70},
Abstract = {Placidia, Wobbia ~ Bicoec., "MAST" p.p. ~ Bicoecida},
File = {massana2004b.pdf}
}
@Article{Massana2008,
Title = {{Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate}},
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Journal = {Environ. Microbiol.},
Year = {2008},
Number = {5},
Pages = {1335--1343},
Volume = {10},
Abstract = {FBB25 ~ Perkinsids and/or basal dinoflegellates},
Doi = {10.1111/j.1462-2920.2007.01549.x},
File = {massana2008.pdf}
}
@Article{Massard2008,
Title = {{Global diversity of bryozoans (Bryozoa or Ectoprocta) in freshwater}},
Author = {J. A. Massard and G. Geimer},
Journal = {Hydrobiologia},
Year = {2008},
Pages = {93--99},
Volume = {595},
Abstract = {Phylactolaemata may be closer to Phor and Brach then two other classes},
Doi = {10.1007/s10750-007-9007-3},
File = {massard2008.pdf}
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@Article{Masta2008,
Title = {{Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses}},
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Journal = {Mol. Phyl. Evol.},
Year = {2009},
Number = {1},
Pages = {117--128},
Volume = {50},
Abstract = {Solfigida are basal, ~ Merostr.},
Doi = {10.1016/j.ympev.2008.10.010},
File = {masta2008.pdf}
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@Article{Masuzaki2010,
Title = {{Systematic position of the enigmatic liverwort Mizutania (Mizutaniaceae, Marchantiophyta) inferred from molecular phylogenetic analyses}},
Author = {H. Masuzaki and M. Shimamura and T. Furuki and H. Tsubota and T. Yamaguchi and H. M. A. Majid and H. Deguchi},
Journal = {Taxon},
Year = {2010},
Number = {2},
Pages = {448--458},
Volume = {59},
Abstract = {Reduction from leafy Jungermanniales to secondary thalloid},
File = {masuzaki2010_mizutania_liverworts.pdf}
}
@Article{Matheny2006,
Title = {{Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota}},
Author = {P. B. Matheny and J. A. Gossmann and P. Zalar and T. K. A. Kumar and D. S. Hibbett},
Journal = {Can. J. Bot.},
Year = {2006},
Number = {12},
Pages = {1794--1805},
Volume = {84},
Abstract = {Wall + Entorrh || other Basidio},
Doi = {10.1139/B06-128},
File = {matheny2006a.pdf}
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@Article{Mathews2009,
Title = {{Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data}},
Author = {S. Mathews},
Journal = {American Journal of Botany},
Year = {2009},
Number = {1},
Pages = {228--236},
Volume = {96},
Abstract = {wanted: morphology},
Doi = {10.3732/ajb.0800178},
File = {matthews2009.pdf}
}
@Article{Mathews2010,
Title = {{A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants.}},
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Journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.},
Year = {2010},
Number = {1539},
Pages = {383 - 395},
Volume = {365},
Abstract = {PHY: cycads sister to angiosp., Pinac+ Podoc. || Arauc || Gnetales || other conifers},
Doi = {10.1098/rstb.2009.0233},
File = {mathews2010_seed_plants_rooting.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20047866}
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@Article{Mathur2019,
Title = {{Multiple Independent Origins of Apicomplexan-Like Parasites.}},
Author = {V. Mathur and M. Kol{\'i}sko and E. Hehenberger and N. A. T. Irwin and B. S. Leander and {\'A}. Kristmundsson and M. A. Freeman and P. J. Keeling},
Journal = {Current biology : CB},
Year = {2019},
Number = {17},
Pages = {2936 - 2941 - e5},
Volume = {29},
Abstract = {Platyporeum || Chromerida incl. Piridium},
Doi = {10.1016/j.cub.2019.07.019},
File = {mathur2019_platyproteum_piridium_apicomon.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31422883}
}
@Article{Mathur2021,
Title = {{Phylogenomics identifies a new major subgroup of apicomplexans, Marosporida class. Nov., With extreme apicoplast genome reduction}},
Author = {V. Mathur and W. K. Kwong and F. Husnik and N. A. T. Irwin and {\'A}. Kristmundsson and C. Gestal and M. Freeman and P. J. Keeling},
Journal = {Genome Biology and Evolution},
Year = {2021},
Abstract = {|| Coccidia; e.g.: Aggregata, Margolisiella, Rhytidocystis},
File = {/home/alexey/coll/ref/os/1/mathur2020_marosporida_sister_to_coccidia.djvu}
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@Conference{Matsumoto2008,
Title = {{Katablepharid EFL possess the evolutionary affinity to the homologues of chlorarachniophytes, foraminiferans, and diatoms}},
Author = {T. Matsumoto and M. Sakaguchi and A. Yabuki and T. Hashimoto and Y. Inagaki},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {As stated},
File = {matsumoto2008.txt}
}
@Article{Matsumoto2010,
Title = {{Green-colored Plastids in the Dinoflagellate Genus Lepidodinium are of Core Chlorophyte Origin.}},
Author = {T. Matsumoto and F. Shinozaki and T. Chikuni and A. Yabuki and K. Takishita and M. Kawachi and T. Nakayama and I. Inouye and T. Hashimoto and Y. Inagaki},
Journal = {Protist},
Year = {2010},
Abstract = {As stated},
Doi = {10.1016/j.protis.2010.07.001},
File = {matsumoto2010_lepidodinium_plastids.pdf},
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@Article{Matsuzaki2008,
Title = {{A cryptic algal group unveiled: a plastid biosynthesis pathway in the oyster parasite Perkinsus marinus}},
Author = {M. Matsuzaki and H. Kuroiwa and T. Kuroiwa and K. Kita and H. Nozaki},
Journal = {Mol. Biol. and Evolution},
Year = {2008},
Number = {6},
Pages = {1167--1179},
Volume = {25},
Abstract = {As stated},
File = {matsuzaki2008.pdf}
}
@Article{Matsuzaki2009,
Title = {{A DNA-lacking plastid in the oyster pathogen Perkinsus marinus}},
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Journal = {Phycologia},
Year = {2009},
Number = {4},
Pages = {1--153},
Volume = {48},
Abstract = {As stated},
File = {matsuzaki2009_perkinsus_plastid.txt}
}
@Article{Matsuzaki2021,
Title = {{The enigmatic snow microorganism, Chionaster nivalis, is closely related to Bartheletia paradoxa (Agaricomycotina, Basidiomycota)}},
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Journal = {Microbes Environ.},
Year = {2021},
Number = {2},
Pages = {2021},
Volume = {6},
Abstract = {As stated},
Doi = {10.1264/jsme2.ME21011},
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Pages = {R575--R576},
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@Article{Matus2007,
Title = {{The Hox gene complement of a pelagic chaetognath, \textit{Flaccisagitta enflata}}},
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Pages = {854--864},
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Abstract = {Chaetoghanta either || Ecdys + Loph, or || Loph},
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@Article{Matus2006,
Title = {{Molecular evidence for deep evolutionary roots of bilaterality in animal development}},
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Abstract = {posterior proliferation zone was absent in the last common ancestor of Onychophora and Arthropoda. By comparing our data from Onychophora with those from annelids, arthropods, and chordates, we suggest that the occurrence of a "posterior growth zone" currently cannot be used to support the homology of segmentation between these three animal groups},
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Abstract = {exogenous ovary is the ancestral condition in velvet worms and a synapomorphy of Onychophora and Arthropoda. The embryonic origin, growth, and position of oocytes outside the ovarian lumen in Onychophora and various groups of Arthropoda do not support the Articulata hypothesis},
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Year = {2008},
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Pages = {1456--1500},
Volume = {269},
Abstract = {segmental ganglia have arisen independently in Arthropoda and Annelida and are not a synapomorphy uniting these groups},
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File = {mayer2008.txt}
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Year = {2021},
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Abstract = {As stated},
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File = {mcinerley2011_planctomycetes_and_euk.pdf},
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@Article{McLoughlin2011,
Title = {{Ptilophyllum muelleri (Ettingsh.) Comb. Nov. From the Oligocene of Australia: Last of the Bennettitales?}},
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Abstract = {As stated (only leaves)},
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Year = {2020},
Pages = {55--64},
Volume = {6},
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@Article{Melzer2009,
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Year = {2009},
Abstract = {Sister to Gymnosp},
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@Article{MengYin2011,
Title = {{New macroalgal fossils of the Kaili Biota in Guizhou Province, China}},
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Pages = {93--100},
Volume = {54},
Abstract = {Lower cambrian: differentiated macroalgae},
Doi = {10.1007/s11430-010-4063-3},
File = {wu2011_comples_macroalgae_cambrian.pdf},
Url = {www.springerlink.com}
}
@Article{Mercer1981,
Title = {{Studies with \textit{Cyanidium caldarium}. {I}. The fine structure and systematic position of the organism}},
Author = {F. V. Mercer and L. Bogorad and R. Mullens},
Journal = {J. Cell. Biol.},
Year = {1981},
Number = {3},
Pages = {393--403},
Volume = {13}
}
@Article{Merchant2007,
Title = {{The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions}},
Author = {S. S. Merchant and S. E. Prochnik and O. Vallon and E. H. Harris and S. J. Karpowicz and G. B. Witman and A. Terry and A. Salamov and L. K. Fritz-Laylin and L. Marechal-Drouard and W. F. Marshall and L.-H. Qu and D. R. Nelson and A. A. Sanderfoot and M. H. Spalding and V. V. Kapitonov and Q. Ren and P. Ferris and E. Lindquist and H. Shapiro and S. M. Lucas and J. Grimwood and J. Schmutz and C. A. Team and J. A. Team and I. V. Grigoriev and D. S. Rokhsar and A. R. Grossman},
Journal = {Science},
Year = {2007},
Pages = {245--251},
Volume = {218},
Abstract = {Uniconta, but no Biconta},
File = {merchant2007.pdf}
}
@Article{vonMering2007,
Title = {{Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments}},
Author = {C. von Mering and et al.},
Journal = {Science},
Year = {2007},
Number = {2007},
Pages = {1126--1130},
Volume = {315},
Abstract = {(Cyano, Deino, Chloroflexi, Aquifi, Thermotog)},
File = {mering2007.pdf}
}
@Article{Merkel2012,
Title = {{Spiral cleavage and early embryology of a loxosomatid entoproct and the usefulness of spiralian apical cross patterns for phylogenetic inferences}},
Author = {J. Merkel and T. Wollesen and B. Lieb and A. Wanninger},
Journal = {BMC Developmental Biology},
Year = {2012},
Pages = {11},
Volume = {12},
Abstract = {Unclear},
File = {merkel2012_entoprocta_cleavage.pdf},
Url = {http://www.biomedcentral.com/1471-213X/12/11}
}
@Article{Merker2013,
Title = {{Comparative anatomy of the heart-glomerulus complex of Cephalodiscus gracilis (Pterobranchia): Structure, function, and phylogenetic implications}},
Author = {S. Merker and A. Gruhl and T. Stach},
Journal = {Zoomorphology},
Year = {2013},
Pages = {1--16},
Abstract = {Heart-glomerulus complex does not support a sister-group relationship between Echinodermata and Hemichordata},
Doi = {10.1007/s00435-013-0200-9},
File = {merker2013_cephalodiscus.pdf}
}
@Article{Merola1981,
Title = {{Revision of \textit{Cyanidium caldarium}}},
Author = {Merola},
Journal = {Giorn. Bot. Ital.},
Year = {1981},
Number = {4--5},
Pages = {189--186},
Volume = {115}
}
@Book{Meyen1987,
Title = {The basics of palaeobotany. The reference book},
Author = {S. V. Meyen},
Publisher = {Nedra},
Year = {1987},
Address = {Moscow},
Note = {(In Russian)}
}
@InCollection{Meyen1984,
Title = {The origin of main groups of higher plants},
Author = {S. V. Meyen},
Booktitle = {Actual problems of current biology},
Publisher = {Prosveschenie},
Year = {1984},
Address = {Moscow},
Note = {(In Russian)},
Pages = {127--163},
Abstract = {sistematika, evoljucija, Vegetabilia}
}
@Article{Meyen1982,
Title = {Sexual organs of gymnosperms and their evolution (according to palaeobotany data)},
Author = {S. V. Meyen},
Journal = {Zhurn. Obshch. Biol.},
Year = {1982},
Note = {(In Russian)},
Number = {3},
Pages = {303--323},
Volume = {43},
Abstract = {morfologija, evoljucija, Spermatophyta}
}
@Article{Meyen1978,
Title = {Taxonomy, phylogeny and ecology of propteridophytes},
Author = {S. V. Meyen},
Journal = {Bull. MOIP. Otd. biol.},
Year = {1978},
Note = {(In Russian)},
Number = {4},
Pages = {72--84},
Volume = {83},
Abstract = {sistematika, evoljucija, Pteridophyta}
}
@Article{Meyen1978a,
Title = {The morphology pf propteridophytes("psilophytes")},
Author = {S. V. Meyen},
Journal = {Bull. MOIP. Otd. biol.},
Year = {1978},
Note = {(In Russian)},
Number = {2},
Pages = {96--107},
Volume = {83},
Abstract = {morfologija, Pteridophyta}
}
@Article{Meyer2010a,
Title = {{Respiratory proteins in Sipunculus nudus--implications for phylogeny and evolution of the hemerythrin family}},
Author = {A. Meyer and B. Lieb},
Journal = {Comp. Biochem. Physiol. B: Biochem. Mol. Biol.},
Year = {2010},
Number = {2},
Pages = {171 - 177},
Volume = {155},
Abstract = {Separate from Annelida},
Doi = {10.1016/j.cbpb.2009.11.001},
File = {meyer2010_sipunc_hem.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19897048}
}
@Article{Meyer2010b,
Title = {{Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity}},
Author = {A. Meyer and C. Todt and N. T. Mikkelsen and B. Lieb},
Journal = {BMC Evol. Biol.},
Year = {2010},
Pages = {70},
Volume = {10},
Abstract = {18S: Cycl + Kampt; Polyplac + Monoplac sister; Scaph || Caudofov || Solen || Ceph placed wrongly due to substitutuon rates},
Doi = {10.1186/1471-2148-10-70},
File = {meyer2010_solenogastres_18s.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20214780}
}
@Article{Meyer2010,
Title = {{Selecting ribosomal protein genes for invertebrate phylogenetic inferences: How many genes to resolve the Mollusca?}},
Author = {A. Meyer and A. Witek and B. Lieb},
Journal = {Methods in Ecology \& Evolution},
Year = {2010},
Abstract = {18 genes; Kampto ~ Platyz; Bryoz || Phor + Brach || Moll || Nemert || Ann; Caudofov || Polyplac || Bivalv || Gastr},
Doi = {10.1111/j.2041-210X.2010.00052.x},
File = {meyer2010_mollusca.pdf},
Url = {http://www.respond2articles.com/MEE/}
}
@Article{Meyer2000,
Title = {{The development of Archaeopteris: new evolutionary characters from the structural analysis of an Early Famennian trunk from southeast Morocco1}},
Author = {B. Meyer-Berthaud and S. E. Scheckler and J.-L. Bousquet},
Journal = {Amer. J. Bot.},
Year = {2000},
Pages = {456--468},
Volume = {87}
}
@Article{MeyerWachsmuth2012,
Title = {{The muscular system of Nemertoderma westbladi and Meara stichopi (Nemertodermatida, Acoelomorpha)}},
Author = {I. Meyer-Wachsmuth and {\'A}. U. Jondelius and O. I. Raikova and O. I. Raikova},
Journal = {Zoomorphology},
Year = {2012},
Abstract = {Diagonal musculature: against Acoelomorpha},
Doi = {10.1007/s00435-013-0191-6},
File = {meyer-wachsmuth2013_nemertodermatida_musc_system.pdf}
}
@Article{MeyerWachsmuth,
Title = {{Interrelationships of Nemertodermatida}},
Author = {I. Meyer-Wachsmuth and U. Jondelius},
Journal = {Org Divers Evol},
Abstract = {As stated, monophyletic},
Doi = {10.1007/s13127-015-0240-8},
File = {meyer-wachsmuth2015_nemertodermatida.pdf}
}
@Article{Miadlikowska2014a,
Title = {{A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 Fungi representing 1139 infrageneric taxa, 317 genera and 66 families.}},
Author = {J. Miadlikowska and F. Kauff and F. H{\"o}gnabba and J. C. Oliver and K. Moln{\'a}r and E. Fraker and E. Gaya and J. Hafellner and V. Hofstetter and C. Gueidan and M. Kukwa and R. L{\"u}cking and C. Bj{\"o}rk and H. J. M. Sipman and A. R. Burgaz and A. Thell and A. Passo and L. Myllys and T. Goward and S. Fern{\'a}ndez-Brime and G. Hestmark and J. Lendemer and H. T. Lumbsch and M. Schmull and C. Schoch and E. S{\'e}rusiaux and D. R. Maddison and A. E. Arnold and F. Lutzoni and S. Stenroos},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2014.04.003},
File = {miadlikowska2014_lecanoromycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24747130}
}
@Article{Miadlikowska2014,
Title = {{A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 Fungi representing 1139 infrageneric taxa, 317 genera and 66 families.}},
Author = {J. Miadlikowska and F. Kauff and F. H{\"o}gnabba and J. C. Oliver and K. Moln{\'a}r and E. Fraker and E. Gaya and J. Hafellner and V. Hofstetter and C. Gueidan and M. A. G. Ot{\'a}lora and B. Hodkinson and M. Kukwa and R. L{\"u}cking and C. Bj{\"o}rk and H. J. M. Sipman and A. R. Burgaz and A. Thell and A. Passo and L. Myllys and T. Goward and S. Fern{\'a}ndez-Brime and G. Hestmark and J. Lendemer and H. T. Lumbsch and M. Schmull and C. L. Schoch and E. S{\'e}rusiaux and D. R. Maddison and A. E. Arnold and F. Lutzoni and S. Stenroos},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Pages = {132--168},
Volume = {79},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2014.04.003},
File = {miadlikowska2014_lecanoromycetes.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24747130}
}
@Article{Michel1974,
Title = {{Phyletic lines in modern ferns}},
Author = {J. T. Michel},
Journal = {Ann. Miss. Bot. Gard.},
Year = {1974},
Pages = {474--482},
Volume = {61}
}
@Article{Michel2009,
Title = {{Isolation of the Amoeba Thecamoeba quadrilineata Harbouring Intranuclear Spore Forming Endoparasites Considered as Fungus-like Organisms}},
Author = {R. Michel and B. Hauroeder and L. Zoeller},
Journal = {Acta Protozool.},
Year = {2009},
Pages = {41--49},
Volume = {48},
Abstract = {Nucleophaga ~ ? Microsporidia},
File = {michel2009_nucleophaga.pdf}
}
@Article{Michel2007,
Title = {{Phylogenetic position and notes on the ultrastructure of Sappinia diploidea (Thecamoebidae)}},
Author = {R. Michel and C. Wylezich and B. Haurader and A. V. Smirnov},
Journal = {Protistology},
Year = {2007},
Number = {4},
Pages = {319--325},
Volume = {4},
Abstract = {Thecam. ~ Acanthop.},
File = {michel2007_sappinia.pdf}
}
@Article{Mignot1975,
Title = {{Etude ultrastructurale du flagelle phagotrophe \textit{Colponema loxodes} Stein}},
Author = {J. P. Mignot and G. Brugerolle},
Journal = {Protistologica},
Year = {1975},
Number = {4},
Pages = {429--444},
Volume = {22}
}
@Article{Mikhailov2007,
Title = {{Resolving the position of Rhizaria on the basis of multigene analysis}},
Author = {K. V. Mikhailov and V. V. Aleoshin},
Journal = {Protistology},
Year = {2007},
Pages = {9--91},
Volume = {5},
Abstract = {Bigelowiella || Heteroconta},
File = {mikhailov2007.txt}
}
@Article{Mikhailov2009,
Title = {{The origin of Metazoa: A transition from temporal to spatial cell differentiation}},
Author = {K. V. Mikhailov and A. V. Konstantinova and M. A. Nikitin and P. V. Troshin and L. Y. Rusin and V. A. Lyubetsky and Y. V. Panchin and A. P. Mylnikov and L. L. Moroz and S. Kumar and V. V. Aleoshin},
Journal = {Bioessays},
Year = {2009},
Number = {7},
Pages = {758--768},
Volume = {31},
Abstract = {Zakhvatkin hypothese},
Doi = {10.1002/bies.200800214},
File = {mikhailov2009_irig_metazoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19472368}
}
@Article{Mikhailov2016a,
Title = {{Genomic survey of a hyperparasitic microsporidian Amphiamblys sp. (Metchnikovellidae).}},
Author = {K. V. Mikhailov and T. G. Simdyanov and V. V. Aleoshin},
Journal = {Genome Biol Evol},
Year = {2016},
Abstract = {More or less core Microsporidia},
Doi = {10.1093/gbe/evw235},
File = {mikhailov2016_metchnikovellidae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27694476}
}
@Article{Mikhailov2016,
Title = {{The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians.}},
Author = {K. V. Mikhailov and G. S. Slyusarev and M. A. Nikitin and M. D. Logacheva and A. A. Penin and V. V. Aleoshin and Y. V. Panchin},
Journal = {Curr. Biol.},
Year = {2016},
Number = {13},
Pages = {1768 - 1774},
Volume = {26},
Abstract = {Synderm + Gnath || Gastr || Plath || Ortho || Ecto + Ento, Cycl || higher},
Doi = {10.1016/j.cub.2016.05.007},
File = {mikhailov2016_orthonectida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27374341}
}
@Article{Mikhailyuk2018,
Title = {{New Taxa of Streptophyte Algae (Streptophyta) from Terrestrial Habitats Revealed Using an Integrative Approach}},
Author = {T. Mikhailyuk and A. Luke{\v{s}}ov{\'a} and K. Glaser and A. Holzinger and S. Obwegeser and S. Nyporko and T. Friedl and U. Karsten},
Journal = {Protist},
Year = {2018},
Abstract = {Streptofilum (covered with scales + mucilage) sister to all other Streptophyta || Mesostigma + Spirotaenia + Chlorokybus},
Doi = {10.1016/j.protis.2018.03.002},
File = {mikhailyuk2018_streptosarcina_streptofilum.pdf},
Url = {https://doi.org/10.1016/j.protis.2018.03.002}
}
@Article{Mikhailyuk2008,
Title = {{New streptophyte green algae from terrestrial habitats and an assessment of the genus interfilum (Klebsormidiophyceae, Streptophyta)}},
Author = {T. I. Mikhailyuk and H. J. Sluiman and A. Massalski and O. Mudimu and E. M. Demchenko and S. Y. Kondratyuk and T. Friedl},
Journal = {J. Phycol.},
Year = {2008},
Pages = {1586--1603},
Volume = {44},
Abstract = {Re-establishing genus ~ Klebsormidium, transition from Trebouxiophyceae},
Doi = {10.1111/j.1529-8817.2008.00606.x},
File = {mikhailyuk2008.pdf}
}
@Article{Mikkelsen2018,
Title = {{Mitogenomics reveals phylogenetic relationships of caudofoveate aplacophoran molluscs.}},
Author = {N. T. Mikkelsen and K. M. Kocot and K. M. Halanych},
Journal = {Mol. Phylogenet. Evol.},
Year = {2018},
Abstract = {Solenogastres + Caudofoveata},
Doi = {10.1016/j.ympev.2018.04.031},
File = {mikkelsen2018_caudofoveata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29702218}
}
@Article{Mikrjukov2000,
Title = {{Taxonomy and Phylogeny of Heliozoa. I. The Order Desmothoracida Hertwig et Lesser, 1874}},
Author = {K. A. Mikrjukov},
Journal = {Acta Protozool.},
Year = {2000},
Pages = {81--97},
Volume = {39}
}
@Article{Mikrjukov2000b,
Title = {Taxonomy and phylogeny of heliozoans},
Author = {K. A. Mikrjukov},
Journal = {Zool. Zhurn.},
Year = {2000},
Note = {(In Russian)},
Number = {8},
Pages = {891--894},
Volume = {79},
Annote = {xerox}
}
@Article{Mirkrjukov2000,
Title = {{Taxonomy and Phylogeny of Heliozoa. II. The Order Dimorphida Siemensma, 1991 (Cercomonadea classis n.): Diversity and Relatedness with Cercomonads}},
Author = {Kirill A. Mikrjukov},
Journal = {Acta Protozool.},
Year = {2000},
Pages = {99--115},
Volume = {39}
}
@Article{Mikrjukov1999,
Title = {The study of ultrastructure and the comparison of ribosomal RNA genes as methods for building the classification of protists},
Author = {K. A. Mikrjukov},
Journal = {Zool. Zhurn.},
Year = {1999},
Note = {(In Russian)},
Number = {8},
Pages = {901--915},
Volume = {78},
Annote = {xerox}
}
@Article{Mikrjukov1998b,
Title = {{On the Biology of Heliozoa: The Origin of Radial Forms in the Benthic Sarcodines}},
Author = {K. A. Mikrjukov},
Journal = {Rus. J. Zool.},
Year = {1998},
Number = {1},
Pages = {15--24},
Volume = {2}
}
@Article{Mikrjukov1995a,
Title = {{Structure, function, and formation of extrusive organelles~--- microtoxicysts in the rhizopod Penardia cometa}},
Author = {K. A. Mikrjukov},
Journal = {Protoplasma},
Year = {1995},
Pages = {186--191},
Volume = {188}
}
@Article{Mikrjukov1998,
Title = {{A Study of the Structure and the Life Cycle of \textit{Gymnophrys cometa} Cienkowski, 1876 (Gymnophrea cl. n.) with Remarks on the Taxonomy of the Amoebo-flagellated Genera \textit{Gymnophrys} and \textit{Borkovia}}},
Author = {K. A. Mikrjukov and A. P. Mylnikov},
Journal = {Acta Protozool.},
Year = {1998},
Pages = {179--189},
Volume = {37}
}
@Article{Mikrjukov1998a,
Title = {{The Fine Structure of a Carnivorous Multiflagellar Protist, \textit{Multicilia marina} Cienkowski, 1881 (Flagellata Incertae Sedis)}},
Author = {K. A. Mikrjukov and A. P. Mylnikov},
Journal = {Eur. J. Protistol.},
Year = {1998},
Pages = {391--401},
Volume = {34}
}
@Article{Mikrjukov1996,
Title = {{Protist \textit{Multicilia marina} Cienk.: mastigophore or heliozoan?}},
Author = {K. A. Mikrjukov and A. P. Mylnikov},
Journal = {Doklady Akademii Nauk},
Year = {1996},
Note = {(In Russian)},
Number = {1},
Pages = {136--139},
Volume = {346},
Annote = {xerox}
}
@Article{Mikrjukov1996a,
Title = {New data about morphology and life cycle of athalamic amoebae ({P}rotista, {A}thalamida)},
Author = {K. A. Mikrjukov and A. P. Mylnikov},
Journal = {Zool. Zhurn.},
Year = {1996},
Note = {(In Russian)},
Number = {9},
Pages = {1283--1293},
Volume = {75},
Annote = {xerox}
}
@Article{Mikrjukov1995,
Title = {{Fine structure of an unusual rhizopod, \textit{Penardia cometa}, containing extrusomes and kinetosomes}},
Author = {K. Mikrjukov and A. Mylnikov},
Journal = {Eur. J. Protistol.},
Year = {1995},
Pages = {90--96},
Volume = {31}
}
@Article{Millanes2011,
Title = {{Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)}},
Author = {A. M. Millanes and P. Diederich and S. Ekman and M. Wedin},
Journal = {MOLECULAR PHYLOGENETICS AND EVOLUTION},
Year = {2011},
Doi = {10.1016/j.ympev.2011.05.014},
File = {millanes2011_tremellomycetes.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2011.05.014}
}
@Article{Min1998,
Title = {{Molecular phylogeny of arthropods and their relatives: polyphyletic origin of arthropodization.}},
Author = {G. S. Min and S. H. Kim and W. Kim},
Journal = {Mol Cells},
Year = {1998},
Number = {1},
Pages = {75--83},
Volume = {8}
}
@Article{Min2009,
Title = {{Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata).}},
Author = {G.-S. Min and J.-K. Park},
Journal = {BMC Genomics},
Year = {2009},
Pages = {533},
Volume = {10},
Abstract = {Monog || Bdell + Acanth},
Doi = {10.1186/1471-2164-10-533},
File = {min2009_rotatoria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19919696}
}
@Article{Mindell1999,
Title = {{Interordinal relationships of birds and other reptiles bases on whole mitochondrial genomes}},
Author = {D. P. Mindell and M. D. Sorenson and D. E. Dimcheff and M. Hasegawa and J. C. Ast and T. Yuri},
Journal = {Syst. Biol.},
Year = {1999},
Number = {1},
Pages = {138--152},
Volume = {48}
}
@Article{Minelli2010,
Title = {{The origins of larval forms: What the data indicate, and what they don't.}},
Author = {A. Minelli},
Journal = {Bioessays},
Year = {2010},
Number = {1},
Volume = {32},
Abstract = {Against Williamson},
Doi = {10.1002/bies.200900133},
File = {minelli2009_against_williamson.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19953590}
}
@Book{Minelli2003,
Title = {{The Development of Animal Form: Ontogeny, Morphology, and Evolution}},
Author = {A. Minelli},
Publisher = {Cambridge University Press},
Year = {2003},
Address = {Cambridge},
ISBN = {0521808510},
Pages = {1--323}
}
@Conference{Minge2008,
Title = {{Evolutionary position of breviate amoebae illuminates the primary eukaryote divergence}},
Author = {M. A. Minge and J. D. Silberman and R. J. S. Orr and T. Cavalier-Smith and K. Shalchian-Tabrizi and F. Burki and ??. Skj??veland and K. S. Jakobsen},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {In our trees, Breviata is placed as sister to the remaining Amoebozoa. Maybe has a modified mitochondrion.},
File = {minge2008.txt}
}
@Article{Minge2008b,
Title = {{Evolutionary position of breviate amoebae and the primary eukaryote divergence}},
Author = {M. A. Minge and J. D. Silberman and R. J. S. Orr and T. Cavalier-Smith and K. Shalchian-Tabrizi and F. Burki and A. Skjaeveland and K. S. Jakobsen},
Journal = {Proc. R. Soc. B},
Year = {In press},
Abstract = {As stated, + support for bikonts (!), Excavates (minus all amitoch.), low support for plants+crypto, no unikonts},
Doi = {10.1098/rspb.2008.1358},
File = {minge2008.pdf}
}
@Article{Minichev1979,
Title = {Subclasses of gastropods and their phylogeny},
Author = {Ju. Minichev and Ja. I. Starobogatov},
Journal = {Zool. Zhurn.},
Year = {1979},
Note = {(In Russian)},
Number = {3},
Pages = {293--305},
Volume = {58},
Abstract = {sistematika, Gastropoda, Mollusca}
}
@InCollection{Minichev1975,
Title = {About phylogenetic relations inside molluscan phylum},
Author = {Ju. Minichev and Ja. I. Starobogatov},
Booktitle = {The condition of exploration degree of living world},
Publisher = {Institute of Palaeontology},
Year = {1975},
Address = {Moscow},
Note = {(In Russian)},
Pages = {205--276},
Abstract = {sistematika, Mollusca}
}
@Article{Miquelis2000,
Title = {{Performance of 18S rDNA helix E23 for phylogenetic relationships within and between the Rotifera-Acanthocephala clades.}},
Author = {A. Miquelis and J. F. Martin and E. W. Carson and G. Brun and A. Gilles},
Journal = {C. R. Acad. Sci. III},
Year = {2000},
Number = {10},
Pages = {925--941},
Volume = {323}
}
@Article{Mirabdullaev1994,
Title = {{About origin and placement of fungi in the scassification of living things}},
Author = {I. M. Mirabdullaev},
Journal = {Uspekhi sovremennoj biologii},
Year = {1994},
Number = {1},
Pages = {30--41},
Volume = {114}
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Pages = {983--992},
Volume = {100},
Abstract = {Tetracapsuloides bryosalmonae is the myxozoan parasite responsible for proliferative kidney disease (PKD) of salmonid fishes. This disease affects farmed species in North America and Western Europe where it results in significant economic losses for the rainbow trout industry. The parasite has two hosts in its life cycle, salmonid fish, and freshwater bryozoans. In this study, we describe the development of the parasite at the ultrastructural level within the bryozoan host Fredericella sultana. Single celled, presaccular stages form aggregates within the metacoel of this host which resolve into spore sacs. Within these sacs sporogenesis is initiated with the differentiation of presporogonic cells into sporogonic and valvogenic cells. These latter cells surround a sporogonic cell which subsequently divides to form a sporoplasmogenic cell and a capsulogenic cell. The capsulogenic cell divides further to form four cells each with a polar capsule, while the sporoplasmogenic cell divides resulting in four cells, two primary cells and two secondary cells. The secondary cells are engulfed by the primary cells resulting in a mature sporoplasm. It is hypothesized that autogamy occurs during the initial formation of the spore sac and that allogamy is also possible during this time.},
Doi = {10.1007/s00436-006-0371-0},
File = {morris2007a.pdf}
}
@Article{Morris2018,
Title = {{The timescale of early land plant evolution.}},
Author = {J. L. Morris and M. N. Puttick and J. W. Clark and D. Edwards and P. Kenrick and S. Pressel and C. H. Wellman and Z. Yang and H. Schneider and P. C. J. Donoghue},
Journal = {Proceedings of the National Academy of Sciences of the United States of America},
Year = {2018},
Number = {10},
Pages = {E2274 - E2283},
Volume = {115},
Abstract = {Bryophytes as a whole are basal},
Doi = {10.1073/pnas.1719588115},
File = {morris2018_land_plant_evol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27325830}
}
@InCollection{Moshkova1989,
Title = {Brown algae~--- Phaeophyta},
Author = {I. A. Moshkova},
Booktitle = {Algae: the reference},
Publisher = {Naukova Dumka},
Year = {1989},
Address = {Kiev},
Note = {(In Russian)},
Pages = {386--408}
}
@Article{Mouchaty2000,
Title = {{The Phylogenetic Position of the Talpidae Within Eutheria Based on Analysis of Complete Mitochondrial Sequences}},
Author = {S. K. Mouchaty and A. Gullberg and A. Janke and U. Arnason},
Journal = {Mol. Biol. Evol.},
Year = {2000},
Number = {1},
Pages = {60--67},
Volume = {17}
}
@Article{Moustafa2008,
Title = {{Chlamydiae Has Contributed at Least 55 Genes to Plantae with Predominantly Plastid Functions}},
Author = {A. Moustafa and and A. Reyes-Prieto and D. Bhattacharya},
Journal = {PLoS One},
Year = {2008},
Number = {5},
Pages = {1--9},
Volume = {3},
Abstract = {As stated},
Doi = {10.1371/journal.pone.0002205},
File = {moustafa2008.pdf}
}
@Article{Mowbrey2009,
Title = {{Evolution and diversity of the Golgi body}},
Author = {K. Mowbrey and J. B. Dacks},
Journal = {FEBS Lett.},
Year = {In press},
Pages = {8},
Abstract = {Stacked is basal then several (8) independent unstack events},
Doi = {10.1016/j.febslet.2009.10.025},
File = {mowbrey2009_golgi_body_phylog.pdf},
ISSN = {0014-5793},
Url = {http://dx.doi.org/10.1016/j.febslet.2009.10.025}
}
@Article{MozleyStandridge2009,
Title = {{Cladochytriales~--- a new order in Chytridiomycota}},
Author = {S. E. Mozley-Standridge and P. M. Letcher and J. E. Longcore and D. Porter and D. R. Simmons},
Journal = {Myc. Res.},
Year = {2009},
Number = {4},
Pages = {498--507},
Volume = {113},
Abstract = {As stated},
Doi = {10.1016/j.mycres.2008.12.004},
File = {mozley-standridge2009_cladochytriales.pdf},
ISSN = {0953-7562},
Url = {http://dx.doi.org/10.1016/j.mycres.2008.12.004}
}
@Article{Msiska2009,
Title = {{Phylogenetic analysis of the Glomeromycota by partial beta-tubulin gene sequences.}},
Author = {Z. Msiska and J. B. Morton},
Journal = {Mycorrhiza},
Year = {In press},
Abstract = {Sister to core Zygo},
Doi = {10.1007/s00572-008-0216-z},
File = {msiska2008.pdf}
}
@Article{MunozGomez2017,
Title = {{The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known.}},
Author = {S. A. Mu{\~n}oz-G{\'o}mez and F. G. Mej{\'i}a-Franco and K. Durnin and M. Colp and C. J. Grisdale and J. M. Archibald and C. H. Slamovits},
Journal = {Curr. Biol.},
Year = {2017},
Number = {11},
Pages = {1677 - 1684 - e4},
Volume = {27},
Abstract = {Cyanidi || (Proteorhodophytina: Porphyr + Compsog || Rhodello + Stylonemato) || Eurhodophytina: Bang + Florid},
Doi = {10.1016/j.cub.2017.04.054},
File = {munoz-gomez2017_proteorhodophytina.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28528908}
}
@Article{Mueller2008,
Title = {{Neurophylogeny of Chaetognatha: Can Neuroanatomical Characters Shed Light on the Phylogenetic Position of Arrow Worms?}},
Author = {C. H. G. Mueller and V. Rieger and Y. Perez and N. Hansson and S. Harzsch},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {We suggest to place the Chaetognatha within the Protostomia and argue against hypotheses proposing a deuterostome affinity of Chaetognatha or a sister-group relationship to all other Bilateria.},
Doi = {10.1002/jmor.10683},
File = {carsten2008.txt}
}
@Article{Mueller2007,
Title = {{The unique skeleton of siliceous sponges (Porifera; Hexactinellida and Demospongiae) that evolved first from the Urmetazoa during the Proterozoic: a review}},
Author = {W. E. G. Mueller and J. Li and H. C. Schroder and L. Qiao and X. Wang},
Journal = {Biogeosciences},
Year = {2007},
Pages = {219--232},
Volume = {4},
Abstract = {Hexact of ediacarian origin; Hexact + Demo || Calcarea || Archaeocyatha},
File = {mueller2007.pdf},
Url = {www.biogeosciences.net/4/219/2007/}
}
@Article{Muller2010,
Title = {{First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat}},
Author = {F. Muller and T. Brissac and N. Le Bris and H. Felbeck and O. Gros},
Journal = {Environ. Microbiol.},
Year = {2010},
Number = {8},
Pages = {2371 - 2383},
Volume = {12},
Abstract = {(Cenarchaeum || Giganthauma || Nitrosopumilus) || Crenarchaeota},
Doi = {10.1111/j.1462-2920.2010.02309.x},
File = {muller2010_giganthauma.pdf}
}
@Article{Muller2001,
Title = {{Ribosomal RNA phylogeny of the Bangiophycidae (Rhodophyta) and the origin of secondary plastids}},
Author = {K. M. Muller and M. C. Oliveira and R. G. Sneath and D. Bhattacharya},
Journal = {Amer. J. Bot.},
Year = {2001},
Pages = {1390--1400},
Volume = {88}
}
@Article{Munoz2016,
Title = {{Corrigendum to "Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. Nov." [Syst. Appl. Microbiol. 39 (5) (2016) 281-296].}},
Author = {R. Munoz and R. Rossell{\'o}-M{\'o}ra and R. Amann},
Journal = {Syst. Appl. Microbiol.},
Year = {2016},
Number = {7},
Pages = {491 - 492},
Volume = {39},
Abstract = {Nomenclatural types corrected},
Doi = {10.1016/j.syapm.2016.08.006},
File = {munoz2016_rhodothermaeota_corr.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27639921}
}
@Article{Munoz2016a,
Title = {{Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. Nov.}},
Author = {R. Munoz and R. Rossell{\'o}-M{\'o}ra and R. Amann},
Journal = {Syst. Appl. Microbiol.},
Year = {2016},
Number = {5},
Pages = {281 - 296},
Volume = {39},
Abstract = {Rhodothermaeota at the base, incl. Salinibacter},
Doi = {10.1016/j.syapm.2016.04.004},
File = {munoz2016_rhodothermaeota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27287844}
}
@Article{Muona2003,
Title = {{Abstracts of the 21st Annual Meeting of the Willi Hennig Society}},
Author = {J. Muona},
Journal = {Cladistics},
Year = {2003},
Pages = {148--163},
Volume = {19},
Abstract = {Cycliophora morph. and combined ~ Entoprocta, mol. ~ Rotifera; non-Acoela Bilat.=Nephrozoa; Loricifera > Scalidophora (incl. also Priap \& Kino); Sipuncula: absence of suport for classes; Gnatifera (Gnath, Microg, Rotif, Seison, Acanthoc) and Cycloneuralia (Nemat., Nemath, Scalidoph.), Gastrotr. morph. || Gn, mol || Cycl; supertree support only Bilateria,Deuterostomia,Brachiopoda-Phoronida,Cephalorhyncha, Nematoida,Panarthropoda,Trochozoa},
File = {muona2003_21whs.pdf}
}
@Article{Murdock2008,
Title = {{Phylogeny of marattioid ferns (Marattiaceae): Inferring a root in the absence of a closely related outgroup}},
Author = {A. G. Murdock},
Journal = {Amer. J. Bot.},
Year = {2008},
Number = {5},
Pages = {626--641},
Volume = {95},
Abstract = {Danaea basal, Marattia polyphyletic},
Doi = {10.3732/ajb.2007308},
File = {murdock2008.pdf}
}
@Article{Murdock2008b,
Title = {{A taxonomic revision of the eusporangiate fern family Marattiaceae, with description of a new genus \textit{Ptisana}}},
Author = {A. G. Murdock},
Journal = {Taxon},
Year = {2008},
Number = {3},
Pages = {737--755},
Volume = {2008},
Abstract = {Angiopteris, Christensenia, Danaea, Eupodium, Marattia, Marattiaceae, Ptisana},
File = {murdock2008.pdf}
}
@InCollection{Murphy1995,
Title = {{Classification And Nomenclature Of Viruses. Sixth Report of the International Committee on Taxonomy of Viruses}},
Author = {F. A. Murphy and C. M. Fauquet and D. H. L. Bishop and S. A. Ghabrial and A. W. Jarvis and G. P. Martelli and M. A. Mayo and M. D. Summers (eds.)},
Booktitle = {Archives od Virology. 15.},
Publisher = {Springer},
Year = {1995}
}
@Book{Mushegian2007,
Title = {{Foundations of Comparative Genomics}},
Author = {A. R. Mushegian},
Publisher = {Academic Press},
Year = {2007},
Address = {Amsterdam},
ISBN = {0120887940},
Pages = {1--280}
}
@Article{Mwinyi2010,
Title = {{The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis.}},
Author = {A. Mwinyi and X. Bailly and S. J. Bourlat and U. Jondelius and D. T. J. Littlewood and L. Podsiadlowski},
Journal = {BMC Evol. Biol.},
Year = {2010},
Pages = {309},
Volume = {10},
Abstract = {Monophyletic Acoelomorpha with Xeno ?sister},
Doi = {10.1186/1471-2148-10-309},
File = {mwinyi2010_acoela.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20942955}
}
@Article{Mwinyi2009,
Title = {{Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida}},
Author = {A. Mwinyi and A. Meyer and C. Bleidorn and B. Lieb and T. Bartolomaeus and L. Podsiadlowski},
Journal = {BMC Genomics},
Year = {2009},
Pages = {27},
Volume = {10},
Abstract = {Myz || Sipun || Annel},
Doi = {10.1186/1471-2164-10-27},
File = {mwinyi2009_sipunculida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19149868}
}
@Article{Mylnikov2011,
Title = {{The Cell Structure of the Reticulopodial Amoeba Filoreta marina Bass et Cavalier Smith (Cercozoa)}},
Author = {A. P. Myl'nikov and A. A. Myl'nikov},
Journal = {Science},
Year = {2011},
Number = {4},
Pages = {440--445},
Volume = {4},
Abstract = {~ foram, vampyrell},
Doi = {10.1134/S1995082911040146},
File = {mylnikov2011_filoreta.pdf},
Keywords = {filoreta marina, ultrastructure, reticulopodia, multinucleate plasmodia, cercozoa}
}
@Article{Mylnikova1995,
Title = {{Ultrastructure of the Marine Predatory Flagellate Metromonas simplex Larsen et Patterson, 1990 (Cercozoa)}},
Author = {A. A. Myl'nikova and A. P. Myl'nikov},
Journal = {BIOLOGY, MORPHOLOGY, AND SYSTEMATICS OF HYDROBIONTS},
Year = {1995},
Number = {2},
Pages = {105--110},
Volume = {4},
Abstract = {Metromonas ~ Metopion and Cryomonadida},
Doi = {10.1134/S1995082911020155},
File = {mylnikova2011_metromonas.pdf}
}
@Article{Mylnikov2009,
Title = {{Ultrastructure and Phylogeny of Colpodellids (Colpodellida, Alveolata)}},
Author = {A. P. Mylnikov},
Journal = {Biology Bulletin},
Year = {2009},
Number = {6},
Pages = {582--590},
Volume = {36},
Abstract = {~ CA of sporoz + dinofl},
Doi = {10.1134/S1062359009060065},
File = {mylnikov2009_colpodellids.pdf}
}
@Article{Mylnikov2008,
Title = {{The structure of extrusive organelles in alveolate and other heterotrophic flagellates}},
Author = {A. P. Mylnikov and A. A. Mylnikov},
Journal = {Tsitologiya},
Year = {2008},
Number = {5},
Pages = {406--412},
Volume = {50},
Abstract = {Extrusomes of Colpodella and Colponema are close to infusorian},
File = {mylnikov2008.pdf}
}
@Article{Mylnikov1998,
Title = {The peculiarities of ultrastructure of carnivorous flagellate \textit{Katablepharis} sp.},
Author = {A. P. Mylnikov and Z. M. Mylnikova and A. I. Cvetkov},
Journal = {Tsitologiya},
Year = {1998},
Note = {(In Russian)},
Number = {4},
Pages = {315--320},
Volume = {40},
Abstract = {sistematika, morfologija, Katablepharis, Dinozoa},
Annote = {Bolee vsego pohozhi na: kriptofitov (no kristy), spiromonadid (no slabo razvityj rotovoj apparat), dinomonad (no net teki, a tolko cheshujki, net trihocist). U dinomonad nedavno obraruzhet bolee ili menee razvityj rotovoj apparat. U Katablepharis i blizkogo Leucocryptos razvity kortikalnye alveoly, celljuloznye cheshujki, poroshica i spiral v perehodnoj zone.}
}
@Article{Mylnikov1999,
Title = {The ultrastructure of carnivorous marine flagellate \textit{Metopion fluens}},
Author = {A. P. Mylnikov and Z. P. Mylnikova and A. I. Cvetkov},
Journal = {Tsitologiya},
Year = {1999},
Note = {(In Russian)},
Pages = {581--585},
Volume = {41},
Annote = {xerox}
}
@Article{Nagahama2011,
Title = {{Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments.}},
Author = {T. Nagahama and E. Takahashi and Y. Nagano and M. A. Abdel-Wahab and M. Miyazaki},
Journal = {Environmental Microbiology},
Year = {2011},
Number = {8},
Pages = {2359 - 2370},
Volume = {13},
Abstract = {Basal Clone Group I ~ Blastocl / Chytrid},
Doi = {10.1111/j.1462-2920.2011.02507.x},
File = {nagahama2011_basal_clone_group_1.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21605311}
}
@Article{Nagalingum2008,
Title = {{Assessing phylogenetic relationships in extant heterosporous ferns (Salviniales), with a focus on \textit{Pilularia} and \textit{Salvinia}}},
Author = {N. S. Nagalingum and M. D. Nowak and K. M. Pryer},
Journal = {Botanical Journal of the Linnean Society},
Year = {2008},
Pages = {673--685},
Volume = {2008},
Abstract = {Monophyletic, Regnell ~ Pilularia},
File = {nagalingum2008.pdf}
}
@Article{Nagy2018,
Title = {{Complex multicellularity in fungi: Evolutionary convergence, single origin, or both?}},
Author = {L. G. Nagy and G. M. Kov{\'a}cs and K. Krizs{\'a}n},
Journal = {Biol Rev Camb Philos Soc},
Year = {2018},
Abstract = {Do not ephasize tissues, only cell types},
Doi = {10.1111/brv.12418},
File = {nagy2018_complex_multicell_fungi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29675836}
}
@Article{Nakai2016,
Title = {{Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria}},
Author = {R. Nakai and T. Fujisawa and Y. Nakamura and T. Baba and M. Nishijima and F. Karray and S. Sayadi and H. Isoda and T. Naganuma and H. Niki},
Journal = {Stand Genomic Sci},
Year = {2016},
Pages = {90},
Volume = {11},
Abstract = {Oligoflexia > core Proteobacteria},
Doi = {10.1186/s40793-016-0210-6},
File = {nakai2016_oligoflexia_proteob.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20019144}
}
@Article{Nakamura2015,
Title = {{Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa)}},
Author = {Y. Nakamura and I. Imai and A. Yamaguchi and A. Tuji and F. Not and N. Suzuki},
Journal = {Protist},
Year = {2015},
Abstract = {Chrorar + Granofilos || Phaeod || Glisso || Cryo + Ebri || Spongom + Thaum || Euglyph + Cercom},
Doi = {10.1016/j.protis.2015.05.004},
File = {nakamura2015_phaeodaria.pdf},
Url = {http://dx.doi.org/doi:10.1016/j.protis.2015.05.004}
}
@Article{Nakano2017,
Title = {{A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella}},
Author = {H. Nakano},
Year = {2017},
Number = {1},
Pages = {1080 - 1082},
Volume = {17},
Abstract = {As stated; belongs to "shalow clade"},
Doi = {10.1186/s12862-017-1080-2},
File = {nakano2017_xenoturbella_japonica.pdf},
Url = {http://creativecommons.org/licenses/by/4.0/),}
}
@Article{Nakano2015,
Title = {{What is Xenoturbella?}},
Author = {H. Nakano},
Journal = {Zoological Letters},
Year = {2015},
Abstract = {Review},
Doi = {10.1186/s40851-015-0018-z},
File = {nakano2015_what_is_xenoturnbella.pdf},
ISSN = {2056-306X},
Url = {http://dx.doi.org/10.1186/s40851-015-0018-z}
}
@Article{Nakayama2009,
Title = {{Diversity of the bicosoecids: Implication to the evolution of the stramenopiles}},
Author = {T. Nakayama and M. Sato and H. Yamaguchi and I. Inouye},
Journal = {Phycologia},
Year = {2009},
Number = {4},
Pages = {1--153},
Volume = {48},
Abstract = {Distant relationship between Labromonas and Boroka suggests that common ancestor of the Bicosoecea would possess similar appearance to these genera. The flagellar apparatus of L. fenchelii and other bicosoecids has considerable similarities (e.g. splitting R2) to that of excavates such as Malawimonas},
File = {nakayama2009_bicosoecids.txt}
}
@Article{Nakayama2007,
Title = {{Phylogeny and ultrastructure of Nephroselmis and Pseudoscourfieldia (Chlorophyta), including the description of Nephroselmis anterostigmatica sp. nov. and a proposal for the Nephroselmidales ord. nov.}},
Author = {T. Nakayama and S. Suda and M. Kawachi},
Journal = {Phycologia},
Year = {2007},
Number = {6},
Pages = {680--697},
Volume = {46},
Abstract = {Mamiellales-Pyraminomon vs. Nephroselmidales-Pycnococc},
Doi = {10.2216/04-25.1},
File = {nakayama2007.pdf}
}
@Article{Nanglu2020,
Title = {{Cambrian Tentaculate Worms and the Origin of the Hemichordate Body Plan}},
Author = {K. Nanglu and J.-B. Caron and C. B. Cameron},
Journal = {Current Biology},
Year = {2020},
Abstract = {Gyaltsenglossus as basal Hemichordata},
Doi = {10.1016/j.cub.2020.07.078},
File = {nangluetal2020_cambrian_hemichordata.pdf}
}
@Article{NaranjoOrtiz2019,
Title = {{Fungal evolution: Diversity, taxonomy and phylogeny of the Fungi.}},
Author = {M. A. Naranjo-Ortiz and T. Gabald{\'o}n},
Journal = {Biological reviews of the Cambridge Philosophical Society},
Year = {2019},
Number = {6},
Pages = {2101 - 2137},
Volume = {94},
Abstract = {Hyaloraphidiomycetes ~ Monoblepharid.; Nephridiophagida separate class; Caulochytrium ~ Olpidium},
Doi = {10.1111/brv.12550},
File = {naranjo_ortiz_2019_fungi.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31659870}
}
@Article{Narasingarao2012,
Title = {{De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.}},
Author = {P. Narasingarao and S. Podell and J. A. Ugalde and C. Brochier-Armanet and J. B. Emerson and J. J. Brocks and K. B. Heidelberg and J. F. Banfield and E. E. Allen},
Journal = {ISME J},
Year = {2012},
Number = {1},
Pages = {81--93},
Volume = {6},
Abstract = {~ Halobacteriales},
Doi = {10.1038/ismej.2011.78},
File = {narasingarao2012_nanohaloarchea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17468765}
}
@Article{Narrowe2018,
Title = {{Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids.}},
Author = {A. B. Narrowe and A. Spang and C. W. Stairs and E. F. Caceres and B. J. Baker and C. S. Miller and T. J. G. Ettema},
Journal = {Genome Biol Evol},
Year = {2018},
Number = {9},
Pages = {2380--2393},
Volume = {10},
Doi = {10.1093/gbe/evy154},
File = {narrowe2018_ef2_archaea_parabasalids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26582926}
}
@Article{Nasir2016,
Title = {{Arguments Reinforcing the Three-Domain View of Diversified Cellular Life.}},
Author = {A. Nasir and K. M. Kim and V. D. Cunha and G. Caetano-Anoll{\'e}s},
Journal = {Archaea},
Year = {2016},
Pages = {1851865},
Volume = {2016},
Abstract = {As stated},
Doi = {10.1155/2016/1851865},
File = {nasir2016_three_domains.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/11391013}
}
@Article{Nazina2006,
Title = {{Phylogenetic Diversity and Activity of Anaerobic Microorganisms of High-Temperature Horizons of the Dagang Oil Field (P. R. China)}},
Author = {T. N. Nazina and N. M. Shestakova and A. A. Grigor'yan and E. M. Mikhailova and T. P. Tourova and A. B. Poltaraus and C. Feng and F. Ni and S. S. Belyaev},
Journal = {Microbiology},
Year = {2006},
Number = {1},
Pages = {55--65},
Volume = {75},
Abstract = {Thermotog ~ Clostridia},
File = {nazina2006.pdf}
}
@Article{Near2009,
Title = {{Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes}},
Author = {T. J. Near},
Journal = {J. Exp. Zoolog. B Mol. Dev. Evol.},
Year = {In press},
Abstract = {Still not resolved},
Doi = {10.1002/jez.b.21293},
File = {near2009_lower_chordata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19402130}
}
@Article{Near1998,
Title = {{Phylogenetic Relationships of the Acanthocephala Inferred from 18{S} Ribosomal {DNA} Sequences}},
Author = {T. J. Near and J. R. Garey and S. A. Nadler},
Journal = {Mol. Phyl. Evol.},
Year = {1998},
Number = {3},
Pages = {287--298},
Volume = {10}
}
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Title = {{``Candidatus Lumbricincola'', a novel lineage of uncultured Mollicutes from earthworms of family Lumbricidae}},
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Year = {2009},
Number = {4},
Pages = {1016--1026},
Volume = {11},
Abstract = {Lumbricincola is the otstanding group of Mollicutes},
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Pages = {1852--1860},
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File = {nedelcu2008.pdf}
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Url = {www.plosone.org}
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Year = {2013},
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Pages = {e54576},
Volume = {8},
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Title = {{The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships.}},
Author = {M. P. Nesnidal and M. Helmkampf and I. Bruchhaus and B. Hausdorf},
Journal = {BMC Genomics},
Year = {2011},
Number = {1},
Pages = {572},
Volume = {12},
Abstract = {Bryozoa monophyletic, everything else unclear},
Doi = {10.1186/1471-2164-12-572},
File = {nesnidall2011_flustra_mt_gen.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22111761}
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@Article{Nesnidal2010,
Title = {{Compositional heterogeneity and phylogenomic inference of metazoan relationships}},
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Year = {2010},
Abstract = {If bias removed: Entopr + Ectopr, Brachioz + Mollusca},
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Title = {{New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias}},
Author = {M. P. Nesnidal and M. Helmkampf and A. Meyer and A. Witek and I. Bruchhaus and I. Ebersberger and T. Hankeln and B. Lieb and T. H. Struck and B. Hausdorf},
Journal = {BMC Evolutionary Biology},
Year = {2013},
Pages = {253},
Volume = {13},
Abstract = {Cycliophora + Entoprocta (sometimes || Syndermata + Plathelm); Lophophorata: Brach || Phor || Ectoprocta (frequently with Nemert.)},
Doi = {10.1186/1471-2148-13-253},
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Url = {http://www.biomedcentral.com/1471-2148/13/253}
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Abstract = {Closer to Nemat. and Kinorh. then to Priap.},
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@Article{Neves2010b,
Title = {{Expression of synapsin and co-localization with serotonin and RFamide-like immunoreactivity in the nervous system of the chordoid larva of Symbion pandora (Cycliophora)}},
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Journal = {Invertebrate Biology},
Year = {2010},
Number = {1},
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Volume = {129},
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File = {neves2010_symbion_serotonin_2.pdf}
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@Article{Neves2010a,
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Author = {R. C. Neves and R. M. Kristensen and A. Wanninger},
Journal = {Zoologischer Anzeiger},
Year = {2010},
Pages = {1--12},
Abstract = {Nothing},
Doi = {10.1016/j.jcz.2010.02.002},
File = {neves2010_symbion_serotonin_1.pdf},
ISSN = {0044-5231},
Url = {http://dx.doi.org/10.1016/j.jcz.2010.02.002}
}
@Article{Neves2008,
Title = {{Three-Dimensional Reconstruction of the Musculature of Various Life Cycle Stages of the Cycliophoran Symbion americanus}},
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Year = {2009},
Number = {3},
Pages = {257--270},
Volume = {270},
Abstract = {Distant from Rotifera},
Doi = {10.1002/jmor.10681},
File = {neves2008.pdf}
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Title = {{Origin of the Maxillopoda; urmalacostracan ontogeny and progenesis}},
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@Article{Newton2000,
Title = {{Evolution of the Major Moss Lineages: Phylogenetic Analyses Based on Multiple Gene Sequences and Morphology}},
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@Article{Nian2009,
Title = {{Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes}},
Author = {L. Nian and Zh. Yong and W.ZongXian and Ch. Jie and W. QingBiao and J. ShuGuang and Zh. DangWei and Sh. Jing and Y. Yong and Zh. Yang},
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Year = {2009},
Number = {2005},
Pages = {2648--2655},
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@Article{Nickel2008,
Title = {{Re-Evaluating the Elementary (pre-)Nervous System: New Morphological, Physiological, and Genomic Evidence from Sponges}},
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Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {the presence of complex networks of regulatory circuits within a system of effectors, signal conductors, and pacemakers},
Doi = {10.1002/jmor.10683},
File = {nickel2008.txt}
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@Article{Nickela2010,
Title = {{Evolutionary emergence of synaptic nervous systems: What can we learn from the non-synaptic, nerveless Porifera?}},
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Year = {2010},
Number = {1},
Pages = {1--16},
Volume = {129},
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@Article{Nicks2018,
Title = {{The sperm of Xenacoelomorpha revisited: Implications for the evolution of early bilaterians}},
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Year = {2018},
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@Article{Nielsen2019,
Title = {{Early animal evolution: A morphologist's view.}},
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Journal = {Royal Society open science},
Year = {2019},
Number = {7},
Pages = {190638},
Volume = {6},
Abstract = {Porifera-first},
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Url = {https://www.ncbi.nlm.nih.gov/pubmed/31417759}
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@Article{Nielsen2013,
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Doi = {10.1186/1471-2148-13-171},
File = {nielsen2013_life_cycle_evol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18315817}
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File = {nielsen2010_spiralian_development.pdf}
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@Article{Nielsen2010b,
Title = {{After all: Xenoturbella is an acoelomorph!}},
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Year = {2010},
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Volume = {3},
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File = {nielsen2010_xenoturbella.pdf}
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@Article{Nielsen2008,
Title = {{Six major steps in animal evolution: are we derived sponge larvae?}},
Author = {C. Nielsen},
Journal = {Evol. Devel.},
Year = {2008},
Pages = {241--257},
Volume = {10},
Abstract = {Choano || Silicea || Calcarea || Homosceromorpha || Placozoa || Cnidaria || Ctenophora || Acoelomorpha || others},
File = {nielsen2008.pdf}
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@Article{Nielsen2005,
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File = {nielsen2004.pdf}
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@Article{Nielsen2003,
Title = {{Defining phyla: morphological and molecular clues to metazoan evolution}},
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File = {nielsen2003b.pdf}
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@Article{Nielsen2003b,
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File = {nielsen2003.pdf}
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@Article{Nielsen1996,
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Title = {{Gymnophrys cometa and Lecythium sp. are Core Cercozoa: Evolutionary Implications}},
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Abstract = {Amoebozoa: Tubulinea, Acanthopodida+Mayorella+'Platyamoeba', Flabellinea, Conosea (suph.?): Phalansterium || Multicilia+Gephyramoeba || Filamoeba || Archamoebae || Mycetozoa (Dictyo + Myxog); Crypto+Glauco; Hapto+Centroh; Breviata+Jacob; Diphyll+Metam},
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Journal = {Cell},
Year = {2018},
Number = {2},
Pages = {448--464--e24},
Volume = {174},
Doi = {10.1016/j.cell.2018.06.033},
File = {nishiyama2018_chara_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30007417}
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@Article{Nitsche2011,
Title = {{Higher Level Taxonomy and Molecular Phylogenetics of the Choanoflagellatea}},
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Year = {2011},
Number = {1144},
Pages = {1--11},
Abstract = {One class, two orders},
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@Article{Nitschke2010,
Title = {{The "green" phylogenetic clade of Rieske/cytb complexes}},
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Year = {2010},
Abstract = {Firmicutes were photosynthetic},
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File = {nitschke2010_heliobact.pdf},
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@Article{Noah2020,
Title = {{Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates}},
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Journal = {Evolutionary Bioinformatics},
Year = {2020},
Abstract = {Xiphosura in},
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Title = {{Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.}},
Author = {M. K. Nobu and J. A. Dodsworth and S. K. Murugapiran and C. Rinke and E. A. Gies and G. Webster and P. Schwientek and P. Kille and R. J. Parkes and H. Sass and B. B. J{\o}rgensen and A. J. Weightman and W.-T. Liu and S. J. Hallam and G. Tsiamis and T. Woyke and B. P. Hedlund},
Journal = {ISME J},
Year = {2015},
Abstract = {Firmicutes || OP9 || JS1},
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File = {nobu2015_atribacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26090992}
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Title = {{Molecular phylogeny of parabasalids with emphasis on the order Cristamonadida and its complex morphological evolution}},
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Title = {{Molecular phylogeny and evolution of parabasalia with improved taxon sampling and new protein markers of actin and elongation factor-1$\alpha$.}},
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Journal = {PLoS ONE},
Year = {2012},
Number = {1},
Pages = {e29938},
Volume = {7},
Abstract = {Same orders},
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Url = {http://www.ncbi.nlm.nih.gov/pubmed/22253832}
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Title = {{Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis}},
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Volume = {23},
Abstract = {As stated},
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Title = {{Deep metazoan phylogeny: When different genes tell different stories.}},
Author = {T. Nosenko and F. Schreiber and M. Adamska and M. Adamski and M. Eitel and J. Hammel and M. Maldonado and W. E. G. M{\"u}ller and M. Nickel and B. Schierwater and J. Vacelet and M. Wiens and G. W{\"o}rheide},
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Pages = {223--233},
Volume = {67},
Abstract = {Genomic + EST, minus some fast evolving ribosomal: Porifera*: Demosp + Hexact ||| Homoscl + Calcarea ||| Placozoa ||| Ctenophora + Cnidaria ||| Bilateria},
Doi = {10.1016/j.ympev.2013.01.010},
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Url = {http://www.ncbi.nlm.nih.gov/pubmed/23353073}
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Journal = {Science},
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Number = {4},
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Year = {2005},
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@Article{Nozaki2007,
Title = {{Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes}},
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Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {8},
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Title = {{Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes}},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2009},
Abstract = {Rhodo (+ Excav, or outside) || Glauco || Chlor || Hapt || Chromalv},
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Title = {{The Phylogenetic Position of Red Algae Revealed by Multiple Nuclear Genes from Mitochondria-Containing Eukaryotes and an Alternative Hypothesis on the Origin of Plastids}},
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Year = {2003},
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Year = {2019},
Number = {4},
Pages = {349 - 357},
Volume = {170},
Abstract = {As stated},
Doi = {10.1016/j.protis.2019.06.002},
File = {ntakou2019_artodiscus_multicilia.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31295666}
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Url = {http://creativecommons.org/licenses/}
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@Article{Obst2011,
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Year = {2011},
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Journal = {PLoS ONE},
Year = {2009},
Number = {9},
Pages = {e7080},
Volume = {4},
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File = {okamoto2009_hacrobia.pdf},
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@Article{Okamoto2012,
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Journal = {PLoS ONE},
Year = {2012},
Number = {6},
Pages = {e34900},
Volume = {7},
Abstract = {Perkinsida || Psammosa || Oxyrrhis || Ellob || Noctiluca, Syndinium and others},
Doi = {10.1371/journal.pone.0034900},
File = {okamoto2012_psammosa_early_dinoflagellates.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22719825}
}
@Article{Okamoto2006,
Title = {{\textit{Hatena arenicola} gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition}},
Author = {N. Okamoto and I. Inouye},
Journal = {Protist},
Year = {2006},
Pages = {401--419},
Volume = {27},
Abstract = {Hatena > Katablepharida},
File = {okamoto2006.pdf}
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@Article{Okamoto2005,
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Author = {N. Okamoto and I. Inouye},
Journal = {Protist},
Year = {2005},
Pages = {163--179},
Volume = {156},
Abstract = {Rhodo || Centrohe || Glau || Kata || Crypto; Hapto between Chlo and Alveo w/o support},
File = {okamoto2005.pdf}
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Number = {2},
Pages = {339--351},
Volume = {69},
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Year = {2012},
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@Article{Panek2014a,
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Year = {2014},
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Abstract = {As stated},
Doi = {10.1016/j.protis.2014.05.005},
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Pages = {41--51},
Volume = {98},
Abstract = {Macromycetozoa || Entamoeba || (Pelomyxa + Mastigella) + other Pelobiontida},
Doi = {10.1016/j.ympev.2016.01.011},
File = {panek2016_archamoebae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26826602}
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Pages = {830--836},
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Doi = {10.1016/j.tim.2010.11.001},
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Year = {2011},
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@MastersThesis{P2016,
Title = {{Labyrinthulomycetes diversity meta-analysis}},
Author = {J. Pan},
Year = {2016},
Abstract = {LABs || Oblongichytrium || LABs || Aplanochytrium + Labytinthula || LABs || Amphitremida incl. Diplophrys || Amphifilidae || Thrausto},
File = {pan2016_labyrhinthulomycetes.pdf},
Institution = {THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver)}
}
@Article{Pan2016,
Title = {{Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes}},
Author = {J. Pan and J. del Campo and P. J. Keeling},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2016},
Abstract = {Amphitremida (incl. Diplophrys) + Thraustochytr},
Doi = {10.1111/jeu.12342-4783},
File = {pan2016_labyrinhulomycetes.pdf}
}
@Article{Panek2011,
Title = {{Molecular Systematics of the Psalteriomonadidae, the Main Lineage of Anaerobic/Microaerophilic Heteroloboseans (Excavata: Discoba)}},
Author = {T. Panek and J. D. Silberman and N. Yubuki and B. S. Leander and I. Cepicka},
Journal = {Protist},
Year = {2011},
Abstract = {Stephanopogon ~ Vahlkampfia},
Doi = {10.1016/j.protis.2011.11},
File = {panek2011_psalteriomonadidae.djvu},
Url = {http://www.elsevier.de/protis}
}
@Article{Pantou2008,
Title = {{The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution}},
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Journal = {Gene},
Year = {2008},
Number = {1-2},
Pages = {7--15},
Volume = {419},
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File = {pantou2008.pdf}
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@Article{Papillon2004,
Title = {{Identification of Chaetognaths as Protostomes Is Supported by the Analysis of Their Mitochondrial Genome}},
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Journal = {Mol. Biol. and Evolution},
Year = {2004},
Number = {11},
Pages = {2122--2129},
Volume = {21},
Abstract = {Chaeto > Lophotrochozoa},
File = {papillon2004.pdf}
}
@Article{Paps2009,
Title = {{Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes}},
Author = {J. Paps and J. Baguna and M. Riutort},
Journal = {Proc. Biol. Sci.},
Year = {In press},
Abstract = {18 + 28S: Cnid ||| Acoel ||| Nemertd || Deut || Ecdys incl. Chaetog || Gnathost || Gastr || (Clade III: Micr + Rot/Aca) || (Clade II: Plat || Bry || Cycl + Entopr) || (Clade I: Nem || Annel s.l. || Moll || Brach + Phor)},
Doi = {10.1098/rspb.2008.1574},
File = {paps2009.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19129141}
}
@Article{Paps2009b,
Title = {{Bilaterian Phylogeny: A Broad Sampling of 13 Nuclear Genes Provides a New Lophotrochozoa Phylogeny and supports a paraphyletic basal Acoelomorpha}},
Author = {J. Paps and J. Baguna and M. Riutort},
Journal = {Mol. Biol. Evol.},
Year = {In press},
Abstract = {Gastr + Gnath || Synd + Bryoz || Entopr || Platyh || Nemert || Annel || Moll || Brachizoa (Brach + Phoron) vs. Cephalorh (!) || Chaetogn + Onych || Nemat || Paradox || Crust || Hexa},
File = {paps2009_bilateria.pdf}
}
@Article{Paps2012,
Title = {{Molecular Phylogeny of Unikonts: New Insights into the Position of Apusomonads and Ancyromonads and the Internal Relationships of Opisthokonts{\'i}}},
Author = {J. Paps and L. A. Medina-Chacon and W. Marshall and H. Suga and I. Ruiz-Trillo},
Journal = {Protist},
Year = {2012},
Abstract = {Ancyro || Apuso || Holomycota || Ichth || Coralloch || Filasterea || Choano || Metazoa},
Doi = {10.1016/j.protis.2012.09.002},
File = {paps2012_unikonts.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2012.09.002}
}
@Article{Paps2011,
Title = {{Molecular phylogeny of the phylum Gastrotricha: New data brings together molecules and morphology.}},
Author = {J. Paps and M. Riutort},
Journal = {Molecular phylogenetics and evolution},
Year = {2011},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2011.12.010},
File = {paps2011_gastrotricha.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22198640}
}
@Article{Paquin1996,
Title = {{The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus}},
Author = {B. Paquin and B. F. Lang},
Journal = {J. Mol. Biol.},
Year = {1996},
Number = {5},
Pages = {688--701},
Volume = {255}
}
@Article{Parfrey2006,
Title = {{Evaluating Support for the Current Classification of Eukaryotic Diversity}},
Author = {L. W. Parfrey and E. Barbero and E. Lasser and M. Dunthorn and D. Bhattacharya and D. J. Patterson and L. A. Katz},
Journal = {PLoS Genet.},
Year = {2006},
Number = {12},
Pages = {2062--2073},
Volume = {2},
Abstract = {Chromalveolata supported only in ~50% cases},
File = {parfrey2006.pdf}
}
@Article{Parfrey2010,
Title = {{Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.}},
Author = {L. W. Parfrey and J. Grant and Y. I. Tekle and E. Lasek-Nesselquist and H. G. Morrison and M. L. Sogin and D. J. Patterson and L. A. Katz},
Journal = {Syst. Biol.},
Year = {2010},
Number = {5},
Pages = {518--533},
Volume = {59},
Abstract = {SAR, Micrinuclearia + Ancyro, Diphylleia + Breviata, Telo + Glauco; Jacobids inc. Soginia || Percolom || Staphanopog; Polycystina paraph.; Metopion ~ Metro; Theratomyxa + Vampyrellidae || Plasmodioph; (?pseudo-)Corallomyxa ~ Filoreta},
Doi = {10.1093/sysbio/syq037},
File = {parfrey2010_euk.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20656852}
}
@Article{Parfrey2008,
Title = {{The Dynamic Nature of Eukaryotic Genomes}},
Author = {L. W. Parfrey and D. J. Lahr and L. A. Katz},
Journal = {Mol. Biol. Evol.},
Year = {2008},
Number = {4},
Pages = {787--794},
Volume = {25},
Abstract = {DNA is variable, especially in protists},
File = {parfrey2008.pdf}
}
@Article{Parfrey2013,
Title = {{Multicellularity arose several times in the evolution of eukaryotes (response to DOI 10.1002/Bies.201100187).}},
Author = {L. W. Parfrey and D. J. G. Lahr},
Journal = {Bioessays},
Year = {2013},
Number = {4},
Pages = {339--347},
Volume = {35},
Abstract = {As stated; Sorodiplophrys multicellular},
Doi = {10.1002/bies.201200143},
File = {parfrey2013_multicellularity_euk.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22930590}
}
@Article{Parfrey2011,
Title = {{Estimating the timing of early eukaryotic diversification with multigene molecular clocks}},
Author = {L. W. Parfrey and D. J. G. Lahr and A. H. Knoll and L. A. Katz},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2011},
Abstract = {Panalgae but no Unikonta: Opist || Amoeb || Exca || Panalgae},
Doi = {10.1073/pnas.1110633108},
File = {parfrey2011_euk_timing.pdf},
Url = {www.pnas.org/cgi/doi/10.1073/pnas.1110633108}
}
@Article{Park2021,
Title = {{Revisiting the phylogeny of microsporidia}},
Author = {E. Park and R. Poulin},
Journal = {International Journal for Parasitology},
Year = {2021},
Abstract = {Aphelida | Rozellida | Paramicrosporidium | Mitosporidium | Chytridiopsis | Metchnikovellids | others},
Doi = {10.1016/j.ijpara.2021.02.005},
File = {/home/alexey/coll/ref/os/1/park2021_microsporidia.pdf},
ISSN = {0020-7519},
Keywords = {microsporidia}
}
@Conference{Park2008,
Title = {{The isolation and identification of three extremely halophilic Heterolobosea from high salinity waters}},
Author = {J. S. Park and B. C. Cho and A. G. Simpson},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {Pleurostomum is assigned to Heterolobosea},
File = {park2008.txt}
}
@Article{Park2012,
Title = {{Characterization of Selenaion koniopes n. Gen., N. Sp., An Amoeba that Represents a New Major Lineage within Heterolobosea, Isolated from the Wieliczka Salt Mine.}},
Author = {J. S. Park and J. F. De Jonckheere and A. G. B. Simpson},
Journal = {J. Eukaryot. Microbiol.},
Year = {2012},
Abstract = {As stated},
Doi = {10.1111/j.1550-7408.2012.00641.x},
File = {park2012_selenaion_heterolobosea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22888835}
}
@Article{Park2009,
Title = {{Light Microscopic Observations, Ultrastructure, and Molecular Phylogeny of Hicanonectes teleskopos n. Gen., N. Sp., A Deep-Branching Relative of Diplomonads}},
Author = {J. S. Park and M. Kolisko and A. A. Heiss and A. G. B. Simpson},
Journal = {Journal of Eukaryotic Microbiology},
Year = {In press},
Abstract = {~ Carpediem.},
Doi = {10.1111/j.1550-7408.2009.00412.x},
File = {park2009_hicanonectes.pdf}
}
@Article{Park2010b,
Title = {{Cell Morphology and Formal Description of Ergobibamus cyprinoides n. G., N. Sp., Another Carpediemonas-Like Relative of Diplomonads.}},
Author = {J. S. Park and M. Kolisko and A. G. B. Simpson},
Journal = {J. Eukaryot. Microbiol.},
Year = {2010},
Number = {6},
Pages = {520--528},
Volume = {57},
Abstract = {~ Carpedieomonas and Kipferlia},
Doi = {10.1111/j.1550-7408.2010.00506.x},
File = {park2010_ergobibamus.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20880032}
}
@Article{Park2011a,
Title = {{Characterization of Pharyngomonas kirbyi (= "Macropharyngomonas halophila" nomen nudum), a Very Deep-branching, Obligately Halophilic Heterolobosean Flagellate}},
Author = {J. S. Park and A. G. B. Simpson},
Journal = {Protist},
Year = {2011},
Abstract = {As stated},
Doi = {10.1016/j.protis.2011.05.004},
File = {park2011_pharyngomonas.djvu},
Url = {http://www.elsevier.de/protis}
}
@Article{Park2010a,
Title = {{Characterization of halotolerant Bicosoecida and Placididea (Stramenopila) that are distinct from marine forms, and the phylogenetic pattern of salinity preference in heterotrophic stramenopiles}},
Author = {J. S. Park and A. G. B. Simpson},
Journal = {Environ. Microbiol.},
Year = {2010},
Abstract = {MAST 1, 2 and ? 4, 6, 7, 8, 9, 11 ~ to Hyphoch., Placididea || Bicosoec},
Doi = {10.1111/j.1462-2920.2010.02158.x},
File = {park2010_placididea_env.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20132281}
}
@Article{Park2007b,
Title = {{Ultrastructure and Phylogenetic Placement within Heterolobosea of the Previously Unclassified, Extremely Halophilic Heterotrophic Flagellate Pleurostomum flabellatum (Ruinen 1938)}},
Author = {J. S. Park and A. G. B. Simpson and W. J. Lee and B. C. Cho},
Journal = {Protist},
Year = {2007},
Number = {3},
Pages = {397--413},
Volume = {158},
Abstract = {Pleurostomum > Heterolobosea},
File = {park2007.txt}
}
@Article{Park2007,
Title = {{A common origin of complex life cycles in parasitic flatworms: evidence from the complete mitochondrial genome of Microcotyle sebastis (Monogenea: Platyhelminthes)}},
Author = {J.-K. Park and K.-H. Kim and S. Kang and W. Kim and K. S. Eom and D. T. J. Littlewood},
Journal = {BMC Evol. Biol.},
Year = {2007},
Number = {11},
Pages = {1--42},
Volume = {7},
Abstract = {Monogenea || Trematoda+Cestoda},
File = {park2007.pdf}
}
@Article{Park2006,
Title = {{First Molecular Data on the Phylum Loricifera~--- An Investigation into the Phylogeny of Ecdysozoa with Emphasis on the Positions of Loricifera and Priapulida}},
Author = {J.-K. Park and H. S. Rho and R. M. Kristensen and W. Kim and G. Giribet},
Journal = {Zool. Sci.},
Year = {2006},
Pages = {943--954},
Volume = {23},
Abstract = {18S: Loricifera not sister to Priapulida; sometimes basal or close to Nematoph. or Tardigrada; Tardigrada sep. from Onych.; Nematomorpha does not group with Nematoida },
File = {park2006.pdf}
}
@Article{Park2007a,
Title = {{The complete mitochondrial genome of the sea spider \textit{Achelia bituberculata} (Pycnogonida, Ammotheidae): arthropod ground pattern of gene arrangement}},
Author = {S.-J. Park and Y.-S. Lee and U. W. Hwang},
Journal = {BMC Genomics},
Year = {2007},
Number = {343},
Pages = {1--46},
Volume = {8},
Abstract = {Pycnogonidae in Chelic.}
}
@Article{Park2011b,
Title = {{A stem-group cnidarian described from the mid-Cambrian of China and its significance for cnidarian evolution}},
Author = {T.-y. Park and J. Woo and D.-J. Lee and D.-C. Lee and S.-b. Lee and Z. Han and S. K. Chough and D. K. Choi},
Journal = {Nature Communications},
Year = {2011},
Number = {442},
Volume = {2},
Abstract = {As stated},
Doi = {10.1038/ncomms1457},
File = {park2011_stem_group_cnidarian.pdf},
Url = {www.nature.com/naturecommunications}
}
@Article{Parkhaev2017,
Title = {{Origin and the Early Evolution of the Phylum Mollusca}},
Author = {P. Yu. Parkhaev},
Journal = {Paleontological Journal},
Year = {2017},
Number = {6},
Pages = {663 - 686},
Volume = {51},
Abstract = {palaeontology: Polypl + Apl || Gastr || Bivalv || Ceph + Mono + Scaph},
Doi = {10.1134/S003103011706003X},
File = {parkhaev2017_origin_of_mollusca.pdf}
}
@Article{Parks2018,
Title = {{A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.}},
Author = {D. H. Parks and M. Chuvochina and D. W. Waite and C. Rinke and A. Skarshewski and P.-A. Chaumeil and P. Hugenholtz},
Journal = {Nature Biotechnology},
Year = {2018},
Number = {10},
Pages = {996--1004},
Volume = {36},
Abstract = {http://gtdb.ecogenomic.org -- use GTDB to help with taxonomic decisions and double checking new names; Firmicutes and Proteobacteria polyphyletic},
Doi = {10.1038/nbt.4229},
File = {parks2018_stand_bact_taxonomy.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24678308}
}
@Article{Parks2017,
Title = {{Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.}},
Author = {D. H. Parks and C. Rinke and M. Chuvochina and P.-A. Chaumeil and B. J. Woodcroft and P. N. Evans and P. Hugenholtz and G. W. Tyson},
Journal = {Nature microbiology},
Year = {2017},
Number = {11},
Pages = {1533 - 1542},
Volume = {2},
Abstract = {Multiple UAP (Archaea) and UBP (bacteria) phyla; decision so far is not to list them},
Doi = {10.1038/s41564-017-0012-7},
File = {parks2017_uap_ubp_candidate_phyla.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/29234139}
}
@Article{Parry2016,
Title = {{The impact of fossil data on annelid phylogeny inferred from discrete morphological characters.}},
Author = {L. A. Parry and G. D. Edgecombe and D. Eibye-Jacobsen and J. Vinther},
Journal = {Proc. Biol. Sci.},
Year = {2016},
Number = {1837},
Volume = {283},
Abstract = {Support for Sedentaria (incl. Sibolg. and Echiur.) and Errantia, Sipuncula excluded, "Palaeoann" in Sedentaria},
Doi = {10.1098/rspb.2016.1378},
File = {parry2016_annelida_plus_fossils.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27581880}
}
@Article{Parry2014,
Title = {{The origin of annelids}},
Author = {L. Parry and A. Tanner and J. Vinther},
Journal = {Palaeontology},
Year = {2014},
Pages = {1091--1103},
Volume = {57},
Abstract = {Review},
Doi = {10.1111/pala.12129},
File = {parry2014_origin_of_annelids.pdf}
}
@Article{Pascual2016,
Title = {{Longimicrobium terrae gen. Nov., Sp. Nov., An oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers.}},
Author = {J. Pascual and M. Garc{\'i}a-L{\'o}pez and G. F. Bills and O. Genilloud},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2016},
Number = {5},
Pages = {1976--1985},
Volume = {66},
Abstract = {Gemmatimonadetes: Longimicrobia},
Doi = {10.1099/ijsem.0.000974},
File = {pascual2016_longimicrobia.txt},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26873585}
}
@Article{Pashley1993,
Title = {{Systematics of holometabolous insect orders based on 18S ribosomal RNA.}},
Author = {D. P. Pashley and B. A. McPheron and E. A. Zimmer},
Journal = {Mol. Phyl. Evol.},
Year = {1993},
Number = {2},
Pages = {132--142},
Volume = {2}
}
@Article{Passamaneck2006,
Title = {{Lophotrochozoan phylogeny assessed with LSU and SSU data: Evidence of lophophorate polyphyly}},
Author = {Y. Passamaneck and K. M. Halanych},
Journal = {Mol. Phyl. Evol.},
Year = {2006},
Number = {1},
Pages = {20--28},
Volume = {40},
Abstract = {LSU+SSU: Bryozoa || Sipuncul || Phoro+Brachi (polyph.) || Mollusca || Annelida || Nemertea || Entopr+Cycl || Platyh || Rotif+Acanth; LSU: monoph. Phoro+Brachi; Sipun+Anne},
File = {passamaneck2006.pdf}
}
@Article{Passamaneck2004,
Title = {{Evidence from Hox genes that bryozoans are lophotrochozoans}},
Author = {Y. J. Passamaneck and K. M. Halanych},
Journal = {Evol. Dev.},
Year = {2004},
Number = {4},
Pages = {275--281},
Volume = {6},
Abstract = {As stated},
File = {passamaneck2004b.pdf}
}
@Article{Passamaneck2004b,
Title = {{Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences}},
Author = {Y. J. Passamaneck and C. Schander and K. M. Halanych},
Journal = {Mol. Phyl. Evol.},
Year = {2004},
Pages = {25--38},
Volume = {32},
Abstract = {Neomenio+Polypl+Bivalv (polyph.) || Gastro || Cephal+Chaet+Scapho},
File = {passamaneck2004a.pdf}
}
@Article{Pastrana2019,
Title = {{Sponges Lack ParaHox Genes.}},
Author = {C. C. Pastrana and M. B. DeBiasse and J. F. Ryan},
Journal = {Genome Biol Evol},
Year = {2019},
Number = {4},
Pages = {1250 - 1257},
Volume = {11},
Abstract = {As stated, so likely basal},
Doi = {10.1093/gbe/evz052},
File = {pastrana2019_sponges_lack_parahox.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30859199}
}
@Article{Patil2009,
Title = {{Revisiting the Phylogenetic Position of Synchroma grande}},
Author = {V. Patil and J. Brate and K. Shalchian-Tabrizi and K. S. Jakobsen},
Journal = {Journal of Eukaryotic Microbiology},
Year = {In press},
Abstract = {||| Picophagus || Synchroma + Chlamydomyxa || Synura snd other Chrysophyceae},
Doi = {10.1111/j.1550-7408.2009.00389.x},
File = {patil2009_synchroma.pdf}
}
@Article{Patron2007,
Title = {{Multiple Gene Phylogenies Support the Monophyly of Cryptomonad and Haptophyte Host Lineages}},
Author = {N. J. Patron and Y. Inagaki and P. J. Keeling},
Journal = {Curr. Biol.},
Year = {2007},
Number = {10},
Pages = {887--891},
Volume = {17},
Abstract = {Slow-evolving proteins: Chrom+Excav+Alv vs. Crypto+Hapto || Rhod || Glauc || Viridi},
File = {patron2006.pdf}
}
@Article{Patterson1985,
Title = {{The fine structure of Opalina ranarum (Family Opalinidae): opalinid phylogeny and classification}},
Author = {D. Patterson},
Journal = {Protistologica},
Year = {1985},
Number = {4},
Pages = {413--428},
Volume = {21}
}
@InCollection{Patterson1986,
Title = {{The actinophryid heliozoa (Sarcodina, Actinopoda) as chromophytes}},
Author = {D. J. Patterson},
Booktitle = {Chromophytes: aspects and problems},
Publisher = {Cambridge University Press},
Year = {1986},
Address = {Cambridge},
Editor = {J. Kristiansen and R. A. Anderson},
Pages = {49--67}
}
@Article{Patterson2000,
Title = {{The Lineages of Eukaryotes}},
Author = {D. J. Patterson},
Journal = {Tree of Life Project},
Year = {2000},
Abstract = {Genera of protists for which no clear identity has been developed (after Patterson, 1999) are listed here},
File = {patterson2000_lineages_of_eukaryotes.htm}
}
@Article{Patterson1999,
Title = {{The Diversity of Eukaryotes}},
Author = {David J. Patterson},
Journal = {Amer. Nat.},
Year = {1999},
Pages = {S96--S124},
Volume = {65}
}
@Conference{Patterson1993,
Title = {{Protozoa: evolution and systematics}},
Author = {D. J. Patterson},
Booktitle = {{Hausmann K., Hulsmann N. Progress in protozoology. Proceedings of the IX International Congress of Protozoology}},
Year = {1993},
Address = {Berlin},
Pages = {1--14}
}
@Article{Patterson1993a,
Title = {{The Current Status of the Free-Living Heterotrophic Flagellates}},
Author = {D. J. Patterson},
Journal = {J. Euk. Microbiol.},
Year = {1993},
Number = {5},
Pages = {606--609},
Volume = {40}
}
@Article{Patterson1988a,
Title = {The evolution of protozoa},
Author = {D. J. Patterson},
Journal = {Mem. Inst. Oswaldo Cruz},
Year = {1988},
Number = {1 Suppl.},
Pages = {593--594},
Volume = {83}
}
@Article{Patterson1985a,
Title = {{On the Organization and Affinities of the Amoeba, Pompholyxophrys punicea Archer, Based on Ultrastructural Examination of Individual Cells from Wild Material}},
Author = {D. J. Patterson},
Journal = {J. Protozool.},
Year = {1985},
Number = {2},
Pages = {241--246},
Volume = {32}
}
@Article{Patterson1990,
Title = {{Massisteria marina Larsen \& Patterson 1990, a widespread and abundant bacterivorous protist associated with marine detritus}},
Author = {D. J. Patterson and T. Fenchel},
Journal = {Mar. Ecol. Prog. Ser.},
Year = {1990},
Pages = {11--19},
Volume = {62}
}
@Article{Pavan2018,
Title = {{Proposal for a new classification of a deep branching bacterial phylogenetic lineage: Transfer of Coprothermobacter proteolyticus and Coprothermobacter platensis to Coprothermobacteraceae fam. Nov., Within Coprothermobacterales ord. Nov., Coprothermobacteria classis nov. And Coprothermobacterota phyl. Nov. And emended description of the family Thermodesulfobiaceae}},
Author = {M. E. Pavan and E. E. Pavan and S. P. Glaeser and C. Etchebehere and P. K{\"a}mpfer and M. J. Pettinari and N. I. L{\'o}pez},
Year = {2018},
Abstract = {Firmicutes::Coprothermobacteria (note Jumas-Bilak et al., 2009 placed them in OP1, now Acetotermia, but only on figure)},
Doi = {10.1099/ijsem.0.002720},
File = {pavan2018_coprothermobacteria.txt},
Url = {http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002720}
}
@Article{Pawlowski2013,
Title = {{The new micro-kingdoms of eukaryotes}},
Author = {J. Pawlowski},
Journal = {BMC Biology},
Year = {2013},
Pages = {40},
Volume = {11},
Abstract = {Review; most of small Hacrobia lineages are "kingdoms"},
Doi = {10.1126/science.ns-11.260.40},
File = {pawlowski2013_micro_kingdoms_euk.pdf},
Url = {http://creativecommons.org/licenses/by/2.0),}
}
@Article{Pawlowski2013a,
Title = {{New supraordinal classification of Foraminifera: Molecules meet morphology}},
Author = {J. Pawlowski},
Journal = {Marine Micropaleontology},
Year = {2013},
Abstract = {Monothalamids* (ncl. Allogromiida, Astrorhizida, Xenoph), Tubothalamea (Spirillina), Globothalamea (Globigerina)},
Doi = {10.1016/j.marmicro.2013.04.002},
File = {pawlowski2013_foraminifera.pdf},
ISSN = {0377-8398},
Url = {http://dx.doi.org/10.1016/j.marmicro.2013.04.002}
}
@Article{Pawlowski2008,
Title = {{The twilight of Sarcodina: a molecular perspective on the polyphyletic origin of amoeboid protists}},
Author = {J. Pawlowski},
Journal = {Protistology},
Year = {2008},
Number = {4},
Pages = {281--302},
Volume = {5},
Abstract = {Amoebozoa: Lobosa: Tubulinea, Flabellinea, Acanthopodida, Thecamoebida, Mayorella, Cochliopodium, Trichosphaerium, Vermistella; Conosa: Eumycetozoa, Archamoeba, Protostelida excl. Ceratiomyxa, Filamoeba, Acramoeba, Multicilia, Phalansterium, "Arachnula" ATCC},
File = {pawlowski2008.pdf}
}
@Article{Pawlowski1996a,
Title = {{Early origin of foraminifera suggested by {SSU} r{RNA} gene sequences}},
Author = {J. Pawlowski and I. Bolivar and J. F. Fahrni and T. Cavalier-Smith and M. Gouy},
Journal = {Mol. Biol. Evol.},
Year = {1996},
Number = {3},
Pages = {445--450},
Volume = {13}
}
@Article{Pawlowski2009,
Title = {{Untangling the Phylogeny of Amoeboid Protists}},
Author = {J. Pawlowski and F. Burki},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2009},
Pages = {16--25},
Volume = {56},
Abstract = {Tubulinea, Dermamoeba + Mayorella, Flabellinea, Variosea (Multic, Acra, Phalan, Filam, "Arachn"), Mayorella, Thecamoebida, Conosea (Mycet, Archam); Retaria: (Acantharea || Taxop (incl. Larcopyle) || Spumellaria || Collodaria + Nassellaria) + ((Phytomyxea+Vampyrellida [Platyreta] || Foraminifera [incl. Reticulomyxa] || Filoreta || Gromia Haplosporidia + Paradinium) || Cercozoa)},
File = {pawlowski2009_amoeboid.pdf}
}
@Article{Pawlowski2007,
Title = {{Phylogenetic position of Trichosidae}},
Author = {J. Pawlowski and J. F. Fahrni},
Journal = {Protistology},
Year = {2007},
Pages = {9--91},
Volume = {5},
Abstract = {Trichosphaerium > Amoebozoa i.s.},
File = {pawlowski2007.txt}
}
@Article{Pawlowski2002,
Title = {{Molecular phylogeny of Foraminifera~--- a review}},
Author = {J. Pawlowski and M. Holzmann},
Journal = {Eur. J. Protistol.},
Year = {2002},
Pages = {1--10},
Volume = {38}
}
@Article{Pawlowski1996,
Title = {{Origin of the Mesozoa inferred from 18S rRNA gene sequences}},
Author = {J. Pawlowski and J. I. Montoya-Burgos and J. F. Fahrni and J. Wuest and L. Zaninetti},
Journal = {Mol. Biol. Evol.},
Year = {1996},
Pages = {1128--1132},
Volume = {13}
}
@Unpublished{Pawlowski2003,
Title = {{\textit{Reticulamoeba} sp., the closest naked relative to testate Gromia and Foraminifera}},
Author = {J. Pawlowski and S. Nikolaev and C. Berney and J. Fahrni and A. Mylnikov and N. Petrov},
Note = {http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore\&val=33641927},
Year = {2003},
Abstract = {GenBank submission AY268044},
Url = {http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=33641927}
}
@Article{Pawson2007,
Title = {{Phylum Echinodermata}},
Author = {D. L. Pawson},
Journal = {Zootaxa},
Year = {2007},
Pages = {749--764},
Volume = {1668},
Abstract = {Astero incl. Concentr.},
File = {pawson2007.pdf}
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@Article{Paxton2005,
Title = {{Molting polychaete jaws--ecdysozoans are not the only molting animals}},
Author = {H. Paxton},
Journal = {Evol. Dev.},
Year = {2005},
Number = {4},
Pages = {337--340},
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Abstract = {Subj},
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@Article{Pearse2007,
Title = {{Field biology of placozoans (\textit{Trichoplax}): distribution, diversity, biotic interactions}},
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Journal = {Integr. Comp. Biol.},
Year = {2007},
Number = {5},
Pages = {677--692},
Volume = {47},
File = {pearse2007.pdf}
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Year = {2018},
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Doi = {10.1002/ajb2.1016},
File = {pease2018_quartet_sampling_plant_tol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29746719}
}
@Article{Peer1996,
Title = {The evolution of Stramenopiles and Alveolates as derived by rate calibration of small ribosomal subunit {RNA}},
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Journal = {J. Mol. Evol.},
Year = {1996},
Pages = {201--210},
Volume = {42}
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@Article{Peer1996a,
Title = {{Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae}},
Author = {Y. van de Peer and S. A. Rensing and U.-G. Maier and R. de Wachter},
Journal = {Proc. Natl. Acad. Sci. USA},
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Volume = {93}
}
@Article{Peer1997,
Title = {Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18s r{RNA}},
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Journal = {J. Mol. Evol.},
Year = {1997},
Pages = {619--630},
Volume = {45}
}
@Article{Peer2000,
Title = {{An Updated and Comprehensive rRNA Phylogeny of (Crown) Eukaryotes Based on Rate-Calibrated Evolutionary Distances}},
Author = {Yves Van de Peer and Sandra L. Baldauf and W. Ford Doolittle and Axel Meyer},
Journal = {J. Mol. Evol.},
Year = {2000},
Pages = {565--576},
Volume = {51}
}
@Article{Pekkarinen2003,
Title = {{Phylogenetic Position and Ultrastructure of Two \textit{Dermocystidium} Species (Ichthyosporea) from the Common Perch (Perca fluviatilis)}},
Author = {M. Pekkarinen and J. Lom and C. Murphy and M. Ragan and I. Dykova},
Journal = {Acta Protozool.},
Year = {2003},
Pages = {287--307},
Volume = {42},
Abstract = {have the anucleate stage of development},
File = {pekkarinen2003.pdf}
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@Article{Pena2008,
Title = {{Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by hornworts and vascular plants}},
Author = {M. J. Pena and A. G. Darvill and S. Eberhard and W. S. York and M. A. O'Neill},
Journal = {Glycobiology},
Year = {2008},
Number = {11},
Pages = {891--904},
Volume = {18},
Abstract = {As stated},
Doi = {10.1093/glycob/cwn078},
File = {pena2008.txt}
}
@Article{PereaAtienza2015,
Title = {{The nervous system of Xenacoelomorpha: A genomic perspective.}},
Author = {E. Perea-Atienza and B. Gavil{\'a}n and M. Chiodin and J. F. Abril and K. J. Hoff and A. J. Poustka and P. Martinez},
Journal = {J. Exp. Biol.},
Year = {2015},
Number = {Pt--4},
Pages = {618--628},
Volume = {218},
Abstract = {As stated},
Doi = {10.1242/jeb.110379},
File = {perea-atienza2015_xenacoelomorpha.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25696825}
}
@Article{Perestenko1972,
Title = {{Ontogenesis of Phaeophyta and ontogenetic principle of cunstructing phylogenetic systems}},
Author = {L. P. Perestenko},
Journal = {Botanicheskij Zhurnal},
Year = {1972},
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File = {perestenko1972_indiv_razv_byr_vod.pdf}
}
@Article{PerezLosada2009,
Title = {{Remarkable convergent evolution in specialized parasitic Thecostraca (Crustacea)}},
Author = {M. Perez-Losada and J. T. Hoeg and K. A. Crandall},
Journal = {BMC Biol.},
Year = {In press},
Number = {1},
Pages = {15},
Volume = {7},
Abstract = {Coipepoda + Malac, Faceto || Ascoth || Acrothor || Cirripedia},
Doi = {10.1186/1741-7007-7-15},
File = {perez-losada2009_thecostraca.pdf}
}
@Article{PerezLosada2012,
Title = {{Deep phylogeny and character evolution in thecostraca (Crustacea: Maxillopoda).}},
Author = {M. Perez-Losada and J. T. Hoeg and K. A. Crandall},
Journal = {Integr. Comp. Biol.},
Year = {2012},
Number = {3},
Pages = {430--442},
Volume = {52},
Abstract = {Faceto || Ascoth || Cirripedia},
Doi = {10.1093/icb/ics051},
File = {perez-losada2012_thecostraca.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22532607}
}
@Article{PerezLosada2002,
Title = {{Reanalysis of the relationships among the Cirripedia and the Ascothoracida and the phylogenetic position of the Facetotecta (Maxillopoda: Thecostraca) using 18s rDNA sequences}},
Author = {M. Perez-Losada and J. T. Hoeg and G. A. Kolbasov and K. A. Crandall},
Journal = {J. Crust. Biol.},
Year = {2002},
Number = {3},
Pages = {661--669},
Volume = {22},
Abstract = {Facetotecta || Asco || Cirri},
File = {perez-losada2002.pdf}
}
@Article{Pernice2013,
Title = {{General patterns of diversity in major marine microeukaryote lineages.}},
Author = {M. C. Pernice and R. Logares and L. Guillou and R. Massana},
Journal = {PLoS ONE},
Year = {2013},
Number = {2},
Pages = {e57170},
Volume = {8},
Abstract = {MAST-8,9,7,12,3 + Bicos || MAST-4 + Oo || MAST-2,1 + Labyr + Pirso || Heter; RAD A and RAD B},
Doi = {10.1371/journal.pone.0057170},
File = {pernice2013_microeukaryotes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/12136088}
}
@Article{Perron2000,
Title = {{Evidence from sequence-tagged-site markers of a recent progenitor-derivative species pair in conifers}},
Author = {M. Perron and D. J. Perry and C. Andalo and J. Bousquet},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2000},
Number = {21},
Pages = {11331--11336},
Volume = {97}
}
@Article{Perseke2010,
Title = {{Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata}},
Author = {M. Perseke and D. Bernhard and G. Fritzsch and F. Br{\"u}mmer and P. F. Stadler and M. Schlegel},
Journal = {Molecular phylogenetics and evolution},
Year = {2010},
Abstract = {Crino || Oph || Aster || Echin || Holotur},
Doi = {10.1016/j.ympev.2010.01.035},
File = {perseke2010_echinodermata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20152912}
}
@Article{Perseke2013,
Title = {{The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny.}},
Author = {M. Perseke and A. Golombek and M. Schlegel and T. H. Struck},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Number = {3},
Pages = {898--905},
Volume = {66},
Abstract = {weird},
Doi = {10.1016/j.ympev.2012.11.019},
File = {perseke2013_mt_deuterostomes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23228546}
}
@Article{Perseke2012,
Title = {{The Impact of Mitochondrial Genome Analyses on the Understanding of Deuterostome Phylogeny}},
Author = {M. Perseke and A. Golombek and M. Schlegel and T. H. Struck},
Journal = {Molecular Phylogenetics and Evolution},
Year = {2012},
Abstract = {Xenoturb weakly with Deuterost, Tunicata basal (!)},
Doi = {10.1016/j.ympev.2012.11.019},
File = {perseke2012_mt_genome_deuterostomia.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2012.11.019}
}
@Article{Perseke2007,
Title = {{The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis}},
Author = {M. Perseke and T. Hankeln and B. Weich and G. Fritzsch and P. F. Stadler and O. Israelsson and D. Bernhard and M. Schlegel},
Journal = {Theor. Biosci.},
Year = {2007},
Pages = {16--18},
Volume = {126},
Abstract = {Sister to Ambulacraria + Chordata},
File = {perseke2007.pdf}
}
@Article{Perseke2011,
Title = {{The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria}},
Author = {M. Perseke and J. Hetmank and M. Bernt and P. F. Stadler and M. Schlegel and D. Bernhard},
Journal = {BMC Evol. Biol.},
Year = {2011},
Pages = {134},
Volume = {11},
Abstract = {|| Ophiuroidea (!) ("hampered"?)},
Doi = {10.1186/1471-2148-11-134},
File = {perseke2011_rhabdopleura.pdf},
Url = {http://www.biomedcentral.com/1471-2148/11/134}
}
@Article{Pester2011,
Title = {{The Thaumarchaeota: An emerging view of their phylogeny and ecophysiology}},
Author = {M. Pester and C. Schleper and M. Wagner},
Journal = {Current Opinion in Microbiology},
Year = {2011},
Pages = {1--7},
Volume = {14},
Abstract = {At least 7 subgroups},
Doi = {10.1016/j.mib.2011.04.007},
File = {pester2011_thaumarchaeota.pdf},
ISSN = {1369-5274},
Url = {http://dx.doi.org/10.1016/j.mib.2011.04.007}
}
@Article{Petersen2014,
Title = {{Chromera velia, endosymbioses and the rhodoplex hypothesis--plastid evolution in cryptophytes, alveolates, stramenopiles, and haptophytes (CASH lineages).}},
Author = {J. Petersen and A.-K. Ludewig and V. Michael and B. Bunk and M. Jarek and D. Baurain and H. Brinkmann},
Journal = {Genome Biol Evol},
Year = {2014},
Number = {3},
Pages = {666--684},
Volume = {6},
Abstract = {Independent},
Doi = {10.1093/gbe/evu043},
File = {petersen2014_chromera_and_independent_symbioses.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18288187}
}
@Article{Petersen2006,
Title = {{A ``Green'' Phosphoribulokinase in Complex Algae with Red Plastids: Evidence for a Single Secondary Endosymbiosis Leading to Haptophytes, Cryptophytes, Heterokonts, and Dinoflagellates}},
Author = {J. Petersen and R. Teich and H. Brinkmann and R. Cerff},
Journal = {J. Mol. Evol.},
Year = {2006},
Pages = {143--157},
Volume = {62},
Abstract = {Hapto+Crypto+Chrom+Dino},
File = {petersen2006.pdf}
}
@Article{Peterson2001,
Title = {{Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S DNA gene sequences}},
Author = {K.J. Peterson and D.J. Eernisse},
Journal = {Evol. Dev.},
Year = {2001},
Pages = {170--205},
Volume = {3}
}
@Article{Peterson2007,
Title = {{Poriferan ANTP genes: primitively simple or secondarily reduced?}},
Author = {K. J. Peterson and E. A. Sperling},
Journal = {Evol. Dev.},
Year = {2007},
Number = {5},
Pages = {405--408},
Volume = {9},
Abstract = {ANTP genes may be lost in Porifera and Placozoa; Porifera are paraphyletic},
File = {peterson2007.pdf}
}
@Article{Peterson2013,
Title = {{MicroRNAs support the monophyly of enteropneust hemichordates.}},
Author = {K. J. Peterson and Y.-H. Su and M. I. Arnone and B. Swalla and B. L. King},
Journal = {J. Exp. Zool. B Mol. Dev. Evol.},
Year = {2013},
Number = {6},
Pages = {368--374},
Volume = {320},
Abstract = {As stated},
Doi = {10.1002/jez.b.22510},
File = {peterson2013_hemichordates_mirna.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23703796}
}
@Article{Petitjean2015a,
Title = {{Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.}},
Author = {C. Petitjean and P. Deschamps and P. L{\'o}pez-Garc{\'i}a and D. Moreira},
Journal = {Genome Biol Evol},
Year = {2015},
Number = {1},
Pages = {191--204},
Volume = {7},
Abstract = {Eutyarchaeota: Archeoglobi, Methanobacteria, Methanococci, Methanomicrobia (incl. Halo), Methanopyri, Nanoarchaea, Parvarchaea, Thermococci, Thermoplasmata; Proteoarchaeota: Aigiarchaea, Crenarchaea, Korarchaea, Thaumarchaea},
Doi = {10.1093/gbe/evu274},
File = {petitjean2014_proteroarchaeota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/1545865}
}
@Article{Petitjean2015b,
Title = {{Extending the conserved phylogenetic core of Archaea disentangles the evolution of the third domain of Life}},
Author = {C. Petitjean and P. Deschamps and P. L{\'o}pez-Garc{\'i}a and D. Moreira and C. Brochier-Armanet},
Journal = {Molecular Biology and Evolution},
Year = {2015},
Abstract = {Methamonada: Methanopyrales, Methanobacteriales, Methanococcales; Diaforarchaea: Thermoplasmatae, Aciduliprofundum; Methanogens class II: Methanocellales, Methanosarcinales, Methanomicrobiales (+ Archaeoglobales and Halobacteriales)},
File = {petitjean2015_archaea.pdf}
}
@Article{Petrov2010,
Title = {{New Insight into the Phylogeny of Mesozoa: Evidence from the 18S and 28S rRNA Genes}},
Author = {N. B. Petrov and V. V. Aleshin and A. N. Pegova and M. V. Ofitserov and G. S. Slyusarev},
Journal = {Moscow University Biological Sciences Bulletin},
Year = {2010},
Number = {4},
Pages = {167--169},
Volume = {65},
Abstract = {18+28S: Nemert || Moll || Mesozoa || Annel},
Doi = {10.3103/S0096392510040127},
File = {petrov2010_mesozoa.pdf}
}
@Conference{Petrov2007,
Title = {{Combined 18 and 28S rRNA gene sequences suggest relatedness gastrotrichs and dicyemids to flat worms, and orthonectids~--- to annelids}},
Author = {N. B. Petrov and V. V. Aleshin and I. P. Vladychenskaya and O. G. Manylov and G. S. Slyusarev and A. N. Pegova and L. Y. Rusin and M. V. Ophitserov},
Booktitle = {{Computational phylogenetics and genosystematics. Moscow State University, 16--19 November 2007}},
Year = {2007}
}
@Article{Petrov2005,
Title = {{Phylogeny of Molting Protostomes (Ecdysozoa) as Inferred from 18S and 28S rRNA Gene Sequences}},
Author = {N. B. Petrov and N. S. Vladychenskaya},
Journal = {Mol. Biol.},
Year = {2005},
Number = {4},
Pages = {503--513},
Volume = {39},
Abstract = {Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, and Crustacea + Hexapoda},
File = {petrov2005.pdf}
}
@Article{Petrunina2013,
Title = {{Tantulocarida versus Thecostraca: Inside or outside? First attempts to resolve phylogenetic position of Tantulocarida using gene sequences}},
Author = {A. Petrunina and T. Neretina and N. Mugue and G. Kolbasov},
Journal = {J Zoolog Syst Evol Res},
Year = {2013},
Abstract = {Ceph + Remip; Ostrac + Brachiura + Pentast + Mystac; Thecostraca: Cirr + Tantulocarida || Facetotecta + Ascothoracida; Copep + Brachiop},
Doi = {10.1111/jzs.12045},
File = {petrunina2014_tantulocarida.pdf},
Keywords = {tantulocarida, cirripedia, thecostraca, phylogeny, molecular genetics, 18s rdna, cement adhesion, rootlet system}
}
@Article{Petrushevskaja1982,
Title = {Are Acantharia in the superclassis of Sarcodina or it is a separate phylum of animals?},
Author = {M. G. Petrushevskaja},
Journal = {Zool. Zhurn.},
Year = {1982},
Note = {(In Russian)},
Number = {11},
Pages = {1--11},
Volume = {61},
Abstract = {sistematika, evoljucija, Radiozoa, Protista}
}
@InCollection{Petrushevskaja1981,
Title = {Sarcodines of the Actinopoda superclassis: taxonomy and phylogeny},
Author = {M. G. Petrushevskaja},
Booktitle = {Sistema, evoljucija i stratigraficheskoe znachenie radioljarij},
Publisher = {Nauka},
Year = {1981},
Address = {Moskva},
Note = {(In Russian)},
Pages = {10--17},
Abstract = {sistematika, evoljucija, Radiozoa, Protista}
}
@Article{Petrushevskaja1977,
Title = {About origin of radiolarians},
Author = {M. G. Petrushevskaja},
Journal = {Zool. Zhurn.},
Year = {1977},
Note = {(In Russian)},
Number = {10},
Pages = {1--10},
Volume = {54},
Abstract = {evoljucija, Radiozoa, Protista}
}
@Article{Peyretaillade1998b,
Title = {{Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core}},
Author = {E. Peyretaillade and C. Biderre and P. Peyret and F. Duffieux and G. M. Metenier and M. Gouy and B. Michot and C. P. Vivares},
Journal = {Nucl. Acids Res.},
Year = {1998},
Number = {15},
Pages = {3513--3520},
Volume = {26},
Abstract = {Reduced},
File = {peyretaillade1998.pdf}
}
@Article{Peyretaillade1998,
Title = {{Microsporidia, Amitochondrial Protists, Possess a 70-kDa Heat Shock Protein Gene of Mitochondrial Evolutionary Origin}},
Author = {E. Peyretaillade and V. Broussolle and P. Peyret and G. Motonier and M. Gouy and C. P. Vivares},
Journal = {Mol. Biol. Evol.},
Year = {1998},
Number = {6},
Pages = {683--689},
Volume = {15}
}
@Article{Philippe2011a,
Title = {{Acoelomorph flatworms are deuterostomes related to Xenoturbella}},
Author = {H. Philippe and H. Brinkmann and R. R. Copley and L. L. Moroz and H. Nakano and A. J. Poustka and A. Wallberg and K. J. Peterson and M. J. Telford},
Journal = {Nature},
Year = {2011},
Number = {4},
Pages = {255--258},
Volume = {38},
Abstract = {As stated [but still unclear]},
Doi = {10.1038/nature09676},
File = {philippe2011_xenacoelomorpha.pdf}
}
@Article{Philippe2011b,
Title = {{Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough}},
Author = {H. Philippe and H. Brinkmann and D. V. Lavrov and D. T. J. Littlewood and M. Manuel and G. Worheide and D. Baurain},
Journal = {PLoS Biology},
Year = {2011},
Number = {3},
Pages = {e1000602},
Volume = {9},
Abstract = {Dunn and Schierwater probably artifacts, best is Porif || Placoz || Cten + Cnid},
File = {philippe2011_basal_metazoa.pdf}
}
@Article{Philippe2007,
Title = {{Acoel Flatworms Are Not Platyhelminthes: Evidence from Phylogenomics}},
Author = {H. Philippe and H. Brinkmann and P. Martinez and M. Riutort and J. Baguna},
Journal = {PLoS One},
Year = {2007},
Number = {8},
Pages = {e717},
Volume = {2},
Abstract = {Acoela || Deuterostomia},
Doi = {10.1371/journal.pone.0000717},
File = {philippe2007.pdf}
}
@Article{Philippe2009,
Title = {{Phylogenomics Revives Traditional Views on Deep Animal Relationships}},
Author = {H. Philippe and R. Derelle and P. Lopez and K. Pick and C. Borchiellini and N. Boury-Esnault and J. Vacelet and E. Renard and E. Houliston and E. Queinnec and D. Silva and C and P. Wincker and H. Le Guyader and S. Leys and D. J. Jackson and F. Schreiber and D. Erpenbeck and B. Morgenstern and G. Worheide and M. Manuel},
Journal = {Curr. Biol.},
Year = {2009},
Pages = {706--712},
Volume = {19},
Abstract = {128 genes, protists outgroups: ||| Porifera (|| Homos + Calci ||| Hexa ||| Demo) || Placozoa ||| Eumetazoa (Bilateria ||| Ctenophora || Cnidaria)},
Doi = {10.1016/j.cub.2009.02.052},
File = {philippe2009_phylogenomics.pdf}
}
@Article{Philippe1999,
Title = {{The Rooting of the Universal Tree of Life Is Not Reliable}},
Author = {H. Philippe and P. Forterre},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {509--523},
Volume = {49}
}
@Article{Philippe2019,
Title = {{Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.}},
Author = {H. Philippe and A. J. Poustka and M. Chiodin and K. J. Hoff and C. Dessimoz and B. Tomiczek and P. H. Schiffer and S. M{\"u}ller and D. Domman and M. Horn and H. Kuhl and B. Timmermann and N. Satoh and T. Hikosaka-Katayama and H. Nakano and M. L. Rowe and M. R. Elphick and M. Thomas-Chollier and T. Hankeln and F. Mertes and A. Wallberg and J. P. Rast and R. R. Copley and P. Martinez and M. J. Telford},
Journal = {Current biology : CB},
Year = {2019},
Number = {11},
Pages = {1818 - 1826 - e6},
Volume = {29},
Abstract = {As stated; Xenoacoelomorpha could be simplified Ambulacraria or Deuterostomia diphyletic},
Doi = {10.1016/j.cub.2019.04.009},
File = {philippe2019_xenacoelom_ambulacralia.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31104936}
}
@Article{Philippot2010,
Title = {{The ecological coherence of high bacterial taxonomic ranks}},
Author = {L. Philippot and S. G. E. Andersson and T. J. Battin and J. I. Prosser and J. P. Schimel and W. B. Whitman and S. Hallin},
Journal = {Nature reviews. Microbiology},
Year = {2010},
Number = {7},
Pages = {523 - 529},
Volume = {8},
Abstract = {Some coherence},
Doi = {10.1038/nrmicro2367},
File = {philippot2010_bacterial_high_ranks_ecology.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20531276}
}
@Article{Phillips2008,
Title = {{Resolving evolutionary relationships among the brown algae using chloroplast and nuclear genes}},
Author = {N. Phillips and R. Burrowes and F. Rousseau and B. de Reviers and G. W. Saunders},
Journal = {J. Phycol.},
Year = {2008},
Pages = {394--405},
Volume = {44},
Abstract = {Choristicarpos suster, some support for higher clade (Laminariales, Fucales etc.)},
Doi = {10.1111/j.1529-8817.2008.00473.x},
File = {phillips2008.pdf}
}
@InProceedings{Picard2009,
Title = {{Investigating a Primitive Mycobiont-Photobiont Symbiosis}},
Author = {K. T. Picard and P. M. Letcher and M. Powell},
Booktitle = {{Botany and Mycology 2009. Snowbird, Utah, July 25-29. Abstracts}},
Year = {2009},
Abstract = {Rhizidium phycophilum, a recently delineated saprobic soil-dwelling chytrid from Australia, exhibits a unique mode of nutrition in which the presence of a chlorococcalean green alga is required for maintenance on nutrient media},
File = {picard2009_chytr_lichen.txt}
}
@Article{Sermoli1981,
Title = {{Report of the Subcommittee for family names of Pteridophyta}},
Author = {R. E. G. {Pichi Sermoli}},
Journal = {Taxon},
Year = {1981},
Pages = {163--168},
Volume = {30}
}
@Article{Sermoli1977,
Title = {{Tentamen Pteridophytorum genera in taxonomicum ordinem redigendi}},
Author = {R. E. G. {Pichi Sermoli}},
Journal = {Webbia},
Year = {1977},
Number = {2},
Pages = {313--512},
Volume = {31}
}
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Title = {{The occurrence of hemocyanin in Hexapoda}},
Author = {C. Pick and M. Schneuer and T. Burmester},
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Year = {In press},
Abstract = {Support for Pancrustacea and Hexapoda},
Doi = {10.1111/j.1742-4658.2009.06918.x},
File = {pick2009_hemocyanin_hexapoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19236479}
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@Article{Pilato2005,
Title = {{The clade Ecdysozoa, perplexities and questions}},
Author = {G. Pilato and M. G. Binda and O. Biondi and V. D'Urso and O. Lisi and A. Marletta and S. Maugeri and V. Nobile and G. Rappazzo and G. Sabella and F. Sammartano and G. Turrisi and F. Viglianisi},
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Year = {2005},
Pages = {43--50},
Volume = {244},
Abstract = {Annelida are moulting; Gastrotricha probably similar to them},
File = {pilato2005.pdf}
}
@Article{Pincus2008,
Title = {{Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.}},
Author = {D. Pincus and I. Letunic and P. Bork and W. A. Lim},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {28},
Pages = {9680--9684},
Volume = {105},
Abstract = {TyrK is present in choanofl.},
Doi = {10.1073/pnas.0803161105},
File = {pincus2008.pdf}
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@Article{Pinevich2020,
Title = {{The ambiguity of the basic terms related to eukaryotes and the more consistent etymology based on eukaryotic signatures in Asgard archaea}},
Author = {A. V. Pinevich},
Journal = {BioSystems},
Year = {2020},
Month = {1 November},
Pages = {104178},
Volume = {197},
Abstract = {Caryosignifara for Archaea + euk, "nucleated organisms" for euk},
Doi = {10.1016/j.biosystems.2020.104178},
File = {pinevich2020_caryosignifera.pdf},
ISSN = {0303-2647}
}
@Article{Pinnow2015,
Title = {{Identification and characterisation of hemocyanin of the fish louse Argulus (Crustacea: Branchiura).}},
Author = {P. Pinnow and A. Fabrizius and C. Pick and T. Burmester},
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Year = {2015},
Abstract = {As stated, not far from Ostracoda},
Doi = {10.1007/s00360-015-0943-3},
File = {pinnow2015_argulus_hemocyanin.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26515963}
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@Article{Pinos2016,
Title = {{Compartmentalization in PVC super-phylum: Evolution and impact.}},
Author = {S. Pinos and P. Pontarotti and D. Raoult and J. P. Baudoin and I. Pagnier},
Journal = {Biol. Direct},
Year = {2016},
Pages = {38},
Volume = {11},
Abstract = {Poribacteria in PVC!; compartments in Chlamydia and Verruc},
Doi = {10.1186/s13062-016-0144-3},
File = {pinos2016_pvc_compartmentalization.pdf},
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@Article{Pisani2007,
Title = {{Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes}},
Author = {D. Pisani and J. A. Cotton and J. O. McInerney},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {8},
Pages = {1752--1760},
Volume = {24},
Abstract = {Aquifex || Firmi (incl. Thermot + Fuso) || Dehalocc. + Cyano || Chlorob/Bacteroid + Spiro || Plancto + Dein/Th + Proteobact},
Doi = {10.1093/molbev/msm095},
File = {pisani2007.pdf}
}
@Article{Pisani2011,
Title = {{Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships}},
Author = {D. Pisani and R. Feuda and K. J. Peterson and A. B. Smith},
Journal = {Mol. Phyl. Evol.},
Year = {2011},
Abstract = {Aster (Oph + Echin)},
Doi = {10.1016/j.ympev.2011.08.028},
File = {pisani2011_echinoderms.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2011.08.028}
}
@Article{Pisani2015,
Title = {{Genomic data do not support comb jellies as the sister group to all other animals.}},
Author = {D. Pisani and W. Pett and M. Dohrmann and R. Feuda and O. Rota-Stabelli and H. Philippe and N. Lartillot and G. W{\"o}rheide},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2015},
Number = {50},
Pages = {15402--15407},
Volume = {112},
Abstract = {As stated; Porif || Cten || Plac || Cnidaria},
Doi = {10.1073/pnas.1518127112},
File = {pisani2015_porifera_sister.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21423652}
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@Article{Pittis2016,
Title = {{Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.}},
Author = {A. A. Pittis and T. Gabald{\'o}n},
Journal = {Nature},
Year = {2016},
Number = {7592},
Pages = {101--104},
Volume = {531},
Abstract = {As stated},
Doi = {10.1038/nature16941},
File = {pittis2016_leca_mitochondria_late.pdf},
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@Article{Plazzi2010,
Title = {{Towards a Molecular Phylogeny of Mollusks: Bivalves' Early Evolution as Re??? vealed by Mitochondrial Genes}},
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Year = {2010},
Abstract = {4 mt genes: first good molecular phylogeny of bivalves :)},
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@Article{Pleijel2008,
Title = {{Progress in systematics: from Siboglinidae to Pogonophora and Vestimentifera and back to Siboglinidae}},
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Journal = {C. R. Biologies},
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Abstract = {Review},
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File = {plejiel2009.pdf},
ISSN = {1631-0691}
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@Article{Pleijel2009,
Title = {{Progress in systematics: from Siboglinidae to Pogonophora and Vestimentifera and back to Siboglinidae}},
Author = {F. Pleijel and T. G. Dahlgren and G. W. Rouse},
Journal = {C. R. Biologies},
Year = {2009},
Pages = {140--148},
Volume = {332},
Abstract = {Review},
Doi = {10.1016/j.crvi.2008.10.007},
File = {pleijel2009_pogonophora.pdf},
ISSN = {1631-0691},
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Title = {{Die Klassen und h{\"o}heren Gruppen des tierreichs}},
Author = {F. Poche},
Journal = {Archiv fuer Naturgeschichte},
Year = {1911},
Pages = {63--136},
Volume = {77 (Suppl. 1)},
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}
@Article{Podsiadlowski2009,
Title = {{Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea}},
Author = {L. Podsiadlowski and A. Braband and T. H. Struck and J. von Dohren and T. Bartolomaeus},
Journal = {BMC Genomics},
Year = {2009},
Pages = {364},
Volume = {10},
Abstract = {Tangled; Nemert ~ Moll; Brach ~ Ectoprocta; Entopr ~ Nemert or Phoron},
Doi = {10.1186/1471-2164-10-364},
File = {podsiadlowski2009_nemertea_mt.pdf},
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@Article{Podsiadlowski2007,
Title = {{The complete mitochondrial genome of \textit{Scutigerella causeyae} (Myriapoda: Symphyla) and the phylogenetic position of Symphyla}},
Author = {L. Podsiadlowski and H. Kohlhagen and M. Koch},
Journal = {Mol. Phyl. Evol.},
Year = {2007},
Pages = {251--260},
Volume = {45},
Abstract = {Unclear, weak affinities with Chilopoda (pauropods absent from analysis)},
Doi = {10.1016/j.ympev.2007.07.017},
File = {podsiadlowski2007.pdf}
}
@Article{Polet2004,
Title = {{Small-Subunit Ribosomal RNA Gene Sequences of Phaeodarea Challenge the Monophyly of Haeckel's Radiolaria}},
Author = {S. Polet and C. Berney and J. Fahrni and J. Pawlowski},
Journal = {Protist},
Year = {2004},
Pages = {53--63},
Volume = {155},
Abstract = {Phaeod ~ Filosea},
File = {polet2004.pdf}
}
@Article{Pombert2007,
Title = {{Divergence order of chlorophyte green algal lineages as inferred from the chloroplast and mitochondrial genomes}},
Author = {J. Pombert and A. Belanger and J. De Cambiaire and J. Gagnon and C. Otis and C. Lemieux and M. Turmel},
Journal = {Journal of Phycology},
Year = {2007},
Number = {S1},
Pages = {1--48},
Volume = {42},
Abstract = {Chlorophyceae first},
Doi = {10.1111/j.1529-8817.2006.20064201.x},
File = {pombert2007.txt}
}
@Article{Pombert2010,
Title = {{The Mitochondrial Genome of the Entomoparasitic Green Alga Helicosporidium}},
Author = {J.-F. Pombert and P. J. Keeling},
Journal = {PLoS ONE},
Year = {2010},
Number = {1},
Pages = {e8954},
Volume = {5},
Abstract = {~ Prototheca},
File = {pombert2010_helicosporidium_mt.pdf},
Url = {www.plosone.org}
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@Article{PonceToledo2017,
Title = {{An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids.}},
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Journal = {Curr. Biol.},
Year = {2017},
Number = {3},
Pages = {386 - 391},
Volume = {27},
Abstract = {Gloeomargarita lithophora},
Doi = {10.1016/j.cub.2016.11.056},
File = {ponce_toledo2017_gloeomargarita_sister_to_plastids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28132810}
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Title = {{Facetotecta~--- an undecided riddle of marine biology}},
Author = {E. A. Ponomarenko},
Journal = {Biologiya Morya},
Year = {2006},
Number = {3},
Pages = {163--173},
Volume = {32},
Abstract = {Description of group, Facetotecta are Tantulocarids?},
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@Article{Ponomarenko2008,
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Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {Data on both Balanus crenatus and Peltogasterella gracilis obtained so far do not show the characteristics of the spiral cleavage.},
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Title = {{Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA}},
Author = {T. M. Porter and W. Martin and T. Y. James and J. E. Longcore and F. H. Gleason and P. H. Adler and P. M. Letcher and R. Vilgalys},
Journal = {Mycological Research},
Year = {2011},
Abstract = {Chytr || Blastocl || other (Rozella and Olpidium did not mentioned)},
Doi = {10.1016/j.funbio.2011.02.004},
File = {porter2011_blastocladiomycota.pdf},
ISSN = {1878-6146},
Url = {http://dx.doi.org/10.1016/j.funbio.2011.02.004}
}
@Article{Porter2008,
Title = {{Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life}},
Author = {T. M. Porter and C. W. Schadt and L. Rizvi and A. P. Martin and S. K. Schmidt and L. Scott-Denton and R. Vilgalys and J. M. Moncalvo},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {2},
Pages = {635--644},
Volume = {46},
Abstract = {Taphrinomyc || SCGI || Saccharo || Pezizo},
File = {porter2007.pdf}
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@Article{Postberg2010,
Title = {{The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms.}},
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Year = {2010},
Pages = {259},
Volume = {10},
Abstract = {Excavata have outstanding H4 histone},
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File = {postberg2010_histones.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20738881}
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Year = {2007},
Number = {11},
Pages = {1625--1652},
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Title = {{Phylogenetic relationships of the Raphidophyceae and Xanthophyceae as inferred from nucleotide sequences of the 18S ribosomal RNA gene}},
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Year = {2012},
Pages = {29--54},
Abstract = {Helicosporidium in Monobleph.},
Booktitle = {{Systematics and Evolution of Fungi}},
File = {systematics_and_evolution_of_fungi_2012.pdf},
ISBN = {978-1-57808-723-5},
Publisher = {CRC Press}
}
@Article{Pozdnyakov2013,
Title = {{Flagellar apparatus structure of choanocyte in Sycon sp. And its significance for phylogeny of Porifera}},
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Journal = {Zoomorphology},
Year = {2013},
Pages = {351--357},
Volume = {132},
Abstract = {Calcarea + Homoscl.},
Doi = {10.1007/s00435-013-0193-4},
File = {pozdnyakov2013_sycon_choanocyte.pdf}
}
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Title = {{A community-derived classification for extant lycophytes and ferns}},
Author = {PPG},
Journal = {Journal of Systematics and Evolution},
Year = {2017},
Abstract = {Smaller families, split genera},
Doi = {10.1111/jse.12229},
File = {pteridophyte_phylogeny_group_ppg_1_2016.pdf}
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@Article{Prasanna2020,
Title = {{Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.}},
Author = {A. N. Prasanna and D. Gerber and T. Kijpornyongpan and M. C. Aime and V. P. Doyle and L. G. Nagy},
Journal = {Systematic biology},
Year = {2020},
Number = {1},
Pages = {17 - 37},
Volume = {69},
Abstract = {Wallemiomycetes in Agaricomycotina},
Doi = {10.1093/sysbio/syz029},
File = {prasanna2019_deep_basidiom_phyl_wallemia_agaric.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31062852}
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@Article{Pratlong2017,
Title = {{Monophyly of Anthozoa (Cnidaria): Why do nuclear and mitochondrial phylogenies disagree?}},
Author = {M. Pratlong and C. Rancurel and P. Pontarotti and D. Aurelle},
Journal = {Zoologica Scripta},
Year = {2017},
Abstract = {Monophyletic},
Doi = {10.1111/zsc.12208},
File = {pratlong2016_monophyly_anthozoa.pdf},
ISBN = {3-900051-07-0}
}
@Article{Preisig1999,
Title = {{Systematics and Evolution of the Algae: Phylogenetic Relationships of Taxa Within the Different Groups of Algae}},
Author = {H. R. Preisig},
Journal = {Progr. in Botany},
Year = {1999},
Pages = {369--412},
Volume = {60}
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@Article{Price2017,
Title = {{Robust Dinoflagellata phylogeny inferred from public transcriptome databases}},
Author = {D. C. Price and D. Bhattacharya},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2017},
Abstract = {Standard},
Doi = {10.1111/ijlh.12426},
File = {price2017_dinoflagell_phylog_transcriptomes.pdf}
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@Article{Price2012,
Title = {{Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants.}},
Author = {D. C. Price and C. X. Chan and H. S. Yoon and E. C. Yang and H. Qiu and A. P. M. Weber and R. Schwacke and J. Gross and N. A. Blouin and C. Lane and A. Reyes-Prieto and D. G. Durnford and J. A. D. Neilson and B. F. Lang and G. Burger and J. M. Steiner and W. L{\"o}ffelhardt and J. E. Meuser and M. C. Posewitz and S. Ball and M. C. Arias and B. Henrissat and P. M. Coutinho and S. A. Rensing and A. Symeonidi and H. Doddapaneni and B. R. Green and V. D. Rajah and J. Boore and D. Bhattacharya},
Journal = {Science},
Year = {2012},
Number = {6070},
Pages = {843--847},
Volume = {335},
Abstract = {Between Rhodo and Chloro},
Doi = {10.1126/science.1213561},
File = {price2012_cyanophora_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22344435}
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@Article{Prieto2012,
Title = {{Mazaedium evolution in the Ascomycota (Fungi) and the classification of mazaediate groups of formerly unclear relationship}},
Author = {M. Prieto and E. Baloch and A. Tehler and M. Wedin},
Journal = {Cladistics},
Year = {2012},
Pages = {1--13},
Abstract = {Geoglosso || Coniocybomycetes + Lichniomycetes || Dothideo, Arthonio + Sordario, Leotio || Eurotio || Lecanoro},
Doi = {10.1111/j.1096-0031.2012.00429.x},
File = {prieto2012_coniocybomycetes.pdf}
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Title = {{Dating the Diversification of the Major Lineages of Ascomycota (Fungi)}},
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Journal = {PLOS One},
Year = {2013},
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Pages = {e65576},
Volume = {8},
Abstract = {Geoglossom. after Peziz.},
Doi = {10.1371/journal.pone.0065576.g001},
File = {prieto2013_ascomycota_timetree.pdf},
Url = {www.plosone.org}
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Title = {{Some Aspects of Taxonomy in the Cryptophyceae}},
Author = {E. G. Pringsheim},
Journal = {New Phytologist},
Year = {1944},
Number = {2},
Pages = {143--150},
Volume = {43},
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@Article{Printzen2010,
Title = {{Lichen Systematics: The Role of Morphological and Molecular Data to Reconstruct Phylogenetic Relationships}},
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Journal = {Progress in Botany},
Year = {2010},
Pages = {233--275},
Volume = {71},
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@Article{Probst2017,
Title = {{Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO}},
Author = {A. J. Probst and C. J. Castelle and A. Singh and C. T. Brown and K. Anantharaman and I. Sharon and L. A. Hug and D. Burstein and J. B. Emerson and B. C. Thomas and J. F. Banfield},
Journal = {Environmental Microbiology},
Year = {2017},
Number = {2},
Pages = {459--474},
Volume = {19},
Abstract = {Desantisbacteria ~ Elusi, Wirthbacteria ~ Microgenomates},
Doi = {10.1111/1462-2920.13362},
File = {probst2016_desantisbacteria.pdf},
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Title = {{Systematics of the green algae: conflict of classic and modern approaches}},
Author = {Th. Proeschold and F. Leliaert},
Booktitle = {Unravelling the algae: the past, present and future of algae systematics. The Systematic Association special volume series 75},
Publisher = {CRC Press},
Year = {2007},
Address = {London},
Editor = {J. Brodie and J. Lewis},
Pages = {123--154},
Abstract = {Prasinophyceae VI (Prasinococcus) || I (Pyraminom.) || II (Mamiella) || V (Pseudoscourfiella) || VII (unknown) + VIII (Pilocystis) || III (Nephroselmis) !! IX (Pedinomonas) !! IV (Tetraselmis) || Ulvo || Treboux || Geminella + Chloroph}
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@Unpublished{Prous2009,
Title = {{The Opisthokonta and the Ecdysozoa may be clades: An update on Philip et al. (2005)}},
Author = {M. Prous},
Year = {2009},
Abstract = {As stated},
Doi = {doi:10.1038/npre.2009.3306.1},
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Journal = {Nature Precedings}
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Number = {1},
Pages = {17},
Volume = {5},
Abstract = {...limb-less forms in the Protostomia are derived from limb-bearing forms (!)},
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File = {prpic2008.pdf}
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Journal = {Nature},
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Pages = {618--622},
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Pages = {498--513},
Volume = {63},
Abstract = {Juvenilizarion},
Doi = {10.1111/j.1558-5646.2008.00562.x},
File = {pryer2009_juvenilization_marsilea.pdf}
}
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Title = {{Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences}},
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Journal = {Amer. J. Bot.},
Year = {2004},
Number = {10},
Pages = {1582--1598},
Volume = {91}
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@Article{Ptackova2013,
Title = {{Evolution of Archamoebae: Morphological and molecular evidence for pelobionts including Rhizomastix, Entamoeba, Iodamoeba, and Endolimax.}},
Author = {E. Pt{\'a}{\v{c}}kov{\'a} and A. Y. Kostygov and L. V. Chistyakova and L. Falteisek and A. O. Frolov and D. J. Patterson and G. Walker and I. Cepicka},
Journal = {Protist},
Year = {2013},
Number = {3},
Pages = {380--410},
Volume = {164},
Abstract = {(Rhizomastix || Pelomyxa || Entamoeba) || Mastigomaebidae (incl. Iodamoeba, Endolimax)},
Doi = {10.1016/j.protis.2012.11.005},
File = {ptackova2013_archamoebae.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23312407}
}
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Journal = {Genome Biol Evol},
Year = {2010},
Pages = {745--756},
Volume = {2},
Abstract = {ToL is still viable; the supertree of NUTs is not well resolved},
Doi = {10.1093/gbe/evq062},
File = {puigbo2010_tree_and_net.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20889655}
}
@Article{Puigbo2009,
Title = {{Search for a 'Tree of Life' in the thicket of the phylogenetic forest}},
Author = {P. Puigbo and Y. I. Wolf and E. V. Koonin},
Journal = {Journal of Biology},
Year = {2009},
Pages = {59},
Volume = {8},
Abstract = {Nearly Universal Trees aka NUTs: Cyano, Actino, Dein; Thermot, Firm; Proteo, Acido, Spiro; Bacteroi, Chlorob, Chlamyd; Plancto; Lentisf, Verrocu, Chloroflexi},
Doi = {10.1186/jbiol159)},
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}
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Title = {{Sipunculid-Like Ocellar Tubes in the Polychaete Fauveliopsis (Annelida)}},
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Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {sense organs show a striking similarity to the ocellar tubes of sipunculids especially to those with unpigmented ocelli such as Onchnesoma squamatum},
Doi = {10.1002/jmor.10683},
File = {purschke2008.txt}
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Title = {{The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte.}},
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Year = {2018},
Number = {5},
Pages = {733 - 745 - e2},
Volume = {28},
Abstract = {Same as Morris et al. (2018) in PNAS; whole Bryophyta basal},
Doi = {10.1016/j.cub.2018.01.063},
File = {puttick2018_land_plant_evol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29456145}
}
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Year = {2008},
Number = {3},
Pages = {287--306},
Volume = {46},
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Doi = {10.3724/SP.J.1002.2008.08035},
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@Article{Qiu1998,
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@Article{Qiu2007,
Title = {{A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes}},
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Abstract = {~ Qiu et al., 2006, weak support for Equisetum+Maratt.},
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@Article{Qiu2006,
Title = {{The deepest divergences in land plants inferred from phylogenomic evidence}},
Author = {Y.-L. Qiu and L. Li and B. Wang and Z. Chen and V. Knoop and M. Groth-Malonek and O. Dombrovska and J. Lee and L. Kent and J. Rest and G. F. Estabrook and T. A. Hendry and D. W. Taylor and C. M. Testa and M. Ambros and B. Crandall-Stotler and R. J. Duff and M. Stech and W. Frey and D. Quandt and C. C. Davis},
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Year = {2006},
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Pages = {15511--15516},
Volume = {103},
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Title = {{Oligosphaera ethanolica gen. Nov., Sp. Nov., An anaerobic, carbohydrate-fermenting bacterium isolated from methanogenic sludge, and description of the Oligosphaeria classis nov. In the bacterial phylum Lentisphaerae.}},
Author = {Y.-L. Qiu and M. Muramatsu and S. Hanada and Y. Kamagata and R.-B. Guo and Y. Sekiguchi},
Journal = {International journal of systematic and evolutionary microbiology},
Year = {2012},
Abstract = {Lentisphaeria + Oligosphaeria},
Doi = {10.1099/ijs.0.039545-0},
File = {qiu2012_oligosphaeria_lentisphaerae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22523166}
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Year = {2002},
Pages = {513--531},
Volume = {57}
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Journal = {Acta Protozool.},
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@Article{Radek2017,
Title = {{Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota}},
Author = {R. Radek and others},
Journal = {MycoKeys},
Year = {2017},
Pages = {31 - 50},
Volume = {25},
Abstract = {Three species, within Chytridiomycota main radiation, sister to Nowakowskiella chytrid (support is low)},
Doi = {10.3897/mycokeys.25.12446},
File = {radek2017_nephridiophaga.pdf}
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File = {raff2007.pdf}
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@Article{Ragan1996,
Title = {{A novel clade of protistan parasites near the animal-fungal divergence}},
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@Article{Raghukumar2011,
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Author = {S. Raghukumar and V. S. Damare},
Journal = {Botanica Marina},
Year = {2011},
Pages = {3--11},
Volume = {54},
Abstract = {As stated},
Doi = {10.1515/BOT.2011.008},
File = {raghukumar2011_labyr.pdf}
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@Article{Ragon2014,
Title = {{16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization.}},
Author = {M. Ragon and K. Benzerara and D. Moreira and R. Tavera and P. L{\'o}pez-Garc{\'i}a},
Journal = {Front Microbiol},
Year = {2014},
Pages = {331},
Volume = {5},
Abstract = {Gloeomargarita ~ Synechococcus},
Doi = {10.3389/fmicb.2014.00331},
File = {ragon2014_gloeomargarita_cyanobact_clade.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25071744}
}
@Article{Rahman2009,
Title = {{Evaluating phylogenetic hypotheses of carpoids using stratigraphic congruence indices}},
Author = {I. A. Rahman and M. D. Sutton and M. A. Bell},
Journal = {Lethaia},
Year = {2009},
Pages = {424 - 437},
Volume = {42},
Abstract = {Echinoderm affinities are most stratigraphically congruent},
Doi = {10.1111/j.1502-3931.2009.00161.x},
File = {rahman2009_carpoids_phylogeny.pdf}
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@Article{Rai2010,
Title = {{Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes)}},
Author = {H. S. Rai and S. W. Graham},
Journal = {American Journal of Botany},
Year = {2010},
Number = {9},
Volume = {97},
Abstract = {Lycoph || Sperm (incl Cyc + Ang) || Equis || Oph + Psil || others},
Doi = {10.3732/ajb.0900305.},
File = {rai2010_monilophytes.pdf},
Url = {http://www.amjbot.org/cgi/doi/10.3732/ajb.0900305}
}
@Article{Rai2008,
Title = {{Inference of higher-order conifer relationships from a multi-locus plastid data set}},
Author = {H. S. Rai and P. A. Reeves and R. Peakall and R. G. Olmstead and S. W. Graham},
Journal = {Botany},
Year = {2008},
Pages = {658--669},
Volume = {86},
Abstract = {Pinac || Podoc + Arauc || Scia || Taxa incl. Cephal. || Cupressac. s.l.; in big ML tree chlor. genes unite Cycad. and Angiosp.},
Doi = {10.1139/B08-062},
File = {rai2008.pdf}
}
@Book{Raikov1978,
Title = {{The nucleus of protozoans. Morphology and evolution}},
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Year = {1978},
Address = {Leningrad},
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Pages = {1--328}
}
@Article{Raikova2005,
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Author = {E. V. Raikova},
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Year = {2005},
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Pages = {933--939},
Volume = {47},
Abstract = {Polypodium belongs to separate class},
File = {raikova2005.pdf}
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@Article{Raikova2002,
Title = {{\textit{Polypodium hydriforme} infection in the eggs of acipenseriform fishes}},
Author = {E. V. Raikova},
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Year = {2002},
Pages = {405--415},
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Abstract = {Polypodium differs by gametes, amebocytes etc. -> separate class},
File = {raikova2002.pdf}
}
@Article{Raikova2007,
Title = {{Muscular system of a peculiar parasitic cnidarian \textit{Polypodium hydriforme}: A phalloidin fluorescence study}},
Author = {E. V. Raikova and A. Y. Ibragimov and O. I. Raikova},
Journal = {Tiss. Cell},
Year = {2007},
Pages = {79--87},
Volume = {39},
Abstract = {Triploblastic, as well as some other Cnidaria. Support for Endocnidozoa (Polypodium + Myxozoa)},
Doi = {10.1016/j.tice.2007.01.003},
File = {raikova2005b.pdf}
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@Article{Raikova2008,
Title = {{Neurophylogeny of Early Bilaterians: Acoela, Nemertodermatida, Xenoturbella}},
Author = {O. Raikova},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {Thus, the early bilaterians display only common plesiomorphic features. No synapomorphies in the NS structure for the Acoelomorpha or for Xenoturbella and any other group have been found},
Doi = {10.1002/jmor.10683},
File = {raikova2008.txt}
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Volume = {87},
Abstract = {Hemich CNS and notochord are not homologous with Chordata},
File = {raineri2006.pdf}
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@Book{Rajkov1978,
Title = {The nucleus of protozoans. Morphology and evolution},
Author = {I. B. Rajkov},
Publisher = {Nauka},
Year = {1978},
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Note = {(In Russian)}
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@Article{Rajkova1995,
Title = {Cytological paradoxes in the life cycle of coelenterate {P}olypodium hydriforme, intracellular parasite from oocytes of sturgeons},
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Journal = {Tsitologiya},
Year = {1995},
Note = {(In Russian)},
Number = {4},
Pages = {391--401},
Volume = {37},
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}
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Title = {{Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms}},
Author = {J.-H. Ran and H. Gao and X.-Q. Wang},
Journal = {Mol. Phylogenet. Evol.},
Year = {2009},
Abstract = {Gnet || Conif, then standard phylogeny},
Doi = {10.1016/j.ympev.2009.09.011},
File = {ran2009_conifers.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19761858}
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Year = {2012},
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Pages = {267--281},
Volume = {63},
Abstract = {Review},
Doi = {10.1007/s00248-011-9998-1},
File = {ransom-jones2012_fibrobacteres.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22213055}
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@Article{Raper1978,
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Year = {1978},
Number = {9},
Pages = {1011--1026},
Volume = {65},
Abstract = {Small Copromyxa},
File = {raper1978_copromyxella.pdf},
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@Article{Rappe2003,
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Pages = {369--394},
Volume = {57},
Abstract = {OP1/Dicty/Coproth/Thermot, OP11 group, OP5 ~ Synerg, Chrys ~ Deferri, Calditrix ~ MGA ~ Chlorobi, OP10/Actino, WS2/OP9/Firmi, WS3/OP3 ~ Plancto},
File = {rappe2003.pdf}
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@Article{Rasmussen1999,
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Volume = {96}
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@Article{Rasnicyn1976,
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Journal = {Zhurn. Obshch. Biol.},
Year = {1976},
Note = {(In Russian)},
Number = {4},
Pages = {12},
Volume = {37},
Abstract = {evoljucija, Pterygota, Insecta}
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@Article{Rass1971,
Title = {Current opinions of the natural classification of recent fishes},
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Volume = {11}
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@Article{Ravinesan2013,
Title = {{Molecular Signatures for Members of the Genus Dehalococcoides and the Class Dehalococcoidia}},
Author = {D. A. Ravinesan and R. S. Gupta},
Journal = {International Journal of Systematic and Evolutionary Microbiology},
Year = {2013},
Abstract = {As stated},
File = {ravinesan2014_dehalococcoidia.txt}
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@Article{Raymann2015,
Title = {{The two-domain tree of life is linked to a new root for the Archaea.}},
Author = {K. Raymann and C. Brochier-Armanet and S. Gribaldo},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2015},
Number = {21},
Pages = {6670--6675},
Volume = {112},
Abstract = {Dein-Thermus + Thermotog || Cyanob || Chloroflexi || Firmicutes + Actinobacteria; Spiroch || Chlorobi || PVC || Proteob},
Doi = {10.1073/pnas.1420858112},
File = {raymann2015_two_domains.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25964353}
}
@Article{Rene2017,
Title = {{Evolutionary Trends of Perkinsozoa (Alveolata) Characters Based on Observations of Two New Genera of Parasitoids of dinoflagellates, Dinovorax gen. Nov. And Snorkelia gen. Nov.}},
Author = {A. Re{\~n}{\'e} and E. Alacid and I. Ferrera and E. Garc{\'e}s},
Journal = {Front Microbiol},
Year = {2017},
Pages = {1594},
Volume = {8},
Abstract = {As stated},
Doi = {10.3389/fmicb.2017.01594},
File = {rene2017_perkinsozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26605683}
}
@Article{Redecker2000,
Title = {{Ancestral Lineages of Arbuscular Mycorrhizal Fungi (Glomales)}},
Author = {D. Redecker and J. B. Morton and T. D. Bruns},
Journal = {Mol. Phyl. Evol.},
Year = {2000},
Number = {2},
Pages = {276--284},
Volume = {14}
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@Article{Redl2014,
Title = {{Development of the nervous system in Solenogastres (Mollusca) reveals putative ancestral spiralian features}},
Author = {E. Redl and M. Scherholz and C. Todt and T. Wollesen and A. Wanninger},
Journal = {EvoDevo},
Year = {2014},
Pages = {48},
Volume = {5},
Abstract = {As stated},
Doi = {10.1186/2041-9139-5-48},
File = {redl2015_solenogastres.pdf},
Url = {http://www.evodevojournal.com/content/5/1/48}
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@Article{Redmond2021,
Title = {{Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding}},
Author = {A. K. Redmond and A. McLysaght},
Journal = {Nature Communications},
Year = {2021},
Abstract = {As stated},
Doi = {10.1038/s41467-021-22074-7},
File = {redmond2021_sponges_sister.pdf},
ISSN = {2041-1723}
}
@Article{Reeb2009,
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Journal = {Mol. Phylogenet. Evol.},
Year = {In press},
Abstract = {Telonemia are very basal or close to Stramenopiles; Plastidophila (Hapto, Crypto and Archepl.) is probably result of HGT; EF2 supports Excavata + Plastidiphila; Rhizaria + Cromalv. support},
Doi = {10.1016/j.ympev.2009.04.012},
File = {reeb2009_chromalveolates.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19398025}
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@Article{Reele1997,
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Pages = {1111--1122},
Volume = {90},
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@Article{Regier1997,
Title = {{Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods.}},
Author = {J. C. Regier and J. W. Shultz},
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Year = {1997},
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Volume = {14}
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@Article{Regier2008,
Title = {{Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence}},
Author = {J. C. Regier and J. W. Shultz and A. R. D. Ganley and A. Hussey and D. Shi and B. Ball and A. Zwick and J. E. Stajich and M. P. Cummings and J. W. Martin and C. W. Cunningham},
Journal = {Syst. Biol.},
Year = {2008},
Number = {6},
Pages = {920--938},
Volume = {57},
Abstract = {||| Chelic, Pycnog || Myriap || Ostrac, Branch ||| Cephaloc, Remip || Hexap || Branch || Copep ||| Thecostr ||| Malacostr},
Doi = {10.1080/10635150802570791},
File = {regier2008.pdf}
}
@Article{Regier2005b,
Title = {{Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic}},
Author = {J. C. Regier and J. W. Shultz and R. E. Kambic},
Journal = {Proc. R. Soc. B},
Year = {2005},
Pages = {395--401},
Volume = {272},
Abstract = {Proteins: Ostracoda+Brachiura || Copepoda+(Cirripedia+Malacostraca) || Remipedia+Cephalocar || Branchiopoda || Hexapoda},
File = {regier2005b.pdf}
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@Article{Regier2004,
Title = {{Phylogeny of Basal Hexapod Lineages and Estimates of Divergence Times}},
Author = {J. C. Regier and J. W. Shultz and R. E. Kambic},
Journal = {Ann. Entomol. Soc. Am.},
Year = {2004},
Number = {3},
Pages = {411--419},
Volume = {97},
Abstract = {Hexapoda monophyletic, basal groups unstable},
File = {regier2004.pdf}
}
@Article{Regier2010,
Title = {{Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences}},
Author = {J. C. Regier and J. W. Shultz and A. Zwick and A. Hussey and B. Ball and R. Wetzer and J. W. Martin and C. W. Cunningham},
Journal = {Nature},
Year = {2010},
Number = {7284},
Pages = {1079--1083},
Volume = {463},
Abstract = {Chel (incl. Pyc.) || Myr (Chil + Progon) || Oligostraca (Myodoc, Podoc., Mystac, Ichth) || Vericrustacea (Branch || Copep || Malaco|| Thecostr) || Xenocar (Remi + Cepha) || Hexapoda (incl. Collembola)},
Doi = {10.1038/nature08742},
File = {regier2010_arthropoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20147900}
}
@Article{Regier2005,
Title = {{Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes}},
Author = {J. C. Regier and H. M. Wilson and J. W. Shultz},
Journal = {Mol. Phyl. Evol.},
Year = {2005},
Pages = {147--158},
Volume = {34},
Abstract = {Symphyla, Dignatha, Chilopoda},
File = {regier2005a.pdf}
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@Article{Rehm2014,
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Year = {2014},
Pages = {25--33},
Volume = {77C},
Abstract = {Independent Mandibulata},
Doi = {10.1016/j.ympev.2014.04.007},
File = {rehm2014_myriapoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24732681}
}
@Book{Remane1976,
Title = {{Systematische Zoologie. Stamme des Tierreiches}},
Author = {A. Remane and V. Storch and U. Welsch},
Publisher = {Gustav Fischer Verlag},
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@Article{Rensing2008,
Title = {{The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants}},
Author = {S. A. Rensing and D. Lang and A. D. Zimmer and A. Terry and A. Salamov and H. Shapiro and T. Nishiyama and P.-F. Perroud and E. A. Lindquist and Y. Kamisugi and T. Tanahashi and K. Sakakibara and T. Fujita and K. Oishi and T. Shin-I and Y. Kuroki and A. Toyoda and Y. Suzuki and S.-i. Hashimoto and K. Yamaguchi and S. Sugano and Y. Kohara and A. Fujiyama and A. Anterola and S. Aoki and N. Ashton and W. B. Barbazuk and E. Barker and J. L. Bennetzen and R. Blankenship and S. H. Cho and S. K. Dutcher and M. Estelle and J. A. Fawcett and H. Gundlach and K. Hanada and A. Heyl and K. A. Hicks and J. Hughes and M. Lohr and K. Mayer and A. Melkozernov and T. Murata and D. R. Nelson and B. Pils and M. Prigge and B. Reiss and T. Renner and S. Rombauts and P. J. Rushton and A. Sanderfoot and G. Schween and S.-H. Shiu and K. Stueber and F. L. Theodoulou and H. Tu and Y. Van de Peer and P. J. Verrier and E. Waters and A. Wood and L. Yang and D. Cove and A. C. Cuming and M. Hasebe and S. Lucas and B. D. Mishler and R. Reski and I. V. Grigoriev and R. S. Quatrano and J. L. Boore},
Journal = {Science},
Year = {2008},
Pages = {64--66},
Volume = {319},
Abstract = {whole-genome duplication between chloroph. and mosses},
Doi = {10.1126/science.1150646},
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@Article{Renzaglia2015,
Title = {{Permanent spore dyads are not 'a thing of the past': On their occurrence in the liverwort Haplomitrium (Haplomitriopsida)}},
Author = {K. S. Renzaglia and B. Crandall-Stotler and S. Pressel and J. G. Duckett and S. Schuette and P. K. Strother},
Journal = {Botanical Journal of the Linnean Society},
Year = {2015},
Pages = {658--669},
Volume = {179},
Abstract = {As stated},
File = {renzaglia2015_haplomitrium_dyads.pdf}
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@Article{Renzaglia2015a,
Title = {{Vegetative and reproductive innovations of early land plants: Implications for a unified phylogeny.}},
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Year = {2015},
Abstract = {Spermatozoa; Phylloglossum has multiflagellate},
Doi = {10.1098/rstb.2000.0615},
File = {renzaglia2015_eraly_land_plants_innovations.pdf},
Keywords = {biological evolution, dna, mitochondrial, ribosomal, gametogenesis, phylogeny, plant physiological phenomena, plants, reproduction},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10474899}
}
@Article{Renzaglia2007,
Title = {{Bryophyte phylogeny: Advancing the molecular and morphological frontiers}},
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Journal = {Bryologist},
Year = {2007},
Number = {2},
Pages = {179--213},
Volume = {110},
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}
@InCollection{Renzaglia2008,
Title = {{New insights into morphology, anatomy, and systematics of hornworts}},
Author = {K. S. Renzaglia and J. C. Villarreal and R. J. Duff},
Booktitle = {Bryophyte Biology},
Publisher = {Oxford University Press},
Year = {2008},
Address = {Cambridge},
Editor = {B. Goffinet and A. J. Shaw},
Pages = {139--173},
Abstract = {Leicosporocerotops., Antocerotops.}
}
@Article{Renzaglia2017,
Title = {{Hornwort Stomata: Architecture and Fate Shared with 400-Million-Year-Old Fossil Plants without Leaves.}},
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Year = {2017},
Number = {2},
Pages = {788 - 797},
Volume = {174},
Abstract = {Stomata to dry sporangium},
Doi = {10.1104/pp.17.00156},
File = {renzaglia2017_hornwort_stomata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24117890}
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@Article{vonReumont2011,
Title = {{Pancrustacean phylogeny in the light of new phylogenomic data: Support for Remipedia as the possible sister group of Hexapoda}},
Author = {B. M. von Reumont and R. A. Jenner and M. A. Wills and E. Dell'Ampio and G. Pass and I. Ebersberger and B. Meyer and S. Koenemann and T. M. Iliffe and A. Stamatakis and O. Niehuis and K. Meusemann and B. Misof},
Journal = {Mol. Biol. Evol.},
Year = {2011},
Abstract = {Ostrac || Malac + Cirr + Copep || Branch || Remip || Entognatha || Insecta},
File = {vonreumont2011_pancrustacea.pdf},
Url = {http://mbe.oxfordjournals.org/}
}
@Article{vonReumont2010,
Title = {{A phylogenomic approach to resolve the arthropod tree of life}},
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Year = {2010},
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Abstract = {EST: Tard + Nem || Ony || Myr || Chelic || Crust p.p. || Brach + Hex},
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@InCollection{deReviers2007,
Title = {{Classification of the Phaeophyceae from past to present and current challenges}},
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Year = {2007},
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@Article{ReyesPrieto2007,
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Abstract = {Glauc || Rhod + Chloroph}
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@Article{ReyesPrieto2007a,
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Year = {2007},
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@Article{ReyesPrieto2008,
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@Article{Reynolds2008,
Title = {{Ernst Haeckel's discovery of Magosphaera planula: A vestige of metazoan origins?}},
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Year = {2008},
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@Article{Reynolds2017,
Title = {{Resolving relationships at the animal-fungal divergence: A molecular phylogenetic study of the protist trichomycetes (Ichthyosporea, Eccrinida).}},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2017},
Pages = {447 - 464},
Volume = {109},
Abstract = {Eccrinida: Sphaeroformina + Trichomycina},
Doi = {10.1016/j.ympev.2017.02.007},
File = {reynolds2017_trichomycina_eccrinida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28219758}
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@Article{Rice2006,
Title = {{An Exceptional Horizontal Gene Transfer in Plastids: Gene Replacement by a Distant Bacterial Paralog and Evidence that Haptophyte and Cryptophyte Plastids are Sisters}},
Author = {D. W. Rice and J. D. Palmer},
Journal = {BMC Biology},
Year = {2006},
Number = {31},
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Volume = {4},
Abstract = {Hapto+Crypto},
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@Article{Richards2005,
Title = {{Myosin domain evolution and the primary divergence of eukaryotes}},
Author = {T. A. Richards and T. Cavalier-Smith},
Journal = {Nature},
Year = {2005},
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@Article{Richards2012,
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@Article{Richards2017,
Title = {{What Defines the "Kingdom" Fungi?}},
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Abstract = {Review},
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@Article{Richter2002,
Title = {{The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea}},
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@Article{Rieger1994,
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@Article{Rieger1991a,
Title = {{Neue Organisatiostypen aus der Sandlueckenraumfauna: die Lobatocerebriden und \textit{Jennaria pulchra}}},
Author = {R. M. Rieger},
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Pages = {247--259},
Volume = {84}
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@Article{Rieger1991b,
Title = {{Jennaria pulchra, nov. gen., nov. spec., eine den psammobionten Anneliden nahestehende Gattung aus dem Kuestengrundwasser von North Carolina}},
Author = {R. M. Rieger},
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@Article{Rieger1981,
Title = {{Fine structure of the body wall, nervous system, and digestive tract in the Lobatocerebridae Rieger and the organization of the gliointerstitial system in Annelida}},
Author = {R. M. Rieger},
Journal = {Journal of Morphology},
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Number = {2},
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Volume = {167},
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@Article{Rieger1980,
Title = {{A new group of interstitial annelids, Lobatocerebridae new. fam. and its signification for Metazoan phylogeny}},
Author = {R. M. Rieger},
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Pages = {41--84},
Volume = {94}
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@Article{DiRienzi2013,
Title = {{The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.}},
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Journal = {Elife},
Year = {2013},
Pages = {e01102},
Volume = {2},
Abstract = {Melainabacteria},
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File = {derienzi2013_melainabacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22699609}
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@Article{Riesgo2014,
Title = {{The analysis of eight transcriptomes from all Porifera classes reveals surprising genetic complexity in sponges}},
Author = {A. Riesgo and N. Farrar and P. J. Windsor and G. Giribet and S. P. Leys},
Journal = {Mol. Biol. Evol.},
Year = {2014},
Abstract = {As stated},
File = {riesgo2014_genetic_complexity_sponges.pdf},
Url = {http://mbe.oxfordjournals.org/}
}
@Article{Riesgo2009,
Title = {{An unexpectedly sophisticated, V-shaped spermatozoon in Demospongiae (Porifera): Reproductive and evolutionary implications}},
Author = {A. Riesgo and M. Maldonado},
Journal = {Biological Journal of the Linnean Society},
Year = {2009},
Pages = {413--426},
Volume = {2009},
Abstract = {As stated},
File = {riesco2009_v-shaped_sperm_porifera.pdf}
}
@Article{Riesgo2007,
Title = {{Reproduction in a carnivorous sponge: the significance of the absence of an aquiferous system to the sponge body plan}},
Author = {A. Riesgo and C. Taylor and S. P. Leys},
Journal = {Evol. Devel.},
Year = {2007},
Number = {6},
Pages = {618--631},
Volume = {9},
Abstract = {Cladorhizida: multiciliated cells, striated rootlets as in Hexa and Homoscl (functional similarity); oocyte clusters ("almost gonads") },
File = {riesgo2008.pdf}
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@Article{Riess2015,
Title = {{Identification of a new order of root-colonising fungi in the Entorrhizomycota: Talbotiomycetales ord. Nov. On eudicotyledons.}},
Author = {K. Riess and R. Bauer and R. Kellner and M. Kemler and M. Piątek and K. V{\'a}nky and D. Begerow},
Journal = {IMA Fungus},
Year = {2015},
Number = {1},
Pages = {129--133},
Volume = {6},
Abstract = {As stated},
Doi = {10.5598/imafungus.2015.06.01.07},
File = {riess2015_entorrhizomycota_talbotiomyces.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26203418}
}
@Article{Riess2018,
Title = {{The origin and diversification of the Entorrhizales: Deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae}},
Author = {K. Riess and M. E. Sch{\"o}n and S. Garnica and R. Ziegler and M. Lutz and R. G. Shivas and M. Piątek},
Journal = {Organisms Diversity \& Evolution},
Year = {2018},
Number = {1884},
Pages = {1994},
Volume = {2},
Abstract = {Closer to Basidiomycota},
Doi = {10.1007/s13127-018-0384-4},
File = {riess2019_orig_div_entorrhizales.pdf},
Url = {https://doi.org/10.1007/s13127-018-0384-4}
}
@Article{Riisberg2009,
Title = {{Seven Gene Phylogeny of Heterokonts}},
Author = {I. Riisberg and R. J. Orr and R. Kluge and K. Shalchian-Tabrizi and H. A. Bowers and V. Patil and B. Edvardsen and K. S. Jakobsen},
Journal = {Protist},
Year = {In press},
Abstract = {Chryso || Bacillario || Pingu || Eustig || Dicty + Pelago ||| Rahido ||| Phaeot ||| Xantho ||| Phaeo},
Doi = {10.1016/j.protis.2008.11.004},
File = {riisberg2009_heteroconts.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19213601}
}
@Article{Riisgird2004,
Title = {{Ciliary feeding structures and particle capture mechanism in the freshwater bryozoan Plumatella repens (Phylactolaemata)}},
Author = {H. U. Riisgird and K. K. Nielsen and J. Fuchs and B. F. Rasniussen and M. Obst and P. Funch},
Journal = {Invertebrate Biology},
Year = {2004},
Number = {2},
Pages = {156--167},
Volume = {123},
Abstract = {...The filter feeding apparatus in P. repens, as described in this study, is very similar to that of marine bryozoans, such as the gymnolaemate Flustrellidra hispida (Atkins 1933, Nielsen 2002a). It is also similar to that of the phoronid Phoronis muelleri (Riisgbrd 2002).},
File = {riisgard2004.pdf}
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@Article{RimskayaKorsakova2018,
Title = {{The neuroanatomy of the siboglinid Riftia pachyptila highlights sedentarian annelid nervous system evolution.}},
Author = {N. N. Rimskaya-Korsakova and S. V. Galkin and V. V. Malakhov},
Journal = {PLoS ONE},
Year = {2018},
Number = {12},
Pages = {e0198271},
Volume = {13},
Abstract = {As stated},
Doi = {10.1371/journal.pone.0198271},
File = {rimskaya_korsakova_2018_riftia_neuroanatomy.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30543637}
}
@Article{Rinke2021,
Title = {{A standardized archaeal taxonomy for the Genome Taxonomy Database}},
Author = {C. Rinke and M. Chuvochina and A. J. Mussig and P.-A. Chaumeil and A. A. Dav{\'i}n and D. W. Waite and W. B. Whitman and D. H. Parks and P. Hugenholtz},
Journal = {Nature Microbiology},
Year = {2021},
Pages = {946 - 959},
Volume = {6},
Abstract = {See table on p. 8},
File = {rinke2021_std_archaeal_taxonomy.pdf},
Url = {https://www.nature.com/articles/s41564-021-00918-8}
}
@Article{Rinke2013,
Title = {{Insights into the phylogeny and coding potential of microbial dark matter.}},
Author = {C. Rinke and P. Schwientek and A. Sczyrba and N. N. Ivanova and I. J. Anderson and J.-F. Cheng and A. Darling and S. Malfatti and B. K. Swan and E. A. Gies and J. A. Dodsworth and B. P. Hedlund and G. Tsiamis and S. M. Sievert and W.-T. Liu and J. A. Eisen and S. J. Hallam and N. C. Kyrpides and R. Stepanauskas and E. M. Rubin and P. Hugenholtz and T. Woyke},
Journal = {Nature},
Year = {2013},
Number = {7459},
Pages = {431--437},
Volume = {499},
Abstract = {Too many changes: will be reflected directly in the classification},
Doi = {10.1038/nature12352},
File = {rinke2013_microbial_dark_matter.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23893103}
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@Article{Riser1988,
Title = {{Arhynchonemertes axi gen. n., sp. n.~--- an insight into basic acoelomate bilaterian organology}},
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@Article{Rivera2009,
Title = {{And Lophotrochozoa makes three: Notch/Hes signaling in annelid segmentation}},
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Journal = {Dev. Genes Evol.},
Year = {2009},
Number = {1},
Pages = {37--43},
Volume = {219},
Abstract = {Notch everywhere for segmentation},
Doi = {10.1007/s00427-008-0264-6},
File = {rivera2009_notch_segmentation.pdf},
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@Article{Roberson2011,
Title = {{The hyphal tip structure of Basidiobolus sp.: A zygomycete fungus of uncertain phylogeny}},
Author = {R. W. Roberson and E. Saucedo and D. Maclean and J. Propster and B. Unger and T. A. Oneil and K. Parvanehgohar and C. Cavanaugh and D. Lowry},
Journal = {Mycological Research},
Year = {2011},
Abstract = {Close to Asco/Basidio},
Doi = {10.1016/j.funbio.2011.02.012},
File = {roberson2011_basidiobolus.pdf},
ISSN = {1878-6146},
Url = {http://dx.doi.org/10.1016/j.funbio.2011.02.012}
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@Article{Robertson2005,
Title = {{Phylogenetic diversity and ecology of environmental Archaea}},
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Journal = {Curr. Opin. Microbiol.},
Year = {2005},
Pages = {638--642},
Volume = {8},
Abstract = {Cren: OPA2, YNPFFA, Kora, C2, FGG1--2, C1 (Crenarchaeum); Eury: Nanoarcheota, other groups + 5--6 environmental},
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@Article{Robertson2017,
Title = {{The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae.}},
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Journal = {Sci Rep},
Year = {2017},
Number = {1},
Pages = {1847},
Volume = {7},
Abstract = {With deuterostomes},
Doi = {10.1038/s41598-017-01608-4},
File = {robertson2017_acoelomorph_mt.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17531802}
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@Article{Robertson2018,
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Year = {2018},
Volume = {4},
Doi = {10.1017/pao.2018.12},
File = {robertson2018_mt_genomes_mesozoans.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27374341}
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@Article{Rodin1967,
Title = {{Ontogeny of foliage leaves in Gnetum}},
Author = {R. J. Rodin},
Journal = {Phytomorphology},
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Abstract = {Dichotomic venation initially},
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@Article{RodrguezEzpeleta2005,
Title = {{Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes}},
Author = {N. Rodriguez-Ezpeleta and H. Brinkmann and S. C. Burey and B. Roure and G. Burger and W. Loeffelhardt and H. J. Bohnert and H. Philippe and B. F. Lang},
Journal = {Curr. Biol.},
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Pages = {1325--1330},
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@Article{RodriguezEzpeleta2007,
Title = {{Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans}},
Author = {N. Rodriguez-Ezpeleta and H. Brinkmann and G. Burger and A. J. Roger and M. W. Gray and H. Philippe and B. F. Lang},
Journal = {Biochemistry},
Year = {2007},
Pages = {1420--1425},
Volume = {17},
Abstract = {"Bikonta" (96 Bayes!): (Malawimonadozoa || Jacobozoa || Heter + Eugl) || (Cerc || Stram + Alveol) || (Glauc || Rhod || Viridipl)},
Doi = {10.1016/j.cub.2007.07.036},
File = {rodriguez-ezpeleta2007.pdf}
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@Article{RodriguezEzpeleta2007b,
Title = {{Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta.}},
Author = {N. Rodriguez-Ezpeleta and H. Philippe and H. Brinkmann and B. Becker and M. Melkonian},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {3},
Pages = {723 - 731},
Volume = {24},
Abstract = {Mesostigma basal, pairing with Chlorokybus is an LBA},
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File = {rodriguez-ezpeleta2007.pdf}
}
@Article{Roeding2009,
Title = {{A 454 sequencing approach for large-scale phylogenomic analysis of the Common Emperor Scorpion (Pandinus imperator)}},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2009},
Abstract = {Amino acid genes: Tardigrada ~ Nematoda, Cephalorh., Onych || Myri + Chelic || Crust || Brach + hexap},
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File = {roeding2009_arthropoda.pdf},
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@Article{Roeding2007,
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Journal = {Mol. Phyl. Evol.},
Year = {2007},
Pages = {942--951},
Volume = {45},
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Doi = {10.1016/j.ympev.2007.09.002},
File = {roeding2007.pdf}
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Volume = {48}
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Journal = {Mol. Biol. Evol.},
Year = {1999},
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Volume = {16}
}
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Journal = {Current Biology},
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Abstract = {Against Bikonta},
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Title = {{Evidence for the Heterolobosea from Phylogenetic Analysis of Genes Encoding Glyceraldehyde-3-Phosphate Dehydrogenase}},
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Volume = {43}
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@Article{Roger1998,
Title = {{A mitochondrial-like chaperonin 60 gene in Giardia lamblia: Evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria}},
Author = {A. J. Roger and S. G. Svord and J. Tovar and C. G. Clark and Michael W. Smith and F. D. Gillin and M. L. Sogin},
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Volume = {95}
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@Article{Rogozin2009,
Title = {{Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes}},
Author = {I. B. Rogozin and M. K. Basu and M. Csueroes and E. V. Koonin},
Journal = {Genome Biology and Evolution},
Year = {In press},
Volume = {25},
Abstract = {Plantae, Excavata, Chromalveolata, Unikonts},
Doi = {10.1093/gbe/evp011},
File = {F:/ref/os/1/rogozin2009_euk_phylogeny.pdf}
}
@Article{Rogozin2007,
Title = {{Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements}},
Author = {I. B. Rogozin and Y. I. Wolf and L. Carmel and E. V. Koonin},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {4},
Pages = {1080--1090},
Volume = {24},
Abstract = {Subj, see Irimia et al., 2007},
File = {rogozin2007.pdf}
}
@Article{Rogozin2007a,
Title = {{Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade}},
Author = {I. B. Rogozin and Y. I. Wolf and L. Carmel and E. V. Koonin},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Number = {12},
Pages = {2594--2597},
Volume = {24},
Abstract = {As stated},
Doi = {10.1093/molbev/msm218},
File = {rogozin2007.pdf}
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@Article{Roots2009,
Title = {{The phylogeny of invertebrates and the evolution of myelin.}},
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Journal = {Neuron Glia Biol.},
Year = {2009},
Pages = {1--9},
Abstract = {Myelin has arisen independently at least three times, namely in Annelids, Arthropodas and Chordates},
Doi = {10.1017/S1740925X0900012X},
File = {roots2009_ecdysozoa_myelin.txt},
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@Article{Rosenberg1999,
Title = {{Ribosomal RNA phylogeny of selected major clades in the Mollusca}},
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Year = {1999},
Number = {3},
Pages = {301--309},
Volume = {63}
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@Article{Rosling2011,
Title = {{Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi}},
Author = {A. Rosling and F. Cox and K. Cruz-Martinez and K. Ihrmark and G.-A. Grelet and B. D. Lindahl and A. Menkis and T. Y. James},
Journal = {Science},
Year = {2011},
Pages = {876--879},
Volume = {333},
Abstract = {Sister to Pneumo + Schizosacc; Archaeorhizomyces finlayi},
Doi = {10.1126/science.1206958},
File = {rosling2011_archaeorhizomycetes.pdf},
Url = {www.sciencemag.org}
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@Article{RotaStabelli2010b,
Title = {{A congruent solution to arthropod phylogeny: Phylogenomics, microRNAs and morphology support monophyletic Mandibulata.}},
Author = {O. Rota-Stabelli and L. Campbell and H. Brinkmann and G. D. Edgecombe and S. J. Longhorn and K. J. Peterson and D. Pisani and H. Philippe and M. J. Telford},
Journal = {Proceedings. Biological sciences / The Royal Society},
Year = {2010},
Abstract = {Myriap || Malac || Brachiop || Hexap},
Doi = {10.1098/rspb.2010.0590},
File = {rota-stabelli2010_mandibulata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20702459}
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@Article{RotaStabelli2013,
Title = {{Molecular timetrees reveal a cambrian colonization of land and a new scenario for ecdysozoan evolution.}},
Author = {O. Rota-Stabelli and A. C. Daley and D. Pisani},
Journal = {Curr. Biol.},
Year = {2013},
Number = {5},
Pages = {392--398},
Volume = {23},
Abstract = {Timetree},
Doi = {10.1016/j.cub.2013.01.026},
File = {rota_stabelli2013_ecdysozoa_timetrees.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23518055}
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@Article{RotaStabelli2010a,
Title = {{Ecdysozoan mitogenomics: Evidence for a common origin of the legged invertebrates, the Panarthropoda}},
Author = {O. Rota-Stabelli and E. Kayal and D. Gleeson and J. Daub and J. L. Boore and M. J. Telford and D. Pisani and M. Blaxter and D. V. Lavrov},
Journal = {Genome Biol Evol},
Year = {2010},
Pages = {425 - 440},
Volume = {2},
Abstract = {Tardigrada + Ony consistent; Crustacea (!) + Hexapoda},
Doi = {10.1093/gbe/evq030},
File = {rota-stabelli2010_panarthropoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20624745}
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@Article{RotaStabelli2008,
Title = {{A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics}},
Author = {O. Rota-Stabelli and M. J. Telford},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {1},
Pages = {103--111},
Volume = {48},
Abstract = {Mitochondrial support for Chel + Myriap. may be wrong},
Doi = {doi:10.1016/j.ympev.2008.03.033},
File = {rota-stabelli2008.pdf}
}
@Article{Rothe2010,
Title = {{Structure of the nervous system in Tubiluchus troglodytes (Priapulida)}},
Author = {B. H. Rothe and A. Schmidt-Rhaesa},
Journal = {Invertebrate Biology},
Year = {2010},
Number = {1},
Pages = {39--58},
Volume = {129},
Abstract = {~ Kino},
Doi = {10.1111/j.1744-7410.2010.00185.x},
File = {rothe2010_nerv_priapul.pdf}
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@Article{Rothe2011,
Title = {{Intracellular mineral grains in the xenophyophore Nazareammina tenera (Rhizaria, Foraminifera) from the Nazare Canyon (Portuguese margin, NE Atlantic)}},
Author = {N. Rothe and A. J. Gooday and R. B. Pearce},
Journal = {Deep-Sea Research Part I},
Year = {2011},
Month = {1 December},
Number = {12},
Pages = {1189--1195},
Volume = {58},
Abstract = {As stated},
Doi = {10.1016/j.dsr.2011.09.003},
File = {rothe2011_xenoph.pdf},
ISSN = {0967-0637},
Url = {http://dx.doi.org/10.1016/j.dsr.2011.09.003}
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Title = {{Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns}},
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Journal = {Systematic Biology},
Year = {2012},
Number = {1},
Pages = {1},
Volume = {12},
Abstract = {Polypodium-Gymnocarpium-Woodsia-Thelypteris-Asplenium-Dryopteris-Athyrium-Onoclea-Blechnum-Diplazium},
File = {rothfels2012_eupolypod_ferns.pdf},
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@Article{Rothfels2015,
Title = {{The evolutionary history of ferns inferred from 25 low-copy nuclear genes.}},
Author = {C. J. Rothfels and F.-W. Li and E. M. Sigel and L. Huiet and A. Larsson and D. O. Burge and M. Ruhsam and M. Deyholos and D. E. Soltis and C. N. Stewart Jr and S. W. Shaw and L. Pokorny and T. Chen and C. dePamphilis and L. DeGironimo and L. Chen and X. Wei and X. Sun and P. Korall and D. W. Stevenson and S. W. Graham and G. K.-S. Wong and K. M. Pryer},
Journal = {Am. J. Bot.},
Year = {2015},
Abstract = {As stated; Eq || Oph + Psil || Mar || others},
Doi = {10.3732/ajb.1500089},
File = {rothfels2015_ferns.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26199366}
}
@Article{Rothfels2012b,
Title = {{A revised family-level classification for eupolypod II ferns (Polypodiidae: Polypodiales)}},
Author = {C. J. Rothfels and M. A. Sundue and L.-Y. Kuo and A. Larsson and M. Kato and E. Schuettpelz and K. M. Pryer},
Journal = {Taxon},
Year = {2012},
Number = {3},
Pages = {515--533},
Volume = {60},
Abstract = {As stated},
File = {rothfels2012_polypodiidae.djvu}
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Title = {The Influence of UV Radiation on Protistan Evolution},
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@Article{Rothwell2006,
Title = {{How does the inclusion of fossil data change our conclusions about the phylogenetic history of euphyllophytes?}},
Author = {G. W. Rothwell and K. C. Nixon},
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Pages = {737--749},
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@Article{Rothwell2013,
Title = {{Evolution and Phylogeny of Gnetophytes: Evidence from the Anatomically Preserved Seed Cone Protoephedrites eamesii gen. Et sp. Nov. And the Seeds of Several Bennettitalean Species}},
Author = {G. W. Rothwell and R. A. Stockey},
Journal = {International Journal of Plant Sciences},
Year = {2013},
Number = {3},
Pages = {511--529},
Volume = {174},
Abstract = {Benn. are not close to Gnetales},
Doi = {10.1086/668688},
File = {rothwell2013_gnetophytes_not_bennett.pdf},
Url = {http://www.jstor.org/stable/10.1086/668688}
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@Article{Rouse2007,
Title = {{Annelida}},
Author = {G. W. Rouse},
Journal = {Zootaxa},
Year = {2007},
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Volume = {1668},
Abstract = {Clitellata as a group of Polychaeta; Aelosoma, Echiura unclear; structure unclear},
File = {rouse2007.pdf}
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@Article{Rouse1999,
Title = {{Trochophore concepts: ciliary bands and the evolution of larvae in spiralian Metazoa}},
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Pages = {411--464},
Volume = {66}
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@Article{Rouse2016,
Title = {{New deep-sea species of Xenoturbella and the position of Xenacoelomorpha.}},
Author = {G. W. Rouse and N. G. Wilson and J. I. Carvajal and R. C. Vrijenhoek},
Journal = {Nature},
Year = {2016},
Number = {7588},
Pages = {94--97},
Volume = {530},
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File = {rouse2016_new_xenoturbella.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26842060}
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@Article{Rousset2006,
Title = {{A molecular phylogeny of annelids}},
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Year = {2006},
Pages = {1--23},
Volume = {22},
Abstract = {Echiur., Sipuncul., Clitellata inside; resolution absent},
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@Article{Rousset2004,
Title = {{The phylogenetic position of Siboglinidae (Annelida) inferred from 18S rRNA, 28S rRNA and morphological data}},
Author = {V. Rousset and G. W. Rouse and M. E. Siddall and A. Tillier and F. Pleijel},
Journal = {Cladistics},
Year = {2004},
Pages = {518--533},
Volume = {20},
Abstract = {Sister to Oweniidae},
File = {rousset2004.pdf}
}
@Article{Rowland2001,
Title = {{Archaeocyaths~--- a history of phylogenetic interpretation}},
Author = {S. M. Rowland},
Journal = {J. Paleont.},
Year = {2001},
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@Article{Roy2008,
Title = {{Rare genomic characters do not support Coelomata: Intron loss/gain}},
Author = {S. W. Roy and M. Irimia},
Journal = {Mol. Biol. and Evolution},
Year = {2008},
Number = {4},
Pages = {620--623},
Volume = {25},
Abstract = {As stated},
File = {roy2008.pdf}
}
@Article{Roy2008b,
Title = {{Rare Genomic Characters Do Not Support Coelomata: RGC\_CAMs}},
Author = {S. W. Roy and M. Irimia},
Journal = {J. Mol. Evol.},
Year = {2008},
Number = {3},
Pages = {308--315},
Volume = {66},
Abstract = {As stated},
Doi = {10.1007/s00239-008-9077-5},
File = {roy2008.pdf}
}
@Article{Rozhnov2018,
Title = {{Architectonics of Metazoa as the Basis for the Reconstruction of the Ontogeny and Phylogeny of Extinct Taxa}},
Author = {S. V. Rozhnov},
Journal = {Paleontological Journal},
Year = {2018},
Number = {14},
Pages = {1672 - 1678},
Volume = {52},
Abstract = {Anthozoa possibly oroginally bilateral},
Doi = {10.1134/S0031030118140149},
File = {rozhnov2018_architectonics_of_metazoa.pdf}
}
@Article{Rozhnov2012,
Title = {{The Anteroposterior Axis in Echinoderms and Displacement of the Mouth in Their Phylogeny and Ontogeny}},
Author = {S. V. Rozhnov},
Journal = {Izvestiya Akademii Nauk, Seriya Biologicheskaya},
Year = {2012},
Number = {2},
Pages = {162--171},
Volume = {39},
Abstract = {As stated},
Doi = {10.1134/S1062359012020094},
File = {rozhnov2012_echinoderm_axes.pdf}
}
@Article{Rozhnov2010,
Title = {{From Vendian to Cambrian: The Beginning of Morphological Disparity of Modern Metazoan Phyla}},
Author = {S. V. Rozhnov},
Journal = {Russian Journal of Developmental Biology},
Year = {2010},
Number = {6},
Pages = {357--368},
Volume = {41},
Abstract = {Review},
Doi = {10.1134/S1062360410060032},
File = {rozhnov2010_vendoan_to_cambrian.pdf}
}
@Article{Rubanov2016,
Title = {{A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata.}},
Author = {L. I. Rubanov and A. V. Seliverstov and O. A. Zverkov and V. A. Lyubetsky},
Journal = {BioMed Central Bioinformatics},
Year = {2016},
Pages = {385},
Volume = {17},
Abstract = {Weird results, probably due to highly modified genomes of coccidioid parasites},
Doi = {10.1186/s12859-016-1257-5},
File = {rubanov2016_alveolata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27645252}
}
@Article{Rudall2013,
Title = {{Several developmental and morphogenetic factors govern the evolution of stomatal patterning in land plants.}},
Author = {P. J. Rudall and J. Hilton and R. M. Bateman},
Journal = {New Phytol.},
Year = {2013},
Number = {3},
Pages = {598--614},
Volume = {200},
Abstract = {Review},
Doi = {10.1111/nph.12406},
File = {rudall2013_stomatal_patterns.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23909825}
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@Article{Rueckert2017,
Title = {{Archigregarines of the English Channel revisited: New molecular data on Selenidium species including early described and new species and the uncertainties of phylogenetic relationships.}},
Author = {S. Rueckert and A. Hor{\'a}k},
Journal = {PLoS ONE},
Year = {2017},
Number = {11},
Pages = {e0187430},
Volume = {12},
Abstract = {As stated},
Doi = {10.1371/journal.pone.0187430},
File = {rueckert2017_selenidium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29099876}
}
@Article{RueckertInpress,
Title = {{Molecular Phylogeny and Surface Morphology of Marine Archigregarines (Apicomplexa), Selenidium spp., Filipodium phascolosomae n. Sp., And Platyproteum n. G. Et comb. From North-Eastern Pacific Peanut Worms (Sipuncula)}},
Author = {S. Rueckert and B. S. Leander},
Journal = {Journal of Eukaryotic Microbiology},
Year = {In press},
Abstract = {Piro + Cocci || Gregarines incl. Selenidium, Cryptosp, Rhytido},
Doi = {10.1111/j.1550-7408.2009.00422.x},
File = {rueckert2009_archigregarines.pdf}
}
@Article{Rueckert2008,
Title = {{Morphology and molecular phylogeny of Haplozoon praxillellae n. sp. (Dinoflagellata): A novel intestinal parasite of the maldanid polychaete Praxillella pacifica Berkeley}},
Author = {S. Rueckert and B. S. Leander},
Journal = {Eur. J. Protistol.},
Year = {2008},
Number = {4},
Pages = {299--307},
Volume = {44},
Abstract = {Haplozoon morphology; || (Syndiniales + MAGI) + (MAGII + Noctiluca) ||| Blastodoniales || other},
Doi = {10.1016/j.ejop.2008.04.004},
File = {rueckert2008.pdf}
}
@Article{Rueckert2011,
Title = {{Identification of a divergent environmental DNA sequence clade using the phylogeny of gregarine parasites (Apicomplexa) from crustacean hosts.}},
Author = {S. Rueckert and T. G. Simdyanov and V. V. Aleoshin and B. S. Leander},
Journal = {PLoS ONE},
Year = {2011},
Number = {3},
Pages = {e18163},
Volume = {6},
Abstract = {Gregarines are paraphyletic and mixed...},
Doi = {10.1371/journal.pone.0018163},
File = {rueckert2011_gregarines from_crustaceans.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/12732534}
}
@Article{Ruedinger2008,
Title = {{Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat (PPR) proteins in jungermanniid but not in marchantiid liverworts}},
Author = {M. Ruedinger and M. Polsakiewicz and V. Knoop},
Journal = {Mol. Biol. Evol.},
Year = {2008},
Number = {7},
Pages = {1405--1414},
Volume = {25},
Abstract = {As stated},
Doi = {doi:10.1093/molbev/msn084},
File = {ruedinger2008.pdf}
}
@Article{Ruggiero2015,
Title = {{A higher level classification of all living organisms.}},
Author = {M. A. Ruggiero and D. P. Gordon and T. M. Orrell and N. Bailly and T. Bourgoin and R. C. Brusca and T. Cavalier-Smith and M. D. Guiry and P. M. Kirk},
Journal = {PLoS ONE},
Year = {2015},
Number = {4},
Pages = {e0119248},
Volume = {10},
Abstract = {For CoL},
Doi = {10.1371/journal.pone.0119248},
File = {ruggiero2015_classification_all_life_col.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25152275}
}
@Article{RuizTrillo2006,
Title = {{Insights into the Evolutionary Origin and Genome Architecture of the Unicellular Opisthokonts \textit{Capsaspora owczarzaki} and \textit{Sphaeroforma arctica}}},
Author = {I. Ruiz-Trillo and C. E. Lane and J. M. Archibald and A. J. Roger},
Journal = {J. Euk. Microbiol.},
Year = {2006},
Number = {5},
Pages = {1--6},
Volume = {53},
Abstract = {Nuclearia || Fungi; Ichty || Capsa || Minister || Coralloch || Choano},
File = {ruiz-trillo2006.pdf}
}
@Article{Ruiz-Trillo2002,
Title = {{A phylogenetic analysis of myosin heavy chain type II sequence corroborates that Acoela and Nemetrodermatida are basal bilaterians}},
Author = {I. Ruiz-Trillo and M. Loukota and C. Ribera and U. Jondelius and J. Baguna and M. Riutort},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2002},
Pages = {11246--11251},
Volume = {99}
}
@Article{RuizTrillo2015,
Title = {{Acoelomorpha: Earliest branching bilaterians or deuterostomes?}},
Author = {I. Ruiz-Trillo and J. Paps},
Journal = {Org Divers Evol},
Year = {2015},
Abstract = {Review, no opinion},
Doi = {10.1007/s13127-015-0239-1},
File = {ruiz_trillo2015_acoelomorphs.pdf}
}
@Article{Ruiz1999,
Title = {{Acoel Flatworms: Earliest Extant Bilaterian Metazoans, Not Members of Platyhelminthes}},
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Journal = {Science},
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Journal = {J. Morphol.},
Year = {2003},
Pages = {219--245},
Volume = {257},
Abstract = {Neomeniomorpha have primitive radula},
File = {scheltema2003.pdf}
}
@Article{Scherholz2015,
Title = {{From complex to simple: Myogenesis in an aplacophoran mollusk reveals key traits in aculiferan evolution.}},
Author = {M. Scherholz and E. Redl and T. Wollesen and C. Todt and A. Wanninger},
Journal = {BMC Evol. Biol.},
Year = {2015},
Pages = {201},
Volume = {15},
Abstract = {Apomorphic},
Doi = {10.1186/s12862-015-0467-1},
File = {scherholz2015_neomeniomorpha.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/11748697}
}
@Article{Scheuer2008,
Title = {{Bartheletia paradoxa is a living fossil on Ginkgo leaf litter with a unique septal structure in the Basidiomycota}},
Author = {C. Scheuer and R. Bauer and M. Lutz and E. Stabentheiner and V. A. Mel'nik and M. Grube},
Journal = {Mycol. Res.},
Year = {2008},
Number = {11},
Pages = {1265--1279},
Volume = {112},
Abstract = {Living fossil; Bartheletia || Tremell. incl. Cystophilobasidiales; unusual cell contacts (plasmodesmata)},
Doi = {10.1016/j.mycres.2008.06.008},
File = {scheuer2008.pdf}
}
@Article{Scheuermayer2006,
Title = {{Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ``Verrucomicrobia'', isolated from a sponge (Porifera).}},
Author = {M. Scheuermayer and T. A. M. Gulder and G. Bringmann and U. Hentschel},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2006},
Number = {9},
Pages = {2119--2124},
Volume = {56},
Abstract = {Rubritalea marina > subphylum 1 Verrumicrobia},
File = {santoh2006.pdf}
}
@Article{Schierwater2009b,
Title = {{Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis}},
Author = {B. Schierwater and M. Eitel and W. Jakob and H.-J. Osigus and H. Hadrys and S. L. Dellaporta and S.-O. Kolokotronis and R. Desalle},
Journal = {PLoS Biol.},
Year = {2009},
Number = {1},
Pages = {e20},
Volume = {7},
Abstract = {Placozoa || Porifera | Ctenoph || Cnidaria},
Doi = {10.1371/journal.pbio.1000020},
File = {schierwater2009_urmetazoon.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19175291}
}
@Article{Schierwater2009,
Title = {{Placozoa and the evolution of Metazoa and intrasomatic cell differentiation}},
Author = {B. Schierwater and D. de Jong and R. DeSalle},
Journal = {The International Journal of Biochemistry and Cell Biology},
Year = {2009},
Pages = {370--379},
Volume = {41},
Abstract = {Concatenated evidence: Placo || Spongia || Antho || Cteno + Medusozoa},
Doi = {10.1016/j.biocel.2008.09.023},
File = {schierwater2009.pdf}
}
@Article{Schierwater2010,
Title = {{The early evolution of Hox genes: A battle of belief?}},
Author = {B. Schierwater and K. Kamm},
Journal = {Adv Exp Med Biol.},
Year = {2010},
Pages = {81--90},
Volume = {689},
Abstract = {Review},
File = {shierwater2010_early_hox.txt}
}
@Article{Schierwater2008a,
Title = {{The early ANTP gene repertoire: insights from the placozoan genome}},
Author = {B. Schierwater and K. Kamm and M. Srivastava and D. Rokhsar and R. D. Rosengarten and S. L. Dellaporta},
Journal = {PLoS ONE},
Year = {2008},
Number = {8},
Pages = {e2457},
Volume = {3},
Abstract = {Total evidence for basal Placozoa; Hox: basal sponges are also possibe},
Doi = {10.1371/journal.pone.0002457},
File = {schierwater2008.pdf}
}
@Article{Schierwater1998,
Title = {{Homology of Hox Genes and the Zootype Concept in Early Metazoan Evolution}},
Author = {B. Schierwater and K. Kuhn},
Journal = {Mol. Phyl. Evol.},
Year = {1998},
Number = {3},
Pages = {375--381},
Volume = {9}
}
@Article{Schiffer2018,
Title = {{Orthonectids Are Highly Degenerate Annelid Worms.}},
Author = {P. H. Schiffer and H. E. Robertson and M. J. Telford},
Journal = {Curr. Biol.},
Year = {2018},
Number = {12},
Pages = {1970--1974--e3},
Volume = {28},
Abstract = {Ortho within Annelida; Dicyemida within Lophotrochozoa; likely not a one group},
Doi = {10.1016/j.cub.2018.04.088},
File = {schiffer2018_orthonectids_are_annelids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29861137}
}
@Article{Schirrmeister2011,
Title = {{The origin of multicellularity in cyanobacteria}},
Author = {B. E. Schirrmeister and A. Antonelli and H. C. Bagheri},
Journal = {BMC Evolutionary Biology},
Year = {2011},
Pages = {45},
Volume = {11},
Abstract = {One origin, multiple reversals},
Doi = {10.1186/1471-2148-11},
File = {schirrmeister2011_multicell_cyanobact.djvu},
Url = {http://www.biomedcentral.com/1471-2148/11/45}
}
@Article{Schleper2005,
Title = {{Genomic studies of uncultivated archaea.}},
Author = {C. Schleper and G. Jurgens and M. Jonuscheit},
Journal = {Nat. Rev. Microbiol.},
Year = {2005},
Number = {6},
Pages = {479--488},
Volume = {3},
Abstract = {Korarchaeota ~ AAG, separate group; Nanoarchaeum ~ Crenachaeota; Cenarchaeum ~ Gr. I1A, distinct from other Cren.},
File = {schleper2005.pdf}
}
@Article{Schloss2004,
Title = {{Status of the Microbial Census}},
Author = {P. D. Schloss and J. Handelsman},
Journal = {Microbiology and Mol. Biol. Reviews},
Year = {2004},
Number = {4},
Pages = {686--691},
Volume = {68},
Abstract = {OP11 group ~ Chloroflexi; 10**7 is too much},
File = {schloss2004.pdf}
}
@Article{Schmidt2012,
Title = {{Synchroma pusillum sp. Nov. And other new algal isolates with chloroplast complexes confirm the Synchromophyceae (Ochrophyta) as a widely distributed group of amoeboid algae.}},
Author = {M. Schmidt and S. Horn and K. Flieger and K. Ehlers and C. Wilhelm and R. Schnetter},
Journal = {Protist},
Year = {2012},
Number = {4},
Pages = {544--559},
Volume = {163},
Abstract = {Eustigm || Picophagus || Chryso || Leukarachn || Chlamydomyxa || Synchroma},
Doi = {10.1016/j.protis.2011.11.009},
File = {schmidt2012_new_synchromophyceae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22578425}
}
@Article{Schmidt2002,
Title = {{The Evolution of Gymnosperms Redrawn by Phytochrome Genes: The Gnetatae Appear at the Base of the Gymnosperms}},
Author = {Marion Schmidt and Hansjog A.W. Schneider-Poetsch},
Journal = {J. Mol. Evol.},
Year = {2002},
Pages = {715--724},
Volume = {54}
}
@Book{SchmidtRhaesa2007,
Title = {{The Evolution of Organ Systems}},
Author = {A. Schmidt-Rhaesa},
Publisher = {Oxford University Press},
Year = {2007},
Address = {Oxford},
ISBN = {0198566697},
Pages = {1--368}
}
@Article{SchmidtRhaesa2006,
Title = {{Perplexities concerning the Ecdysozoa: A reply to Pilato et al.}},
Author = {A. Schmidt-Rhaesa},
Journal = {Zool. Anz.},
Year = {2006},
Pages = {205--208},
Volume = {244},
Abstract = {Subj},
File = {schmidt-rhaesa2006.pdf}
}
@Article{SchmidtRhaesa2002,
Title = {{Two Dimensions of Biodiversity Research Exemplified by Nematomorpha and Gastrotricha}},
Author = {A. Schmidt-Rhaesa},
Journal = {Integr. Comp. Biol.},
Year = {2002},
Pages = {633--640},
Volume = {42},
Abstract = {Gastr: ssiter to Spiralia, or, most probably, to Ecdysozoa},
File = {schmidt-rhaesa2003.pdf}
}
@Article{SchmidtRhaesa2001,
Title = {{Tardigrades:~--- are they really miniaturized dwarfs?}},
Author = {A. Schmidt-Rhaesa},
Journal = {Zool. Anz.},
Year = {2001},
Pages = {549--555},
Volume = {240},
Abstract = {Likely Tardigrada primarily small, sister to Cycloneuralia},
File = {schmidt-rhaesa2001.pdf}
}
@Article{Schmitz2000,
Title = {{The Complete Mitochondrial Genome of Tupaia belangeri and the Phylogenetic Affiliation of Scandentia to Other Eutherian Orders}},
Author = {J. Schmitz and M. Ohme and H. Zischler},
Journal = {Mol. Biol. Evol.},
Year = {2000},
Number = {9},
Pages = {1334--1343},
Volume = {17}
}
@Article{Schneider2009,
Title = {{Is Morphology Really at Odds with Molecules in Estimating Fern Phylogeny?}},
Author = {H. Schneider and A. R. Smith and K. M. Pryer},
Journal = {Systematic Botany},
Year = {2009},
Number = {3},
Pages = {455--475},
Volume = {34},
Abstract = {Equis, Psil, Ophio, Maratt are less stable},
File = {schneider2009_ferns.pdf}
}
@Article{Schnepf1997,
Title = {{\textit{Pirsonia}, phagotrophic nanophlagellates incertae sedis, feeding on marine diatoms: host recognition, attachment and fine structure}},
Author = {E. Schnepf and M. Schweikert},
Journal = {Arch. Protistenkd.},
Year = {1997},
Pages = {361--371},
Volume = {147}
}
@Article{Schoch2009b,
Title = {{A class-wide phylogenetic assessment of Dothideomycetes}},
Author = {C. L. Schoch and P. W. Crous and J. Z. Groenewald and E. W. A. Boehm and T. I. Burgess and J. de Gruyter and G. S. de Hoog and L. J. Dixon and M. Grube and C. Gueidan and Y. Harada and S. Hatakeyama and K. Hirayama and T. Hosoya and S. M. Huhndorf and K. D. Hyde and E. B. G. Jones and J. Kohlmeyer and A. Kruys and Y. M. Li and R. L{\"u}cking and H. T. Lumbsch and L. Marvanov{\'a} and J. S. Mbatchou and A. H. McVay and A. N. Miller and G. K. Mugambi and L. Muggia and M. P. Nelsen and P. Nelson and C. A. Owensby and A. J. L. Phillips and S. Phongpaichit and S. B. Pointing and V. Pujade-Renaud and H. A. Raja and E. R. Plata and B. Robbertse and C. Ruibal and J. Sakayaroj and T. Sano and L. Selbmann and C. A. Shearer and T. Shirouzu and B. Slippers and S. Suetrong and K. Tanaka and B. Volkmann-Kohlmeyer and M. J. Wingfield and A. R. Wood and J. H. C. Woudenberg and H. Yonezawa and Y. Zhang and J. W. Spatafora},
Journal = {Stud. Mycol.},
Year = {2009},
Pages = {1 - 15S10},
Volume = {64},
Abstract = {As stated},
Doi = {10.3114/sim.2009.64.01},
File = {schoch2010_dothideomycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20169021}
}
@Article{SchochInpress,
Title = {{The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits}},
Author = {C. L. Schoch and G.-H. Sung and F. L{\'o}pez-Gir{\'a}ldez and J. P. Townsend and J. Miadlikowska and V. Hofstetter and B. Robbertse and P. B. Matheny and F. Kauff and Z. Wang and C. Gueidan and R. M. Andrie and K. Trippe and L. M. Ciufetti and A. Wynns and E. Fraker and B. P. Hodkinson and G. Bonito and J. Z. Groenewald and M. Arzanlou and G. S. de Hoog and P. W. Crous and D. Hewitt and D. H. Pfister and K. Peterson and M. Gryzenhout and M. J. Wingfield and A. Aptroot and S.-O. Suh and M. Blackwell and D. M. Hillis and G. W. Griffith and L. A. Castlebury and A. Y. Rossman and H. T. Lumbsch and R. L{\"u}cking and B. B{\"u}del and A. Rauhut and P. Diederich and D. Ertz and D. M. Geiser and K. Hosaka and P. Inderbitzin and J. Kohlmeyer and B. Volkmann-Kohlmeyer and L. Mostert and O. Kerry and H. Sipman and J. D. Rogers and R. A. Shoemaker and J. Sugiyama and R. C. Summerbell and W. Untereiner and P. R. Johnston and S. Stenroos and A. Zuccaro and P. S. Dyer and P. D. Crittenden and M. S. Cole and K. Hansen and J. M. Trappe and R. Yahr and F. Lutzoni and J. W. Spatafora},
Journal = {Systematic Biology},
Year = {In press},
Abstract = {Neolecto || (Pneumoc + Schizosacc), (Taphrin + Saitoella) || Sacc || Pezizo || Orbilio || Lichn, ?Geoglossales || (Dothideomyceta: ?Symbiotaphrina, Arth, Dothid || Eurot, Lecanor + ?Candelariales), (Sordariomyceta: Leoti || Laboulb || Sordar)}
}
@Article{Schoch2009,
Title = {{Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life}},
Author = {C. L. Schoch and Z. Wang and J. P. Townsend and J. W. Spatafora},
Journal = {Persoonia},
Year = {2009},
Pages = {129--138},
Volume = {22},
Abstract = {As stated},
Doi = {10.3767/003158509X461486},
File = {schoch2009_geoglossomycetes.pdf}
}
@Article{Schockaert2008,
Title = {{Global diversity of free living flatworms (Platyhelminthes, ``Turbellaria'') in freshwater}},
Author = {E. R. Schockaert and M. Hooge and R. Sluys and S. Schilling and S. Tyler and T. Artois},
Journal = {Hydrobiologia},
Year = {2008},
Pages = {41--48},
Volume = {595},
Abstract = {Catenulida (Macrostomida (Polycladida (Neoophora, incl. Neodermata)))},
Doi = {10.1007/s10750-007-9002-8},
File = {schockaert2008.pdf}
}
@Article{Scholtz2002,
Title = {{The Articulata hypothesis~--- or what is a segment?}},
Author = {G. Scholtz},
Journal = {Org. Divers. Evol.},
Year = {2002},
Pages = {197--215},
Volume = {2},
Abstract = {Monophyleric Articulata},
File = {scholz2003.pdf}
}
@Article{Scholtz2006,
Title = {{The evolution of arthropod heads: reconciling morphological, developmental and palaeontological evidence}},
Author = {G. Scholtz and G. D. Edgecombe},
Journal = {Dev. Gen. Evol.},
Year = {2006},
Pages = {395--415},
Volume = {216},
Abstract = {Chelic || Myri || Crust || Hexa, against Paradoxopoda},
File = {scholtz2006.pdf}
}
@Article{Schrodl2014,
Title = {{A review on deep molluscan phylogeny: Old markers, integrative approaches, persistent problems}},
Author = {M. Schr{\"o}dl and I. St{\"o}ger},
Journal = {Journal of Natural History},
Year = {2014},
Abstract = {Gastr | Bivalv || Monopl + Polypl and Scaph || Caudofov || Solenog + Ceph (most of support low)},
Doi = {10.1080/00222933.2014.963184},
File = {schroedl2014_deep_molluscan_phyl_rev.pdf},
Url = {http://dx.doi.org/10.1080/00222933.2014.963184}
}
@InCollection{Schram2004,
Title = {{Are the crustaceans monophyletic?}},
Author = {F. R. Schram and S. Koenemann},
Booktitle = {{Assembling the Tree of Life}},
Publisher = {Oxford Univ. Press},
Year = {2004},
Address = {New York},
Editor = {J. Carcraft and M. J. Donoghue},
Pages = {319--329},
Abstract = {Morphol: Ostracoda in Maxillopoda; but Mystaco+Branchiura separate; Leptostraca in Malacostraca},
File = {schulze2003b.pdf}
}
@Book{Schram2021,
Title = {{Evolution and phylogeny of Pancrustacea : A story of scientific method }},
Author = {F. R. Schram and S. Koenemann and O. Franţescu},
Year = {2021},
Abstract = {Oligostraca (Ostracoda, Mystaco, Branchiura, Pentastomida), Multicrustacea (Copepoda, Thecostraca, Malacostraca), Allotriocarida (Brachiopoda, Phylopoda, Xenocarida: Cephalocarida + Remipedia, Hexapoda)},
File = {schram2021_evolution_and_phylogeny_of_pancrustacea.djvu},
ISBN = {9780195365764}
}
@Article{Schuettpelz2009,
Title = {{Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy}},
Author = {E. Schuettpelz and K. M. Pryer},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2009},
Number = {27},
Pages = {11200--11205},
Volume = {106},
File = {schuettpelz2009_ferns_radiation.pdf}
}
@Article{Schuettpelz2007,
Title = {{Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes}},
Author = {E. Schuettpelz and K. M. Pryer},
Journal = {Taxon},
Year = {2007},
Number = {4},
Pages = {1037--1050},
Volume = {2007},
Abstract = {Good-resolved tree, a little taxonomy},
File = {schuettpelz2007.pdf}
}
@Article{Schuettpelz2018,
Title = {{Are there too many fern genera?}},
Author = {E. Schuettpelz and G. Rouhan and K. M. Pryer and C. J. Rothfels and J. Prado and M. A. Sundue and M. D. Windham and R. C. Moran and A. R. Smith},
Journal = {TAXON},
Year = {2018},
Doi = {10.12705/673.1},
File = {schuettpelz2018_not_too_many_fern_genera.pdf},
Url = {https://doi.org/10.12705/673.1}
}
@Article{Schuler2018a,
Title = {{Description of Armaparvus languidus n. Gen. N. Sp. Confirms Ultrastructural Unity of Cutosea (Amoebozoa, Evosea).}},
Author = {G. A. Schuler and M. W. Brown},
Journal = {J. Eukaryot. Microbiol.},
Year = {2018},
Abstract = {Not "Pessonella" but Armaparvus; Evosea is Cutosea + Eumycetoz + Variosea; Evosea + Tubulinea = Tevosea; Tevosea + Discosea = Amoebozoa},
Doi = {10.1111/jeu.12640},
File = {schuler2018_armaparvus_cutosea_amoebozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29858563}
}
@Article{Schuler2018,
Title = {{Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade.}},
Author = {G. A. Schuler and A. K. Tice and R. A. Pearce and E. Foreman and J. Stone and S. Gammill and J. D. Willson and C. Reading and J. D. Silberman and M. W. Brown},
Journal = {Protist},
Year = {2018},
Number = {6},
Pages = {853--874},
Volume = {169},
Abstract = {Sainouroidea (~ Cercomonas): Cholamonas, Sainouron, Helkesimastix, Guttulinopsis, and Rosculus},
Doi = {10.1016/j.protis.2018.08.002},
File = {schuler2018_sainouroidea.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30415103}
}
@Article{Schulz2007,
Title = {{Evolution of taxodiaceous Cupressaceae (Coniferopsida)}},
Author = {C. Schulz and T. Stutzel},
Journal = {Org. Divers. Evol.},
Year = {2007},
Pages = {124--135},
Volume = {7},
Abstract = {Sciad || Cunnin || others},
Doi = {10.1016/j.ode.2006.03.001},
File = {schulz2007.pdf}
}
@Article{Schulz2017,
Title = {{Towards a balanced view of the bacterial tree of life.}},
Author = {F. Schulz and E. A. Eloe-Fadrosh and R. M. Bowers and J. Jarett and T. Nielsen and N. N. Ivanova and N. C. Kyrpides and T. Woyke},
Journal = {Microbiome},
Year = {2017},
Number = {1},
Pages = {140},
Volume = {5},
Abstract = {As stated, fig. 1 contains the tree},
Doi = {10.1186/s40168-017-0360-9},
File = {schultz2017_balanced_view_bact_tol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27572647}
}
@Article{Schulze2007,
Title = {{Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology}},
Author = {A. Schulze and E. B. Cutler and G. Giribet},
Journal = {Mol. Phyl. Evol.},
Year = {2007},
Pages = {171--192},
Volume = {42},
Abstract = {No support for Sipunculoidea; some support for Phascolosomatidea},
File = {schulze2007.pdf}
}
@Article{Schulze2009,
Title = {{Musculature in sipunculan worms: ontogeny and ancestral states}},
Author = {A. Schulze and M. E. Rice},
Journal = {Evol. Devel.},
Year = {2009},
Pages = {97 - 108},
Volume = {1},
Abstract = {ancestral sipunculan had four introvert retractor muscles, longitudinal body wall musculature in bands; ~ Limbricus},
Doi = {10.1111/j.1525-142X.2008.00306.x},
File = {schulze2009_sipunculid_muscles.pdf}
}
@Article{Schwaha2010,
Title = {{Organogenesis in the Budding Process of the Freshwater Bryozoan Cristatella mucedo Cuvier, 1798 (Bryozoa, Phylactolaemata)}},
Author = {T. Schwaha and S. Handschuh and E. Redl and M. G. Walzl},
Journal = {JOURNAL OF MORPHOLOGY},
Year = {2010},
Abstract = {Nothing fancy},
Doi = {10.1002/jmor.10915},
File = {schwaha2010_cristatella.djvu}
}
@Article{Schweigkofler2002,
Title = {{Analysis of phylogenetic relationships among Ascomycota with yeast phases using ribosomal DNA sequences and cell wall sugars}},
Author = {W. Schweigkofler and K. Lopandic and O. Molnar and H. Prillinger},
Journal = {Org. Divers. Evol.},
Year = {2002},
Pages = {1--17},
Volume = {2}
}
@Article{Schwentner2017,
Title = {{A Phylogenomic Solution to the Origin of Insects by Resolving Crustacean-Hexapod Relationships.}},
Author = {M. Schwentner and D. J. Combosch and J. P. Nelson and G. Giribet},
Journal = {Curr. Biol.},
Year = {2017},
Number = {12},
Pages = {1818 - 1824 - e5},
Volume = {27},
Abstract = {Oligostraca: Mystaco + (Ostrac + Brachiura); Multicrustacea: Thecostr + (Copepoda + Malac); Allotriocarida: Cephaloc || Branchiop || (Labiocarida: Remipedia || Hexapoda)},
Doi = {10.1016/j.cub.2017.05.040},
File = {schwentner2017_crustacea_hexapoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28602656}
}
@Article{Schwentner2018,
Title = {{Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: Highlighting the strength of taxon-specific matrices in phylogenomics.}},
Author = {M. Schwentner and S. Richter and D. C. Rogers and G. Giribet},
Journal = {Proc. Biol. Sci.},
Year = {2018},
Number = {1885},
Volume = {285},
Abstract = {Agrees with their previous publication},
Doi = {10.1098/rspb.2018.1524},
File = {schwentner2018_tetraconata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/11020302}
}
@Article{Scoble2014,
Title = {{Scale evolution, sequence phylogeny, and taxonomy of thaumatomonad Cercozoa: 11 New species and new genera Scutellomonas, Cowlomonas, Thaumatospina and Ovaloplaca.}},
Author = {J. M. Scoble and T. Cavalier-Smith},
Journal = {Eur. J. Protistol.},
Year = {2014},
Number = {3},
Pages = {270--313},
Volume = {50},
Abstract = {Ventrifilosea: Mataza etc. etc.},
Doi = {10.1016/j.ejop.2013.12.005},
File = {scoble2013_thautomonads.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24667165}
}
@Article{SebePedros2013,
Title = {{Insights into the origin of metazoan filopodia and microvilli}},
Author = {A. Seb{\'e}-Pedr{\'o}s and P. Burkhardt and N. S{\'a}nchez-Pons and S. R. Fairclough and B. F. Lang and N. King and I. Ruiz-Trillo},
Journal = {Mol. Biol. Evol.},
Year = {2013},
Pages = {1-33},
Abstract = {From Choanozoa},
File = {sebe_pedros2013_capsaspora_filopodia.pdf}
}
@Article{SebePedros2010,
Title = {{Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki}},
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Journal = {Molecular Biology and Evolution},
Year = {2010},
Abstract = {Amoeboz || Thecamonas || Fungi || Capsa || Choano || Metazoa},
File = {sebe-pedros2010_capsaspora.pdf}
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@Article{Seitz2019,
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@Article{ShalchianTabrizi2007,
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@Article{ShalchianTabrizi2008,
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Pages = {e2098},
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@Article{Shear2009,
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@Article{Shen2018,
Title = {{Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.}},
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Year = {2018},
Number = {2},
Pages = {1 - 11},
Volume = {7},
Abstract = {Equiset || Maratt || Psil + Ophiogl || rest},
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@Article{Shen2009,
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@Article{Shen2016,
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Volume = {5},
Abstract = {Chaeto || Bryoz || Brach || Ann || Nemert, Moll, Entoprocta || Ecdysozoa},
Doi = {10.1111/zsc.12140},
File = {shen2016_cheatognatha.pdf}
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@Article{Shi2011,
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Journal = {PLoS ONE},
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Pages = {2011},
Volume = {21},
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@Article{Shih2013,
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@Article{Shinohara2013,
Title = {{The Use of matK in Ophioglossaceae Phylogeny and the Determination of Mankyua Chromosome Number Shed Light on Chromosome Number Evolution in Ophioglossaceae}},
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Pages = {564--570},
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Abstract = {Platysulcus || Labyr + MAST-20 || MASTs 7,8,9,10,25,11,4,6 || Bicosea + MASTS 22,24,16 || MAST-21 || Placididea || Nanomonadea || MAST-12 + Blasto + Opal || MAST-12 || MAST-23 + Bgyromonadea || MAST-1 + Oo || other Ochrophyta},
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Journal = {Protist},
Year = {2014},
Abstract = {As stated},
Doi = {10.1016/j.protis.2014.10.003},
File = {takashi2014_abollifer.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2014.10.003}
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Year = {2008},
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Pages = {978--990},
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Journal = {Mikologija i fitopatologija},
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Note = {(In Russian)},
Number = {5},
Pages = {1--5},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2016},
Pages = {79--92},
Volume = {96},
Abstract = {As stated in the title},
Doi = {10.1016/j.ympev.2015.11.017},
File = {sielaff2015_syndermata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26702959}
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@Article{Siemer1998,
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Year = {2013},
Abstract = {Plasmodioph || Cercozoa || Gromia-Filoreta || Polycyst || Acanth || Foram},
Doi = {10.1016/j.ympev.2012.12.011},
File = {sierra2013_retaria.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2012.12.011}
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@Article{Siewing1980,
Title = {{Das Archicoelomatenkonzept}},
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@Article{Signorovitch2007,
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@Article{Sigwart2014,
Title = {{Consensus and Confusion in Molluscan Trees: Evaluating Morphological and Molecular Phylogenies}},
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Year = {2014},
Abstract = {No consensus},
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@Article{Sigwart2007,
Title = {{Deep molluscan phylogeny: synthesis of palaeontological and neontological data}},
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Journal = {Proc. R. Soc. B},
Year = {2007},
Number = {1624},
Pages = {2413--2419},
Volume = {274},
Abstract = {Neopil || Polypl + Aplac (diphyletic?)},
File = {sigwart2007.pdf}
}
@Article{Silberfeld2010,
Title = {{A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation"}},
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Year = {2010},
Number = {2},
Pages = {659 - 674},
Volume = {56},
Doi = {10.1016/j.ympev.2010.04.020},
File = {silberfield2010_crown_phaeophyceae.pdf},
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@Article{Silberman1999,
Title = {{Phylogeny of the Genera \textit{Entamoeba} and \textit{Endolimax} as Deduced from Small-Subunit Ribosomal RNA Sequences}},
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Year = {1999},
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Pages = {1740--1751},
Volume = {16}
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@Article{Silberman2004,
Title = {{Ellobiopsids of the Genus \textit{Thalassomyces} are Alveolates}},
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Year = {2004},
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@Article{daSilvaPaiva2013,
Title = {{Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data}},
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Journal = {Genetics and Molecular Biology},
Year = {2013},
Pages = {571--585},
Volume = {4},
Abstract = {Support for Lamellicorticata},
File = {silva2013_armophorea.pdf},
Url = {www.sbg.org.br}
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@Article{daSilva2006,
Title = {{High diversity of deep-sea Gromia from the Arabian Sea revealed by small subunit rDNA sequence analysis}},
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Journal = {Mar. Biol.},
Year = {2006},
Pages = {769--777},
Volume = {148},
Abstract = {Foram sister to Haplo || Gromia || Plasmodioph || other Cercozoa},
File = {silva2006.pdf}
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@Article{daSilva2007,
Title = {{Phylogenetic position of Placozoa based on large subunit (LSU) and small subunit (SSU) rRNA genes}},
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Journal = {Gen. Mol. Biol.},
Year = {2007},
Number = {1},
Pages = {127--132},
Volume = {30},
Abstract = {Placoz || Cnidaria or Bilateria},
File = {silva2007.pdf}
}
@Article{Silva2007,
Title = {{Revisiting the nomenclature of haptophytes}},
Author = {P. C. Silva and J. Throndsen},
Journal = {Phycologia},
Year = {2007},
Number = {4},
Pages = {471--475},
Volume = {46},
Abstract = {Use Coccolithophyceae instead of Prymnesiophyceae},
Doi = {10.2216/07-22.1},
File = {silva2007.pdf}
}
@Article{Simakov2015,
Title = {{Hemichordate genomes and deuterostome origins.}},
Author = {O. Simakov and T. Kawashima and F. Marl{\'e}taz and J. Jenkins and R. Koyanagi and T. Mitros and K. Hisata and J. Bredeson and E. Shoguchi and F. Gyoja and J.-X. Yue and Y.-C. Chen and R. M. Freeman and A. Sasaki and T. Hikosaka-Katayama and A. Sato and M. Fujie and K. W. Baughman and J. Levine and P. Gonzalez and C. Cameron and J. H. Fritzenwanker and A. M. Pani and H. Goto and M. Kanda and N. Arakaki and S. Yamasaki and J. Qu and A. Cree and Y. Ding and H. H. Dinh and S. Dugan and M. Holder and S. N. Jhangiani and C. L. Kovar and S. L. Lee and L. R. Lewis and D. Morton and L. V. Nazareth and G. Okwuonu and J. Santibanez and R. Chen and S. Richards and D. M. Muzny and A. Gillis and L. Peshkin and M. Wu and T. Humphreys and Y.-H. Su and N. H. Putnam and J. Schmutz and A. Fujiyama Jr-K. Yu and K. Tagawa and K. C. Worley and R. A. Gibbs and M. W. Kirschner and C. J. Lowe and N. Satoh and D. S. Rokhsar and J. Gerhart},
Journal = {Nature},
Year = {2015},
Number = {7579},
Pages = {459--465},
Volume = {527},
Abstract = {Acoela (+- Xeno) || Hemi + Echino || Ceph || Uro || Vert},
Doi = {10.1038/nature16150},
File = {simakov2015_hemichordate_genomes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26580012}
}
@Article{Simakov2013,
Title = {{Insights into bilaterian evolution from three spiralian genomes.}},
Author = {O. Simakov and F. Marletaz and S.-J. Cho and E. Edsinger-Gonzales and P. Havlak and U. Hellsten and D.-H. Kuo and T. Larsson and J. Lv and D. Arendt and R. Savage and K. Osoegawa and P. de Jong and J. Grimwood and J. A. Chapman and H. Shapiro and A. Aerts and R. P. Otillar and A. Y. Terry and J. L. Boore and I. V. Grigoriev and D. R. Lindberg and E. C. Seaver and D. A. Weisblat and N. H. Putnam and D. S. Rokhsar},
Journal = {Nature},
Year = {2013},
Number = {7433},
Pages = {526--531},
Volume = {493},
Abstract = {Lophotr. and Spiralia supported, Ecdysozoa with some problems},
Doi = {10.1038/nature11696},
File = {simakov2013_bilateria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23254933}
}
@Article{Simdyanov2018,
Title = {{First Ultrastructural and Molecular Phylogenetic Evidence from the Blastogregarines, an Early Branching Lineage of Plesiomorphic Apicomplexa}},
Author = {T. G. Simdyanov and G. G. Paskerova and A. Valigurov{\'a} and A. Diakin and M. Kov{\'a}{\v{c}}ikov{\'a} and J. Schr{\'e}vel and L. Guillou and A. A. Dobrovolskij and V. V. Aleoshin},
Journal = {Protist},
Year = {2018},
Abstract = {Coccidiomorpha + Gregarines (inc. Selenidium (deeply) and Cryptosporidium (basally))},
Doi = {10.1016/j.protis.2018.04.006},
File = {simdyanov2018_blastogregarines.pdf},
Url = {https://doi.org/10.1016/j.protis.2018.04.006}
}
@Article{Simion2014,
Title = {{Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora}},
Author = {P. Simion and N. Bekkouche and M. Jager and E. Qu{\'e}innec and M. Manuel},
Journal = {Zoology},
Year = {2014},
Abstract = {As stated},
Doi = {10.1016/j.zool.2014.06.004},
File = {simion2014_ctenophora.pdf},
ISSN = {0944-2006},
Url = {http://dx.doi.org/10.1016/j.zool.2014.06.004}
}
@Article{Simion2017,
Title = {{A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals.}},
Author = {P. Simion and H. Philippe and D. Baurain and M. Jager and D. J. Richter and A. Di Franco and B. Roure and N. Satoh and {\'E}. Qu{\'e}innec and A. Ereskovsky and P. Lap{\'e}bie and E. Corre and F. Delsuc and N. King and G. W{\"o}rheide and M. Manuel},
Journal = {Curr. Biol.},
Year = {2017},
Number = {7},
Pages = {958 - 967},
Volume = {27},
Abstract = {Porifera | Ctenophora | Placozoa | Bilateria | Anthozoa + Medusozoa},
Doi = {10.1016/j.cub.2017.02.031},
File = {simion2017_sponges_basal.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28318975}
}
@Article{Simmons2009,
Title = {{Lobulomycetales, a new order in the Chytridiomycota}},
Author = {D. R. Simmons and T. Y. James and A. F. Meyer and J. E. Longcore},
Journal = {Mycol. Res.},
Year = {2009},
Number = {4},
Pages = {450--460},
Volume = {113},
Abstract = {As stated},
Doi = {10.1016/j.mycres.2008.11.019},
File = {simmons2009_lobulomycetales.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19138737}
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@Article{Simon2013,
Title = {{New haptophyte lineages and multiple independent colonizations of freshwater ecosystems.}},
Author = {M. Simon and P. L{\'o}pez-Garc{\'i}a and D. Moreira and L. Jardillier},
Journal = {Environ Microbiol Rep},
Year = {2013},
Number = {2},
Pages = {322--332},
Volume = {5},
Abstract = {Belong to known classes},
Doi = {10.1111/1758-2229.12023},
File = {simon2013_haptophytes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23584973}
}
@Article{Simon2018,
Title = {{Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure.}},
Author = {S. Simon and A. Blanke and K. Meusemann},
Journal = {Arthropod Struct Dev},
Year = {2018},
Number = {4},
Pages = {328--338},
Volume = {47},
Doi = {10.1016/j.asd.2018.05.002},
File = {simon2018_palaeoptera_problem.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29763650}
}
@Article{Simpson1999,
Title = {{The ultrastructure of \textit{Carpediemonas membranifera} (Eukaryota) with reference to the ``Excavate Hypothesis''}},
Author = {A. Simpson and D. J. Patterson},
Journal = {Eur. J. Protistol.},
Year = {1999},
Pages = {353--370},
Volume = {35}
}
@Article{Simpson2003,
Title = {{Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)}},
Author = {A. G. B. Simpson},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2003},
Pages = {1759--1777},
Volume = {53},
Abstract = {Jacobida s.str. also ~ Euglenida?},
File = {simpson2003.pdf}
}
@Article{Simpson1997,
Title = {{The identity and composition of the Euglenozoa}},
Author = {A. G. B. Simpson},
Journal = {Arch. Protistenkd.},
Year = {1997},
Pages = {318--328},
Volume = {148}
}
@Article{Simpson1997a,
Title = {{The ultrastructure and systematic position of the euglenozoon \textit{Postgaardi mariagerensis} Fenchel et al.}},
Author = {A. G. B. Simpson and H. J. van den and C. Bernard and H. Burton and D. J. Patterson},
Journal = {Arch. Protistenkd.},
Year = {1997},
Pages = {213--225},
Volume = {147}
}
@Article{Simpson1997b,
Title = {{The Organisation of \textit{Mastigamoeba schizophrenia} n. sp.: More Evidence of Ultrastructural idiosyncrasy and Simplicity in Pelobont Protists}},
Author = {A. G. B. Simpson and C. Bernard and T. Fenchel and D. J. Patterson},
Journal = {Eur. J. Protistol.},
Year = {1997},
Pages = {87--98},
Volume = {33}
}
@Article{Simpson2002,
Title = {{The evolutionary history of Kinetoplastids and their kinetoplasts}},
Author = {A. G. B. Simpson and J. Lukes and A. J. Roger},
Journal = {Mol. Biol. Evol.},
Year = {2002},
Number = {12},
Pages = {2071--2083},
Volume = {19}
}
@Article{Simpson2001,
Title = {{On Core Jakobids and Excavate Taxa: The Ultrastructure of Jakoba incarcerata}},
Author = {A. G. B. Simpson and D. J. Patterson},
Journal = {J. Euk. Microbiol.},
Year = {2001},
Pages = {480--492},
Volume = {48}
}
@Article{Simpson2008,
Title = {{Lateral transfer of the gene for a widely used marker, alpha-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata)}},
Author = {A. G. B. Simpson and T. A. Perley and E. Lara},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {1},
Pages = {366--377},
Volume = {47},
Abstract = {6--7 proteins: Malawi || ((Andalucia + other Jac.) || (Eugl. + Heter)), and Metamonada near the base; (a-tub.): Crypto || Kata || Hapto, Telonema separ.},
File = {simpson2007.pdf}
}
@Article{Simpson2002b,
Title = {{How Oxymonads Lost Their Groove: An Ultrastructural Comparison of Monocercomonoides and Excavate Taxa}},
Author = {Alastair G. B. Simpson and Renate Radek and Joel B. Dacks and Charles J. O'Kelly},
Journal = {J. Euk. Microbiol.},
Year = {2002},
Pages = {239--248},
Volume = {49}
}
@Article{Simpson2004,
Title = {{Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa}},
Author = {A. G. B. Simpson and A. J. Roger},
Journal = {Mol. Phyl. Evol.},
Year = {2004},
Pages = {201--212},
Volume = {30},
Abstract = {Eugl || Diplo || Kineto},
File = {simpson2004a.pdf}
}
@InBook{Simpson2017,
Title = {{Protist Diversity and Eukaryote Phylogeny}},
Author = {A. G. B. Simpson and C. H. Slamovits and J. M. Archibald},
Year = {2017},
Abstract = {Review},
Booktitle = {{Handbook of the Protists}},
Doi = {10.1007/978-3-319-28149-0_45},
File = {simpson2017_protist_div_phylog.pdf}
}
@Article{Sims1999,
Title = {{Primary and Secondary Structure of the Small-Subunit Ribosomal {RNA} of the Naked, Marine Amoeba \textit{Vannella anglica}: Phylogenetic Implications}},
Author = {Gary P. Sims and Andrew Rogerson and Robert Aitken},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {740--749},
Volume = {48}
}
@Article{Singh2009,
Title = {{Tunicate mitogenomics and phylogenetics: Peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny}},
Author = {T. R. Singh and G. Tsagkogeorga and F. Delsuc and S. Blanquart and N. Shenkar and Y. Loya and E. J. Douzery and D. Huchon},
Journal = {BMC Genomics},
Year = {2009},
Pages = {534},
Volume = {10},
Abstract = {Ceph || Tunic || vertebr},
Doi = {10.1186/1471-2164-10-534},
File = {singh2009_chordata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19922605}
}
@Article{Sinniger2007,
Title = {{Mitochondrial genome of savalia savaglia (Cnidaria, Hexacorallia) and early metazoan phylogeny}},
Author = {F. Sinniger and P. Chevaldonne and J. Pawlowski},
Journal = {J. Mol. Evol.},
Year = {2007},
Pages = {196--203},
Volume = {64},
Abstract = {Demospongia may be close to Cnidaria},
File = {sinniger2007.pdf}
}
@Article{Siver2015,
Title = {{Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches.}},
Author = {P. A. Siver and B. Y. Jo and J. I. Kim and W. Shin and A. M. Lott and A. P. Wolfe},
Journal = {Am. J. Bot.},
Year = {2015},
Abstract = {As stated},
Doi = {10.3732/ajb.1500004},
File = {siver2015_synurophyceae.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26101418}
}
@Article{Sjamsuridzal2002,
Title = {{Phylogenetic position of Mixia osmundae inferred from 28S rDNA comparison}},
Author = {W. Sjamsuridzal and H. Nishida and A. Yokota},
Journal = {J. Gen. Appl. Microbiol.},
Year = {2002},
Pages = {121--123},
Volume = {48},
Abstract = {Major lineage of Urediniomycetes},
File = {sjamsuridzal2002.pdf}
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@InProceedings{Skarlato1979,
Title = {Main features of evolution and taxonomy of classis Bivalvia},
Author = {O. A. Skarlato and Ja. I. Starobogatov},
Booktitle = {Trudy ZIN},
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File = {desousa2018_moss_groups_monophyly.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30411803}
}
@Book{South1987,
Title = {{Introducrion to phycology}},
Author = {G. South and A. Whittick},
Publisher = {Wiley-Blackwell},
Year = {1987},
Address = {Oxford},
Pages = {341}
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@Article{Spang2010,
Title = {{Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota}},
Author = {A. Spang and R. Hatzenpichler and C. Brochier-Armanet and T. Rattei and P. Tischler and E. Spieck and W. Streit and D. A. Stahl and M. Wagner and C. Schleper},
Journal = {Trends in microbiology},
Year = {2010},
Number = {8},
Pages = {331 - 340},
Volume = {18},
Abstract = {Thauma || Eury || Crena + Kora},
Doi = {10.1016/j.tim.2010.06.003},
File = {spang2010_thaumarcheota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20598889}
}
@Article{Spang2015,
Title = {{Complex archaea that bridge the gap between prokaryotes and eukaryotes.}},
Author = {A. Spang and J. H. Saw and S. L. J{\o}rgensen and K. Zaremba-Niedzwiedzka and J. Martijn and A. E. Lind and R. van Eijk and C. Schleper and L. Guy and T. J. G. Ettema},
Journal = {Nature},
Year = {2015},
Number = {7551},
Pages = {173--179},
Volume = {521},
Abstract = {Metanopyrus || Euryarchaeota || DPANN || Thermococcales || TACK: Lokiarchaeum (Lokiarchaeota, DSAG) + Eukarya || Kora || Crena || MCG (Miscellaneous Crenarchaeota Group) || Thauma || Aiga},
Doi = {10.1038/nature14447},
File = {spang2015_lokiarchaea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25945740}
}
@Article{Spatafora2016,
Title = {{A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.}},
Author = {J. W. Spatafora and Y. Chang and G. L. Benny and K. Lazarus and M. E. Smith and M. L. Berbee and G. Bonito and N. Corradi and I. Grigoriev and A. Gryganskyi and T. Y. James and K. O'Donnell and R. W. Roberson and T. N. Taylor and J. Uehling and R. Vilgalys and M. M. White and J. E. Stajich},
Journal = {Mycologia},
Year = {2016},
Number = {5},
Pages = {1028 - 1046},
Volume = {108},
Abstract = {Mucoromycota: Glomerulomycotina, Mortierellomycotina, Mucoromycotina; Zoopagomycota: Zoopagomycotina, Kickxellomycotina, Entomophtoromycotyna: Entomophthorales (Entomophtoromycetes), Basidiobolales (Basidiobolomycetes), Neozygitales (Neozygitomycetes)},
Doi = {10.3852/16-042},
File = {spatafora2016_zygomycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27738200}
}
@Article{Spatafora2006,
Title = {{A five-gene phylogeny of Pezizomycotina}},
Author = {J. W. Spatafora and G.-H. Sung and D. Johnson and C. Hesse and B. O'Rourke and M. Serdani and R. Spotts and F. Lutzoni and V. Hofstetter and J. Miadlikowska and V. Reeb and C. Gueidan and E. Fraker and T. Lumbsch and R. Lucking and I. Schmitt and K. Hosaka and A. Aptroot and C. Roux and A. N. Miller and D. M. Geiser and J. Hafellner and G. Hestmark and A. E. Arnold and B. Budel and A. Rauhut and D. Hewitt and W. A. Untereiner and M. S. Cole and C. Scheidegger and M. Schultz and H. Sipman and C. L. Schoch},
Journal = {Mycologia},
Year = {2006},
Number = {6},
Pages = {1018--1028},
Volume = {98},
Abstract = {These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.},
Doi = {10.3852/mycologia.98.6.1018}
}
@Conference{Sperling2007a,
Title = {{The phylogenetic position of the Brachiopoda: New evidence from nuclear housekeeping genes and microRNAs}},
Author = {E. A. Sperling and D. E. Briggs and T. J. Near and K. J. Peterson},
Booktitle = {2007 GSA Denver Annual Meeting (28--31 October 2007)},
Year = {2007},
Number = {184},
Pages = {28--31},
Volume = {9},
Abstract = {Brashiopoda + Phoronida > Lophotrochozoa},
File = {sperling2007.txt}
}
@Article{Sperling2007,
Title = {{Poriferan Paraphyly and its Implications for Precambrian Paleobiology}},
Author = {E. A. Sperling and K. J. Peterson},
Journal = {Geological Society, London, Special Publications},
Year = {2007},
Pages = {355--368},
Volume = {286},
Abstract = {Silicispongia || Calcispongia || Homoscleromorpha (belong to Epitheliozoa)},
Doi = {10.1144/SP286.25},
File = {sperling2007_draft.pdf}
}
@Article{Sperling2009b,
Title = {{Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa}},
Author = {E. A. Sperling and K. J. Peterson and D. Pisani},
Journal = {Mol. Biol. Evol.},
Year = {In press},
Abstract = {Hexa || Demo || Calca || Homo || Placo || Cnid || Bilateria},
Doi = {10.1093/molbev/msp148},
File = {sperling2009_sponges_paraphyly.pdf}
}
@Article{Sperling2010,
Title = {{A placozoan affinity for Dickinsonia and the evolution of late Proterozoic metazoan feeding modes}},
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Journal = {Evol. Dev.},
Year = {2010},
Number = {2},
Pages = {201 - 209},
Volume = {12},
Abstract = {As stated},
Doi = {10.1111/j.1525-142X.2010.00404.x},
File = {sperling2010_dickinsonia_placozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20433459}
}
@Article{Sperling2009a,
Title = {{MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record}},
Author = {E. A. Sperling and J. Vinther and V. N. Moy and B. M. Wheeler and M. S{\'e}mon and D. E. G. Briggs and K. J. Peterson},
Journal = {Proc. Biol. Sci.},
Year = {2009},
Number = {1677},
Pages = {4315 - 4322},
Volume = {276},
Abstract = {Ann || Sipunc},
Doi = {10.1098/rspb.2009.1340},
File = {sperling2009_annelin_phyl_mirna.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19755470}
}
@Article{Spieck2014,
Title = {{Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. Nov., A member of the newly proposed phylum "Nitrospinae".}},
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Journal = {Syst. Appl. Microbiol.},
Year = {2014},
Number = {3},
Pages = {170--176},
Volume = {37},
Abstract = {~ Elusimicrobium and "Nitrospirae"},
Doi = {10.1016/j.syapm.2013.12.005},
File = {spieck2014_nitrospinae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24581679}
}
@Article{Spring2016,
Title = {{Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.}},
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Journal = {ISME J},
Year = {2016},
Number = {12},
Pages = {2801--2816},
Volume = {10},
Abstract = {Kiritimatiellaeota (Kiritimatiella) ~ Verrucomicrobia s.l.},
Doi = {10.1038/ismej.2016.84},
File = {spring2016_kiritimatiellaeota_sister_verruc.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20531276}
}
@Article{Springer1999,
Title = {{Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes and the impact of data partitions with heterogeneous base composition}},
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Year = {1999},
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@Article{Srivastava2008,
Title = {{The Trichoplax genome and the nature of placozoans}},
Author = {M. Srivastava and E. Begovic and J. Chapman and N. H. Putnam and U. Hellsten and T. Kawashima and A. Kuo and T. Mitros and A. Salamov and M. L. Carpenter and A. Y. Signorovitch and M. A. Moreno and K. Kamm and J. Grimwood and J. Schmutz and H. Shapiro and I. V. Grigoriev and L. W. Buss and B. Schierwater and S. L. Dellaporta and D. S. Rokhsar},
Journal = {Nature},
Year = {2008},
Number = {7207},
Pages = {955 - 960},
Volume = {454},
Abstract = {Genome: Demosp. (Trich. (Cnid + Bilat)))},
Doi = {10.1038/nature07191},
File = {srivastava2008.pdf}
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@Article{Stoger2016,
Title = {{Monoplacophoran mitochondrial genomes: Convergent gene arrangements and little phylogenetic signal}},
Author = {I. St{\"o}ger and K. M. Kocot and A. J. Poustka and N. G. Wilson and D. Ivanov and K. M. Halanych and M. Schr{\"o}dl},
Journal = {BMC Evolutionary Biology},
Year = {2016},
Volume = {16},
Abstract = {As stated},
Doi = {10.1186/s12862-016-0829-3},
File = {stoeger2016_monoplac_mt_genomes_no_answer.pdf},
ISSN = {1471-2148},
Url = {http://dx.doi.org/10.1186/s12862-016-0829-3}
}
@Article{Stoger2013,
Title = {{The continuing debate on deep molluscan phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora).}},
Author = {I. St{\"o}ger and J. D. Sigwart and Y. Kano and T. Knebelsberger and B. A. Marshall and E. Schwabe and M. Schr{\"o}dl},
Journal = {Biomed Res Int},
Year = {2013},
Pages = {407072},
Volume = {2013},
Abstract = {RNA, H3, COI: Mono + Polypl; Scapho || Caudofov || Solenog || Cepha},
Doi = {10.1155/2013/407072},
File = {stoeger2013_serialia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22031330}
}
@InProceedings{Stabelli2009,
Title = {{Arthropods phylogenomics supports Mandibulata and a monophyleltic group of hemimetabolan insects}},
Author = {O. R. Stabelli and H. Brinkmann and G. Edgecombe and M. Telford and H. Philippe},
Booktitle = {{Systematics 2009. Leiden, August 11-14. Abstracts}},
Year = {2009},
Abstract = {support a closer relationships between myriapods and Tetraconata (the Mandibulata hypothesis), suggesting that the grouping of myriapods plus chelicerates is likely due to a long-branch attraction artefact that unites the fast evolving Tetraconata and the outgroup. A monophyletic group of hemimetabolan insects with the branchiopod crustaceans as sistergroup of hexapods to the exclusion of the malacostracans is also strongly supported by these data},
File = {rota_stabelli2009_arthropods.txt}
}
@Article{Stabelli2012,
Title = {{Serine codon usage bias in deep phylogenomics: Pancrustacean relationships as a case study}},
Author = {O. R. Stabelli and N. Lartillot and H. Philippe and D. Pisani},
Journal = {Systematic Biology},
Year = {2012},
Abstract = {Remipedia + Brachiopoda || Hexapoda},
File = {rota-stabelli2012_codon_usage_pancrustacea.pdf},
Url = {http://sysbio.oxfordjournals.org/}
}
@Article{Stach2008b,
Title = {{Chordate phylogeny and evolution: a not so simple three-taxon problem}},
Author = {T. Stach},
Journal = {Journal of Zoology},
Year = {2008},
Pages = {117--141},
Volume = {276},
Abstract = {Tunic || Ceph || Craniota},
Doi = {10.1111/j.1469-7998.2008.00497.x},
File = {stach2008.pdf}
}
@Article{Stach2008c,
Title = {{Electron Microscopic Investigation of the Ontogeny of the Collar Cord of the Enteropneust Saccoglossus kowalevskii: Is it Neurulation?}},
Author = {T. Stach},
Journal = {J. Morphol.},
Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {groove is homologous to the canalis neurentericus in chordates},
Doi = {10.1002/jmor.10683},
File = {stach2008.txt}
}
@Article{Stach2007,
Title = {{Ontogeny of the appendicularian \textit{Oikopleura dioica} (Tunicata, Chordata) reveals characters similar to ascidian larvae with sessile adults}},
Author = {T. Stach},
Journal = {Zoomorphology},
Year = {2007},
Pages = {203--214},
Volume = {126},
File = {stach2007.djvu}
}
@Article{Stach2010,
Title = {{Erosion of phylogenetic signal in tunicate mitochondrial genomes on different levels of analysis.}},
Author = {T. Stach and A. Braband and L. Podsiadlowski},
Journal = {Mol. Phylogenet. Evol.},
Year = {2010},
Number = {3},
Pages = {860 - 870},
Volume = {55},
Abstract = {Tunicata: Appendicularia || Stolidobranchiata || Aplousobranchiata + Phlebobranchiata (~ Thaliacea)},
Doi = {10.1016/j.ympev.2010.03.011},
File = {stach2010_tunicata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20302953}
}
@Article{Stach2005,
Title = {{Nerve cells of \textit{Xenoturbella bocki} (phylum uncertain) and \textit{Harrimania kuperi} (Enteropneusta) are positively immunoreactive to antibodies raised against echinoderm neuropeptides}},
Author = {T. Stach and S. Dupont and O. Israelson and G. Fauville and H. Nakano and T. Kenneby and M. Thorndyke},
Journal = {J. Mar. Biol. Ass. U.K.},
Year = {2005},
Pages = {1519--1524},
Volume = {85},
Abstract = {Xeno ~ Enteropneusta and Echinodermata},
File = {stach2005.pdf}
}
@Article{Stach2002,
Title = {{Phylogeny of Tunicata inferred from molecular and morphological characters}},
Author = {T. Stach and J. M. Turbeville},
Journal = {Mol. Phyl. Evol.},
Year = {2002},
Pages = {408--428},
Volume = {25},
Abstract = {Thaliacea and Append. nested within Ascidiae},
File = {stach2002.pdf}
}
@Article{Stach2008,
Title = {{Embryology of a planktonic tunicate reveals traces of sessility}},
Author = {T. Stach and J. Winter and J.-M. Bouquet and D. Chourrout and R. Schnabel},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2008},
Number = {20},
Pages = {7229--7234},
Volume = {105},
Abstract = {Appendicularia are secondary planctonic},
File = {stach2008.pdf}
}
@Article{Stach2009,
Title = {{Anatomy of the trunk mesoderm in tunicates: Homology considerations and phylogenetic interpretation}},
Author = {T. G. Stach},
Journal = {Zoomorphology},
Year = {2009},
Pages = {97--109},
Volume = {128},
Abstract = {Unique synapomorphy},
Doi = {10.1007/s00435-008-0076-2},
File = {stach2009_tunicates_mesoderm.pdf}
}
@Article{Stackebrandt1997,
Title = {{Proposal for a new hierarchic classification system, Actinobacteria classis nov.}},
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Year = {1997},
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Pages = {479--491},
Volume = {47},
Abstract = {Classification based solely on 16S},
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@Article{Stampar2019,
Title = {{Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia.}},
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Journal = {Sci Rep},
Year = {2019},
Number = {1},
Pages = {6094},
Volume = {9},
Abstract = {Ceriantharia (based on Cerianthus) || Octo + Hexa},
Doi = {10.1038/s41598-019-42621-z},
File = {stampar2019_ceriantharia.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30988357}
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@Article{Starobogatov2000,
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Author = {Ja. I. Starobogatov},
Journal = {Zool. Zhurn.},
Year = {2000},
Note = {(In Russian)},
Number = {1},
Pages = {5--18},
Volume = {79},
Annote = {xerox}
}
@InProceedings{Starobogatov1986,
Title = {About the number of eukaryotic kingdoms},
Author = {Ja. I. Starobogatov},
Booktitle = {Trudy ZIN},
Year = {1986},
Note = {(In Russian)},
Pages = {4--25},
Volume = {144},
Annote = {xerox 13--23 pp.}
}
@Article{Starobogatov1985,
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Journal = {Bull. MOIP. Otd. geol.},
Year = {1985},
Note = {(In Russian)},
Number = {1},
Pages = {80--98},
Volume = {60}
}
@Article{Starobogatov1979,
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Journal = {Zool. Zhurn.},
Year = {1979},
Note = {(In Russian)},
Number = {2},
Pages = {149--160},
Volume = {58},
Abstract = {morfologija, Protostomia, Metazoa}
}
@Article{Starobogatov1995,
Title = {{The position of Flagellated Protists in the system of lower Eukaryotes}},
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Journal = {Tsitologiya},
Year = {1995},
Number = {11},
Pages = {1030--1052},
Volume = {37}
}
@Article{Starobogatov1988,
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Pages = {300--311},
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Abstract = {Branchiopodioides (Speleonectes, Hutchisonella, Daphnia, Branchipus), Carcinioides (Carcinus), Ascothoracioides (Ascothorax, Cyclops, Basipodella/Tant, Derocheilocaris/Mystac), Halicynioides (Cypris, Lepax, Argulus)},
File = {starobogatov1988.pdf}
}
@Article{Stech2008,
Title = {{A morpho-molecular classification of the mosses (Bryophyta)}},
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Journal = {Nova Hedwigia},
Year = {2008},
Pages = {1--21},
Volume = {86},
Abstract = {Takakiophytina, Andraeaea+Andreaeobryum, subcl. Buxb. > Bryopsida, Oed., Tetraph., and Polytr. as classes},
Doi = {10.1127/0029-5035/2008/0086-0001}
}
@Article{Stechmann2003,
Title = {{Phylogenetic Analysis of Eukaryotes Using Heat-Shock Protein Hsp90}},
Author = {A. Stechmann and T. Cavalier-Smith},
Journal = {J. Mol. Evol.},
Year = {2003},
Pages = {408--419},
Volume = {57},
Abstract = {Crypto ~ Viridi ~ Hapto; Apuso ~ Bikonta},
Doi = {10.1007/s00239-003-2490-x},
File = {stechmann2003a.pdf}
}
@Article{Stechmann2003b,
Title = {{The root of the eukaryote tree pinpointed}},
Author = {A. Stechmann and T. Cavalier-Smith},
Journal = {Curr. Biol.},
Year = {2003},
Number = {17},
Pages = {665--666},
Volume = {13},
Abstract = {Amoebozoa ~ Unikonta by carbamoyl phosph synthase/DHO/ACT three-gene fusion; Opist supp. EF1-alpha insertion; Bik. supp. DHFR-TS fusion},
File = {stechmann2003b.pdf}
}
@Article{Stechmann2002,
Title = {{Rooting the Eukaryote Tree by Using a Derived Gene Fusion}},
Author = {A. Stechmann and Th. Cavalier-Smith},
Journal = {Science},
Year = {2002},
Pages = {89--91},
Volume = {297},
Keywords = {pr1}
}
@Article{Stechmann2008,
Title = {{Organelles in Blastocystis that Blur the Distinction between Mitochondria and Hydrogenosomes}},
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Year = {2008},
Pages = {580--585},
Volume = {18},
Abstract = {As stated},
Doi = {10.1016/j.cub.2008.03.037},
File = {stechmann2008.pdf}
}
@Article{Steenkamp2006,
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Pages = {93--106},
Volume = {23},
Abstract = {Nuclearia+Fungi, Coralloch+Mesomyc, Choanofl || Ministeria || Animalia},
File = {steenkamp2006.pdf}
}
@Article{Stefanoviac1998,
Title = {{Phylogenetic relationships of conifers inferred from partial 28{S} r{RNA} gene sequences}},
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@Article{Stegner2014,
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Journal = {Zoomorphology},
Year = {2014},
Abstract = {As stated},
Doi = {10.1007/s00435-014-0248-1},
File = {stegner2015_cephalocarida_neur_syst_devel.pdf}
}
@Article{Steiner2003,
Title = {{Molecular phylogeny of Scaphopoda (Mollusca) inferred from 18S rDNA sequences: support for a Scaphopoda-Cephalopoda clade}},
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Journal = {Zool. Scr.},
Year = {2003},
Number = {4},
Pages = {343--356},
Volume = {32},
Abstract = {Polyplacophora || Bivalvia (not resolved) || Gastr || Cephal + Scaph},
File = {steiner2003.pdf}
}
@Article{Steinmetz2017,
Title = {{Gut-like ectodermal tissue in a sea anemone challenges germ layer homology.}},
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Journal = {Nat Ecol Evol},
Year = {2017},
Number = {10},
Pages = {1535 - 1542},
Volume = {1},
Abstract = {... cnidarian pharyngeal ectoderm corresponds to bilaterian endoderm, and the cnidarian endoderm is homologous to bilaterian mesoderm.},
Doi = {10.1038/s41559-017-0285-5},
File = {steinmetz2017_cnidaria_germ_layers.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/29185520}
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@Article{Stemme2013,
Title = {{Serotonin-immunoreactive neurons in the ventral nerve cord of Remipedia (Crustacea): Support for a sister group relationship of Remipedia and Hexapoda?}},
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Year = {2013},
Pages = {119},
Volume = {13},
Abstract = {Yes},
Doi = {10.1186/1471-2148-13-119},
File = {stemme2013_remipedia_neurons.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22977117}
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@Article{Stenoien2008,
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Journal = {J. Evol. Biol.},
Year = {2008},
Pages = {566--571},
Volume = {21},
Abstract = {As stated},
Doi = {10.1111/j.1420-9101.2007.01479.x},
File = {stenoien2008.pdf}
}
@Article{Stenroos2009,
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Journal = {Cladistics},
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Pages = {1--20},
Volume = {25},
Abstract = {Trizobia acrobia basal to Leotiomycetes},
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Journal = {Mol. Biol. Evol.},
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Journal = {Cladistics},
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Volume = {20},
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@Article{Stiller1998a,
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@Article{Stiller1998,
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@Article{Stiller2009,
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@Article{Stingl2005,
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@Article{Stoecker2009,
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@Article{Stotler2005,
Title = {{A Revised Classification of the Anthocerotophyta and a Checklist of the Hornworts of North America, North of Mexico}},
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Journal = {Bryologist},
Year = {2005},
Number = {1},
Pages = {16--26},
Volume = {108},
Abstract = {Leiosporocerotopsida || Anthocerotopsida},
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@Article{Stott2008,
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Year = {2008},
Number = {8},
Pages = {2030--2041},
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@Article{Strassert2018,
Title = {{New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life}},
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Journal = {biorXiv},
Year = {2018},
Abstract = {TSAR = Telonemia + SAR (Rhizaria, Alveolata, Stramenopila)},
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@Article{Strausfeld2011,
Title = {{A New View of Insect-Crustacean Relationships I. Inferences from Neural Cladistics and Comparative Neuroanatomy}},
Author = {N. J. Strausfeld and D. R. Andrew},
Journal = {Arthropod Structure and Development},
Year = {2011},
Abstract = {Maxill + Remip || Branch || Malac || Insecta},
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@Article{Strausfeld2006,
Title = {{Arthropod phylogeny: onychophoran brain organization suggests an archaic relationship with a chelicerate stem lineage}},
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Year = {2006},
Pages = {1--10},
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@Article{Struck2013,
Title = {{The Impact of Paralogy on Phylogenomic Studies -- A Case Study on Annelid Relationships}},
Author = {T. H. Struck},
Journal = {PLOS One},
Year = {2013},
Number = {5},
Pages = {e62892},
Volume = {8},
Abstract = {Myzo || Oweniidae || Chaetopterididae || Errantia || Sedentaria incl. Clitellata},
Doi = {10.1371/journal.pone.0062892.g001},
File = {struck2013_annelid_paralogy.pdf},
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@Article{Struck2011b,
Title = {{Direction of evolution within Annelida and the definition of Pleistoannelida}},
Author = {T. H. Struck},
Journal = {J Zool Syst Evol Res},
Year = {2011},
Number = {4},
Pages = {340--345},
Volume = {49},
Abstract = {Chaetopterida + Oweniidae || Myzo || ? Magelona, Protodrilida, Polygordiida, Nerillidae, Dinophilidae || Sipunc || Pleistoannelida: Errantia + Sedentaria (incl. Clitellata)},
Doi = {10.1111/j.1439-0469.2011.00640.x},
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}
@Article{Struck2008,
Title = {{Phylogenetic position of Nemertea derived from phylogenomic data}},
Author = {T. H. Struck and F. Fisse},
Journal = {Mol. Biol. and Evolution},
Year = {2008},
Number = {4},
Pages = {728--736},
Volume = {25},
Abstract = {Ento+Ecto; Nemert+Moll},
File = {struck2008.pdf}
}
@Article{Struck2008b,
Title = {{Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa)}},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2008},
Number = {2},
Pages = {628--645},
Volume = {48},
Doi = {10.1016/j.ympev.2008.05.015},
File = {struck2008b.pdf}
}
@Article{Struck2011a,
Title = {{Phylogenomic analyses unravel annelid evolution}},
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Journal = {Nature},
Year = {2011},
Pages = {95--98},
Volume = {471},
Abstract = {Chaetopterus || Myzo || Sipuncula || Errantia || Sedentaria (incl. Sibolg., Echiura, Clitellata)},
Doi = {10.1038/nature09864},
File = {struck2011_annelida.pdf}
}
@Article{Struck2007,
Title = {{Annelid phylogeny and the status of Sipuncula and Echiura}},
Author = {T. H. Struck and N. Schult and T. Kusen and E. Hickman and C. Bleidorn and D. McHugh and K. M. Halanych},
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Year = {2007},
Number = {57},
Pages = {1--11},
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Title = {{Phylogenetic Relationships of the Subclass Peniculia (Oligohymenophorea, Ciliophora) Inferred from Small Subunit rRNA Gene Sequences}},
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Volume = {47}
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@Article{StrulluDerrien2018,
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Volume = {373},
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Year = {2021},
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@Article{Suga2013a,
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Year = {2013},
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@Article{Sugihara2008,
Title = {{Distribution of \textit{Symbiobacterium thermophilum} and Related Bacteria in the Marine Environment}},
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Year = {2008},
Number = {70619},
Pages = {1--8},
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@Article{Sugiyama2007,
Title = {{Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas}},
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Journal = {Mycoscience},
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Pages = {192--198},
Volume = {49},
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Pages = {991-992},
Volume = {57},
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@Article{Sumathi2006,
Title = {{Molecular evidence of fungal signatures in the marine protist Corallochytrium limacisporum and its implications in the evolution of animals and fungi}},
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Journal = {Protist},
Year = {2006},
Number = {4},
Pages = {363--376},
Volume = {157},
Abstract = {As stated},
Doi = {10.1016/j.protis.2006.05.003},
File = {sumathi2006_corallochytrium.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/16899404}
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@Article{Summers2014,
Title = {{Phylogeny of Myzostomida (Annelida) and their relationships with echinoderm hosts.}},
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Year = {2014},
Pages = {170},
Volume = {14},
Abstract = {Endomyzostoma basal},
Doi = {10.1186/s12862-014-0170-7},
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@Article{SumnerRooney2015,
Title = {{A neurophylogenetic approach provides new insight to the evolution of Scaphopoda.}},
Author = {L. H. Sumner-Rooney and M. Schr{\"o}dl and E. Lodde-Bensch and D. R. Lindberg and M. He{\ss} and G. P. Brennan and J. D. Sigwart},
Journal = {Evol. Dev.},
Year = {2015},
Number = {6},
Pages = {337--346},
Volume = {17},
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@Article{Sun2001,
Title = {{Mankyua (Ophioglossaceae): A New Fern Genus from Cheju Island, Korea}},
Author = {B.-Y. Sun and M. H. Kim and C. H. Kim and C.-W. Park},
Journal = {Taxon},
Year = {2001},
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Pages = {1019 - 1024},
Volume = {50},
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@Article{Sun2013,
Title = {{Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity.}},
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Journal = {Appl. Environ. Microbiol.},
Year = {2013},
Number = {19},
Pages = {5962--5969},
Volume = {79},
Abstract = {As stated},
Doi = {10.1128/AEM.01282-13},
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@Article{Sun2010a,
Title = {{The ancient history of the structure of ribonuclease P and the early origins of Archaea}},
Author = {F.-J. Sun and G. Caetano-Anoll{\'e}s},
Journal = {BMC Bioinformatics},
Year = {2010},
Pages = {153},
Volume = {11},
Abstract = {Archaea basal, diversifiaction of ribonucleases before LUCA},
Doi = {10.1186/1471-2105-11-153},
File = {sun2010_ribonucl_p_archaea.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20334683}
}
@Article{Sun2009,
Title = {{The Evolutionary History of the Structure of 5S Ribosomal RNA}},
Author = {F.-J. Sun and G. Caetano-Anolles},
Journal = {J Mol Evol},
Year = {In press},
Abstract = {Mix},
Doi = {10.1007/s00239-009-9264-z},
File = {sun2009_evol_hist_5s_rna.pdf}
}
@Article{Sun2008,
Title = {{Triosephosphate Isomerase Genes in Two Trophic Modes of Euglenoids (Euglenophyceae) and Their Phylogenetic Analysis}},
Author = {G.-L. Sun and W. Shen and J.-F. Wen},
Journal = {J. Euk. Microbiol.},
Year = {2008},
Number = {3},
Pages = {170--177},
Volume = {55},
Abstract = {Eugl. plastids ~ Rhodoph. -> converg. or LGT},
Doi = {10.1111/j.1550-7408.2008.00324.x},
File = {sun2008.pdf}
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@Article{Sun2018,
Title = {{Hyoliths with pedicles illuminate the origin of the brachiopod body plan.}},
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Journal = {Proc. Biol. Sci.},
Year = {2018},
Number = {1887},
Volume = {285},
Abstract = {Hyolitha > Brachiozoa},
Doi = {10.1098/rspb.2018.1780},
File = {sun2018_hyoliths_with_pedicles_pedunculotheca_cf_brachiopods.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21680421}
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@Article{Sun2021,
Title = {{Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages}},
Author = {J. Sun and P. N. Evans and E. J. Gagen and others},
Journal = {ISME COMMUN.},
Year = {2021},
Abstract = {As stated, see review in daCunha et al., 2022},
Doi = {10.1038/s43705-021-00032-0},
File = {sun2021_jordarcheia_sifarcheia.pdf}
}
@Article{Sun2010b,
Title = {{Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach}},
Author = {J. Sun and Z. Xu and B. Hao},
Journal = {Chinese Science Bulletin},
Year = {2010},
Number = {22},
Pages = {2323--2328},
Volume = {55},
Abstract = {Kora ~ Crena, Nano and Thaum may be basal},
Doi = {10.1007/s11434-010-3008-8},
File = {sun2010_archaea_cv.pdf},
Url = {www.springerlink.com}
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@Article{Sundue2013,
Title = {{Stasis and convergence characterize morphological evolution in eupolypod II ferns.}},
Author = {M. A. Sundue and C. J. Rothfels},
Journal = {Ann. Bot.},
Year = {2013},
Abstract = {Morphology for Taxon (2012) paper},
Doi = {10.1093/aob/mct247},
File = {sundie2013_morphol_evol_eupolyp_ii_ferns.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24197753}
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@Article{Sutcliffe2010,
Title = {{Cell envelope architecture in the Chloroflexi: A shifting frontline in a phylogenetic turf war}},
Author = {I. C. Sutcliffe},
Journal = {Environ. Microbiol.},
Year = {2010},
Abstract = {Monoderm; Thermobacteria are diderm but lacks LPS},
Doi = {10.1111/j.1462-2920.2010.02339.x},
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@Article{Sutton2012,
Title = {{A Silurian armoured aplacophoran and implications for molluscan phylogeny}},
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Journal = {Nature},
Year = {2012},
Number = {7418},
Pages = {94--98},
Volume = {490},
Abstract = {Aplacophora ~ Polyplacophora},
Doi = {10.1038/nature11328},
File = {sutton2012_silurian_aplacophore.pdf},
ISSN = {0028-0836}
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@Article{Suzuki2010,
Title = {{Phylogenetic analysis of dicyemid mesozoans (phylum Dicyemida) from innexin amino acid sequences: Dicyemids are not related to Platyhelminthes.}},
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Abstract = {Ambulacralia vs. Chordata (same ranks?)},
Doi = {10.1098/rstb.2007.2246},
File = {swalla2008.pdf}
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@Article{Swanson1989,
Title = {{Ostracod phylogeny and evolution~--- a manawan perspective}},
Author = {K. M. Swanson},
Journal = {Courier Forschungs-Institut Senckenberg},
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@Article{Swithers2011,
Title = {{Reassessment of the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria}},
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@Article{Syed2002,
Title = {{Trichoplax adhaerens: Discovered as a missing link, forgotten as a hydrozoan, re-discovered as a key to metazoan evolution}},
Author = {T. Syed and B. Schierwater},
Journal = {Vie Milieu},
Year = {2002},
Number = {4},
Pages = {177--187},
Volume = {2002},
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@Article{Sytsma2002,
Title = {{Phylogeny of the genus \textit{Coleochaete} (Coleochaetales, Charophyta) and related taxa inferred by analysis of the chloroplast gene rbcL}},
Author = {K. Sytsma},
Journal = {J. Phycol.},
Year = {2002},
Pages = {394--403},
Volume = {38}
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@Article{Syvanen2010,
Title = {{Whole genome comparisons reveals a possible chimeric origin for a major metazoan assemblage}},
Author = {M. Syvanen and J. Ducore},
Journal = {J. Biol. Syst.},
Year = {2010},
Number = {2},
Pages = {261 - 275},
Volume = {18},
Abstract = {As stated},
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@Article{Szucsich2020,
Title = {{Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups}},
Author = {N. U. Szucsich and others},
Year = {2020},
Abstract = {Pauropoda+Symphyla and Chilopoda+Diplopoda},
Doi = {10.1186/s12862-020-01699-0},
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@Article{Taborsky2017,
Title = {{Anaeramoebidae fam. Nov., A Novel Lineage of Anaerobic Amoebae and Amoeboflagellates of Uncertain Phylogenetic Position.}},
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Journal = {Protist},
Year = {2017},
Number = {5},
Pages = {495 - 526},
Volume = {168},
Abstract = {~ Planomonas},
Doi = {10.1016/j.protis.2017.07.005},
File = {taborsky2017_anaeramoeba.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28985627}
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@Article{Tahirov2009,
Title = {{Evolution of DNA polymerases: An inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors}},
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Journal = {Biol. Direct},
Year = {2009},
Pages = {11},
Volume = {4},
Abstract = {As stated},
Doi = {10.1186/1745-6150-4-11},
File = {tahirov2009_euk_rna_polym.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19296856}
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@Article{Tahon2021,
Title = {{Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future}},
Author = {G. Tahon and P. Geesink and T. J. G. Ettema},
Journal = {Annual Review of Microbiology},
Year = {2021},
Abstract = {Review},
Doi = {10.1146/annurev-micro-040921050212},
File = {tahon2021_archaeal_div_review.pdf}
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@Article{Taib2021,
Title = {{Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition}},
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Journal = {Nature Ecology \& Evolution},
Year = {2021},
Abstract = {As stated},
Doi = {10.1038/s41559-020-01299-7},
File = {taib2020_bacteria_diderms_monoderms.pdf},
ISSN = {2397-334X}
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@Article{Tajima2016,
Title = {{Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms).}},
Author = {N. Tajima and K. Saitoh and S. Sato and F. Maruyama and M. Ichinomiya and S. Yoshikawa and K. Kurokawa and H. Ohta and S. Tabata and A. Kuwata and N. Sato},
Journal = {Curr. Genet.},
Year = {2016},
Abstract = {Parmales (Triparma laevis) sister},
Doi = {10.1007/s00294-016-0598-y},
File = {tajima2016_parmales_organellar_genomes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27091756}
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Title = {{Origins of the secondary plastids of Eglenophyta and Chlorarachniophyta as revealed by an analysis of the plastid-targeting, nuclear-encoded gene psbO}},
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Year = {2007},
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Title = {{Conservation and Diversification of Msx Protein in Metazoan Evolution}},
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Year = {2008},
Number = {1},
Pages = {69--82},
Volume = {25},
Abstract = {Cnid || Deuto + (Ecdys + Lopho)},
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File = {takahashi2007.pdf}
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@Article{Takahashi2016,
Title = {{Fibrophrys columna gen. Nov., Sp. Nov: A member of the family Amphifilidae.}},
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Volume = {56},
Abstract = {As stated},
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Url = {http://www.ncbi.nlm.nih.gov/pubmed/27468745}
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Title = {{Diplophrys mutabilis sp. nov., a New Member of Labyrinthulomycetes from Freshwater Habitats}},
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Journal = {Protist},
Year = {2013},
Abstract = {Phylogeny review: numerous genera, four orders},
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Journal = {Genome Biol Evol},
Year = {2017},
Number = {1},
Pages = {93 - 101},
Volume = {9},
Abstract = {As stated},
Doi = {10.1093/gbe/evw288},
File = {takezaki2017_lungfish_sister.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24402279}
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@InCollection{Takhtajan1986,
Title = {Higher taxa of vascular plants, except angiosperms},
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Address = {Leningrad},
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Title = {Higher plants. 1. From psilophytes to conifers},
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Title = {{Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads.}},
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Pages = {344--355},
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@Article{Takishita2006,
Title = {{Genetic Diversity of Microbial Eukaryotes in Anoxic Sediment of the Saline Meromictic Lake Namako-ike (Japan): On the Detection of Anaerobic or Anoxic-tolerant Lineages of Eukaryotes}},
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Year = {2006},
Pages = {237--0061},
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Title = {{Armatimonas rosea gen. Nov., Sp. Nov., A Gram-negative, aerobic, chemoheterotrophic bacterium of a novel bacterial phylum, Armatimonadetes phyl. Nov., Formally called the candidate phylum OP10.}},
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Year = {2010},
Abstract = {~ Chloroflexi and TM7},
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File = {F:/ref/os/1/tamaki2010_armatimonadetes_op10.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20622056}
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Year = {2008},
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Volume = {424},
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Journal = {Nature},
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Title = {{Phylogenetic analyses of GSIII and GSIIi: Evidence for a shared evolutionary history among heterokonts and haptophytes?}},
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Journal = {Journal of Phycology},
Year = {2007},
Number = {S1},
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Volume = {42},
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@Article{Tedersoo2017,
Title = {{Novel soil-inhabiting clades fill gaps in the fungal tree of life.}},
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Year = {2017},
Number = {1},
Pages = {42},
Volume = {5},
Abstract = {Neocalli and Monobleph in Chytrid; lots of undescribed Rozellomycota},
Doi = {10.1186/s40168-017-0259-5},
File = {tedersoo2017_novel_soil_fungal_lineages.pdf},
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Journal = {Fungal Diversity},
Year = {2018},
Abstract = {Nucleariae || Basal Clone Group 2 || Rosellomycota incl. Micr. || Aphelidiomycota || Chytr || Blastocl || Basidiobol, Oplid, Enth, Zoopago, Kickx || Mucoro || Glomero || Dikarya: Asco || Enthorr || Basidio},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2016},
Pages = {144--154},
Volume = {99},
Abstract = {Eudiscosea: Flabellinea (Dactylopodida and Vannellida) + Thecamoebida + Centramoebida; incertae sedis: Himatismenida, Trichosphaerium, Saprocribum and Stygamoeba},
Doi = {10.1016/j.ympev.2016.03.029},
File = {tekle2016_discosea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27015898}
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@Article{Tekle2008,
Title = {{Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within ``Amoebozoa'' upon removal of varying rate classes of SSU-rDNA}},
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Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {1},
Pages = {339--352},
Volume = {47},
Abstract = {Trichosphaerium ~ Phalanst/Filam. gr.; Arachnula ~ Dictyo, Multic; Dermaboeba ~ Flabellinea; Mayorella + Theca + Acanth; Cochliopodium i.s.; Ancyro ~ Jacob.; Stramenopi ~ Cercoz.; Hapto+Crypto+Malawi},
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File = {tekle2007.pdf}
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@Article{Tekle2010,
Title = {{Identification of new molecular markers for assembling the eukaryotic tree of life}},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2010},
Number = {3},
Pages = {1177 - 1182},
Volume = {55},
Abstract = {Reveal most stable groupings: Opistokonta and Alveolates},
Doi = {10.1016/j.ympev.2010.03.010},
File = {tekle2010_euk_tol.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20302952}
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@Article{Tekle2009,
Title = {{Molecular Data Are Transforming Hypotheses on the Origin and Diversification of Eukaryotes}},
Author = {Y. I. Tekle and L. W. Parfrey and L. A. Katz},
Journal = {BioScience},
Year = {2009},
Pages = {471--481},
Volume = {59},
Abstract = {Review},
Doi = {10.1525/bio.2009.59.6.5},
File = {tekle2009_euk_review.pdf}
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@Article{Tekle2017,
Title = {{Longamoebia is not monophyletic: Phylogenomic and cytoskeleton analyses provide novel and well-resolved relationships of amoebozoan subclades.}},
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Journal = {Mol. Phylogenet. Evol.},
Year = {2017},
Pages = {249 - 260},
Volume = {114},
Abstract = {Discosea + Dermamoebida (Dermamoeba, Mayorella) + Semiconosia (Variosea | Mycetozoa); Archamoeba | Tubulinea; Cutosea (Perssonella, Sapocribum)},
Doi = {10.1016/j.ympev.2017.06.019},
File = {tekle2017_amoebozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/28669813}
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}
@Article{Telford2004,
Title = {{Affinity for arrow worms}},
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@Article{Telford2015,
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Url = {http://www.ncbi.nlm.nih.gov/pubmed/26439351}
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Year = {2011},
Abstract = {Review of molecular apomorphies; nothing for Lophotrochozoa!; Deut: Chord || Acoel + Xeno || Echin + Hemi (miRNAs)},
Doi = {10.1016/j.tig.2011.02.003},
File = {telford2011_animal_phyl.pdf},
ISSN = {0168-9525},
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}
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Title = {{Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms}},
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Year = {2000},
Number = {21},
Pages = {11359--11364},
Volume = {97}
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Journal = {Mol. Biol. Evol.},
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Number = {3},
Pages = {660--676},
Volume = {10}
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Year = {2014},
Number = {1786},
Volume = {281},
Abstract = {As stated},
Doi = {10.1098/rspb.2014.0479},
File = {telford2014_asterozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24850925}
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Title = {{Expression of homeobox genes shows chelicerate arthropods retain their deutocerebral segment}},
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Title = {{Development of the nervous system in Phoronopsis harmeri (Lophotrochozoa, Phoronida) reveals both deuterostome- and trochozoan-like features}},
Author = {E. Temereva and A. Wanninger},
Journal = {BMC Evolutionary Biology},
Year = {2012},
Pages = {121},
Volume = {12},
Abstract = {As stated},
File = {temereva2012_phoronopsis.pdf},
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Volume = {14},
Abstract = {As stated},
Doi = {10.15298/invertzool.14.1.12},
File = {temereva2017_lophophorata_monophyly.pdf}
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@PhdThesis{Temereva2008,
Title = {{Phoronids (Phoronida): morphology, development, wolrd fauna, phylogeny}},
Author = {E. N. Temereva},
School = {Moscow State University},
Year = {2008},
Address = {Moscow},
Note = {(In Russian)},
Abstract = {segmented ancestors of Lophophorata || Brachiopoda || Bryozoa + Phoronida},
File = {temereva2008.pdf},
Institution = {Moscow State University}
}
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Title = {{Metamorphic remodeling of morphology and the body cavity in Phoronopsis harmeri (Lophotrochozoa, Phoronida): The evolution of the phoronid body plan and life cycle.}},
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Year = {2015},
Pages = {229},
Volume = {15},
Abstract = {Worm-like ancestor},
Doi = {10.1186/s12862-015-0504-0},
File = {temereva2015_phoronida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18948592}
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Title = {{Organization of the epistome in Phoronopsis harmeri (Phoronida) and consideration of the coelomic organization in Phoronida}},
Author = {E. N. Temereva and V. V. Malakhov},
Journal = {Zoomorphology},
Year = {2011},
Abstract = {Tripartite},
Doi = {10.1007/s00435-011-0126-z},
File = {temereva2011_phoronopsis_coelom.pdf}
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Title = {{Microscopic anatomy and ultrastructure of the nervous system of Phoronopsis harmeri Pixell, 1912 (Lophophorata: Phoronida)}},
Author = {E. N. Temereva and V. V. Malakhov},
Journal = {Mar. Biol.},
Year = {2009},
Number = {5},
Pages = {388--404},
Volume = {35},
Abstract = {phoron || brachiop},
Doi = {10.1134/S1063074009050046},
File = {temereva2009_phoronopsis.pdf}
}
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Title = {{The answer to Thomas Bartolomaeus: Larva of phoronid Phoronopsis harmeri Pixell, 1912 has trimeric coelom organization}},
Author = {E. N. Temereva and V. V. Malakhov},
Journal = {Invertebrate Zoology},
Year = {2006},
Note = {In Russian},
Number = {1},
Pages = {1--21},
Volume = {3},
File = {temereva2006.pdf}
}
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Title = {{Organization and metamorphic remodeling of the nervous system in juveniles of Phoronopsis harmeri (Phoronida): Insights into evolution of the bilaterian nervous system.}},
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Year = {2014},
Pages = {35},
Volume = {11},
Abstract = {Phoronids retained some plesiomorphic traits and can be regarded as one of the most primitive groups of lophotrochozoans.},
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File = {temereva2014_phoronopsis_evol_neur_syst.djvu},
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Year = {2014},
Number = {1},
Pages = {3},
Volume = {11},
Abstract = {phoronids should be extracted from the Trochozoan (=Spiralia) clade and placed at the base of the Lophotrochozoan stem},
Doi = {10.1186/1742-9994-11-3},
File = {temereva2014_phoronida.djvu},
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Abstract = {As stated},
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File = {testo2016_ferns_timetree.pdf},
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Year = {2019},
Number = {5},
Pages = {125682},
Volume = {170},
Abstract = {Platysulcea || Bigyra: Opalozoa: Placidozoa (Opalinata, Nanomonadea + Placididea) and Bicosia (Cantina, Anoecida, Bicoecida); Sagenista (Labyrithulea, Eogyrea) || Pseudofungi (Developayella and Oomycetes) || Chromophyta},
Doi = {10.1016/j.protis.2019.125682},
File = {thakur2019_deep_branch_stramenopiles.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31568885}
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Year = {2014},
Abstract = {genomic: Plath + Gastrotr; Syndermata + Gnathost; Ecto + Entopr/Cycliophora; everuthing else unstable},
Doi = {10.5061/dryad.n435p).},
File = {struck2014_platyzoa.pdf}
}
@Article{Tretter2014,
Title = {{An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales.}},
Author = {E. D. Tretter and E. M. Johnson and G. L. Benny and R. W. Lichtwardt and Y. Wang and P. Kandel and S. J. Novak and J. F. Smith and M. M. White},
Journal = {Mycologia},
Year = {2014},
Number = {5},
Pages = {912--935},
Volume = {106},
Abstract = {As stated},
Doi = {10.3852/13-253},
File = {tretter2014_kickxellom_asellariales.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24891422}
}
@Article{Tretter2013,
Title = {{Examining new phylogenetic markers to uncover the evolutionary history of early-diverging fungi: Comparing MCM7, TSR1 and rRNA genes for single- and multi-gene analyses of the Kickxellomycotina}},
Author = {E. D. Tretter and E. M. Johnson and Y. Wang and P. Kandel and M. M. White},
Journal = {Persoonia},
Year = {2013},
Pages = {106--125},
Volume = {30},
Abstract = {Mucoro ~ Asco, Blastocl || Zoopago || Ento || Kickxe},
Doi = {10.3767/003158513X666394},
File = {tretter2013_kickxellomycotina.pdf},
Url = {www.ingentaconnect.com/content/nhn/pimj}
}
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Title = {{Contribution of Genosystematics to Current Concepts of Phylogeny and Classification of Bryophytes}},
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Journal = {Biochemistry},
Year = {2007},
Number = {12},
Pages = {1675--1689},
Volume = {72},
Abstract = {Takak || Sphagn || Andeaeopsidar + Andreaeobryopsida + (Oedipo || Polytr || (Tetraph + Bryops))},
Doi = {10.1134/S0006297907120115},
File = {troitsky2007.pdf}
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Year = {2009},
Pages = {187},
Volume = {9},
Abstract = {Append || Stolidobranchia || Phlebobranchia || Thaliacea and Salpae || Aplousobranchia},
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File = {tsagkogeorga2009_tunicates.pdf},
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Title = {{Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding}},
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Journal = {Mol. Phyl. Evol.},
Year = {2009},
Number = {1},
Pages = {129--140},
Volume = {50},
Abstract = {Oo + Ochro || Bico + Labyr; traust. paraphyletic},
Doi = {10.1016/j.ympev.2008.09.027},
File = {tsiu2008.pdf}
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@Article{Tsuji2009,
Title = {{Assembling the history of the Parareptilia: Phylogeny, diversification, and a new definition of the clade}},
Author = {L. A. Tsuji and J. M-ller and K. Words},
Journal = {Fossil Record},
Year = {2009},
Number = {1},
Pages = {71--81},
Volume = {12},
Abstract = {Not turtles},
Doi = {10.1002/mmng.200800011},
File = {tsui2009_parareptilia.pdf}
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Title = {{Characterization of the FMO protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum}},
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Year = {2010},
Abstract = {As stated},
Doi = {10.1007/s11120-009-9517-0},
File = {tsukatani2010_chloracidobacterium.pdf},
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Author = {M. Turmel},
Journal = {Int. J. Plant Sci.},
Year = {2007},
Number = {5},
Pages = {679--689},
Volume = {168},
Abstract = {Mesost || Chloroky || Chara || Chaetosph || Zygne || plants},
File = {turmel2007.pdf}
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@Article{Turmel2008,
Title = {{Deep division in the Chlorophyceae (Chlorophyta) revealed by chloroplast phylogenomic analyses}},
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Year = {2008},
Pages = {739--750},
Volume = {44},
Abstract = {44 chloropl. proteins: Prasino ||| Ulvo + Trebouxio ||| Chloro: Chlamydomonas clade and Chaetophora clade},
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Year = {2009},
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Pages = {631--648},
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Abstract = {18S: VI Prasinococc ||| I Pyraminom -> Euglena ||| II Mamiell ||| III Nephrosel (but basal in chloroplast seq) + V Pycnoc ||| VII Picosyct ||| IV Chlorodendr},
File = {turmel2008.pdf},
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Journal = {Plant Cell},
Year = {1999},
Pages = {1717--1730},
Volume = {15},
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File = {turmel1999.pdf}
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Title = {{The Chloroplast Genomes of the Green Algae Pedinomonas minor, Parachlorella kessleri and Oocystis solitaria Reveal a Shared Ancestry between the Pedinomonadales and Chlorellales}},
Author = {M. Turmel and C. Otis and C. Lemieux},
Journal = {Mol. Biol. Evol.},
Year = {In press},
Abstract = {Prasinophyceae incl. Nephr., Pyramin., Monomast., Ostreococc. || Ulvoph + Trebouxiophyc. inc. Pedinomonas || Chlorophyceae},
File = {turmel2009_pedinomonas.pdf}
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Title = {{Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae.}},
Author = {M. Turmel and C. Otis and C. Lemieux},
Journal = {Genome Biol Evol},
Year = {2015},
Number = {7},
Pages = {2062--2082},
Volume = {7},
Abstract = {Pedino || Chlorellales || other},
Doi = {10.1093/gbe/evv130},
File = {turmel2015_pedinophyceae_trebouxiophyceae_cp_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/2258934}
}
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Journal = {Genome Biol Evol},
Year = {2013},
Number = {10},
Pages = {1817--1835},
Volume = {5},
Abstract = {others || Charales || Zygnem || land plants},
Doi = {10.1093/gbe/evt135},
File = {turmel2013_streptophyte_mt.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23335123}
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Title = {{The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes}},
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Year = {In press},
Abstract = {As stated},
Doi = {10.1007/s00435-009-0091-y},
File = {ungerer2009_pycnog_ecdysozoa.pdf}
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Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {last common ancestor of the arthropods exhibited an irregular, putatively total cleavage with gastrulation starting with one or two large immigrating cells},
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File = {ungerer2008.txt}
}
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@Article{Urrutia2022,
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Doi = {10.1186/1745-6150-6-16},
File = {valas2011_achaea_origin.pdf},
Url = {http://www.biology-direct.com/content/6/1/16}
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@Article{Valas2009,
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Journal = {Biol. Direct},
Year = {2009},
Pages = {30},
Volume = {4},
Abstract = {Near Chloroflexi},
Doi = {10.1186/1745-6150-4-30},
File = {valas2009_tol_root.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19706177}
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Journal = {Mycologia},
Year = {2002},
Number = {1},
Pages = {122--131},
Volume = {100},
Abstract = {Asellariales ~ Harpellales},
File = {valle2008.djvu}
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Pages = {16170},
Volume = {1},
Abstract = {Verstraetearchaeota ~ Crenarch},
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File = {vanwonterghem2016_verstaetearchaeota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27694807}
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Abstract = {|| Picobiliphyta ||| Katabl ||| Crypto; Pyraminom || (Prasinococc ||| Mamiell) + Pseudosc ||| Clade VII ||| Chlorodendrales (incl. Tetraselmis) ||| Trebouxio; Pedinophyceae (incl. Resultor and Marsupiomonas) have 1 flagellum and no scales is a class},
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@Article{Vdacny2010,
Title = {{Molecular and morphological evidence for a sister group relationship of the classes Armophorea and Litostomatea (Ciliophora, Intramacronucleata, Lamellicorticata infraphyl. Nov.}},
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Journal = {European Journal of Protistology},
Year = {2010},
Number = {4},
Pages = {298--309},
Volume = {46},
Abstract = {Postciliodesmatophora: Karyorel + Heterotr || Ventrata: (Colpodea || Nassoph* || Phylloph || Oligohy || Prosto + Plagiopy) || Spirotrichia || Lamellicorticata: Armophorea (e.g., Metopus) + Litostomatea},
Doi = {10.1016/j.ejop.2010.07.002},
File = {vdacny2011_ciliophora.pdf},
ISSN = {0932-4739},
Keywords = {apicalization, dileptids, phylogeny, postciliary microtubule ribbons, stomatogenesis, toxicysts},
Url = {http://dx.doi.org/10.1016/j.ejop.2010.07.002}
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Number = {4},
Pages = {445--459},
Volume = {55},
Abstract = {DAP and aa ways: a review},
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File = {velasco2002.pdf}
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Year = {2017},
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Pages = {33},
Volume = {15},
Abstract = {Spiral},
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File = {vellutini2017_bryozoa_spiral.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/17120024}
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Title = {{\textit{Adriamonas peritocrescens} gen. nov., sp. nov., a new Free-living Soil Flagellate}},
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@Article{Verweyen2011,
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Year = {2011},
Number = {12},
Pages = {e28285},
Volume = {6},
Abstract = {As stated},
Doi = {10.1371/journal.pone.0028285},
File = {verweyen2011_acanthocephala.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22163005}
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@Article{Vickerman2005,
Title = {{Aurigamonas solis n. gen., n. sp., a soil-dwelling predator with unusual helioflagellate organisation and belonging to a novel clade within the Cercozoa}},
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Journal = {Protist},
Year = {2005},
Number = {3},
Pages = {335--354},
Volume = {156},
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Pages = {9--24},
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Number = {2},
Pages = {32--37},
Volume = {2},
Abstract = {Cephalochor || Tunic || Vertebr},
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@Article{Vinther2019,
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Abstract = {As stated},
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@Article{Vinther2017,
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Year = {2017},
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Abstract = {Kimberella etc. | Conchifera | Stem Aculifera | Polyplacophora | Aplacophora},
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@Article{Vinther2011a,
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Pages = {711--719},
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Abstract = {Basal to Deuterost.},
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@Article{Waloszek2006,
Title = {{A new Late Cambrian pentastomid and a review of the relationships of this parasitic group}},
Author = {D. Waloszek and J. E. Repetski and A. Maas},
Journal = {Transactions of the Royal Society of Edinburgh: Earth Sciences},
Year = {2006},
Pages = {163--176},
Volume = {96},
Abstract = {Against Ichthyostraca},
File = {waloszek2005b.pdf}
}
@Article{Wang2009,
Title = {{A fungal phylogeny based on 82 complete genomes using the composition vector method}},
Author = {H. Wang and Z. Xu and L. Gao and B. Hao},
Journal = {BMC Evol. Biol.},
Year = {2009},
Number = {1},
Pages = {195},
Volume = {9},
Abstract = {Nothing exiting},
Doi = {10.1186/1471-2148-9-195},
File = {wang2009_fungal_phyl_cv.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19664262}
}
@Article{Wang2021,
Title = {{Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective}},
Author = {J. Wang and Y. Bai and H. Zhao and R. Mu and Y. Dong},
Journal = {PeerJ},
Year = {2021},
Abstract = {Symphyla + Pauropoda},
Doi = {10.7717/peerj.12691},
File = {wang2021_myriapoda.pdf}
}
@Article{Wang2016a,
Title = {{Phylogenetic Analyses of Three Genes of Pedinomonas noctilucae, the Green Endosymbiont of the Marine Dinoflagellate Noctiluca scintillans, Reveal its Affiliation to the Order Marsupiomonadales (Chlorophyta, Pedinophyceae) under the Reinstated Name Protoeuglena noctilucae.}},
Author = {L. Wang and X. Lin and J. I. Goes and S. Lin},
Journal = {Protist},
Year = {2016},
Number = {2},
Pages = {205--216},
Volume = {167},
Abstract = {Pedinophyceae: Marsupiomonadales ana Pedinomonadales},
Doi = {10.1016/j.protis.2016.02.005},
File = {wang2016_protoeuglena_pedinophyceae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27033730}
}
@Article{Wang2007,
Title = {{Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world}},
Author = {M. Wang and L. S. Yafremava and D. Caetano-Anolles and J. E. Mittenthal and G. Caetano-Anolles},
Journal = {Genome Res.},
Year = {2007},
Pages = {1572--1585},
Volume = {17},
Abstract = {LUCA ~ Eukarya},
File = {wang2007.pdf}
}
@Article{Wang2015,
Title = {{Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.}},
Author = {Q.-M. Wang and D. Begerow and M. Groenewald and X.-Z. Liu and B. Theelen and F.-Y. Bai and T. Boekhout},
Journal = {Stud. Mycol.},
Year = {2015},
Pages = {55--83},
Volume = {81},
Abstract = {Exobasid incl. Moniliellomycetes | Malassezio (both -> Exob) || Ustilag},
Doi = {10.1016/j.simyco.2015.10.004},
File = {wang2015_ustilagomycotina.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26955198}
}
@Article{Wang2015a,
Title = {{Phylogeny of yeasts and related filamentous fungi within Pucciniomycotina determined from multigene sequence analyses.}},
Author = {Q.-M. Wang and M. Groenewald and M. Takashima and B. Theelen and P.-J. Han and X.-Z. Liu and T. Boekhout and F.-Y. Bai},
Journal = {Stud. Mycol.},
Year = {2015},
Pages = {27--53},
Volume = {81},
Abstract = {Mixio, Tritirachiomycetes! || Agaricostilb || Pucci + Atractiell + Cystobasid || Classiculo + Microbotr},
Doi = {10.1016/j.simyco.2015.08.002},
File = {wand2015_pucciniomycotina.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26955197}
}
@Article{Wang2014,
Title = {{Moniliellomycetes and Malasseziomycetes, two new classes in Ustilaginomycotina.}},
Author = {Q.-M. Wang and B. Theelen and M. Groenewald and F.-Y. Bai and T. Boekhout},
Journal = {Persoonia},
Year = {2014},
Pages = {41--47},
Volume = {33},
Abstract = {Agarico || Exobasi || Ustilago || Moniliella + Malassezia},
Doi = {10.3767/003158514X682313},
File = {wang2014_moniliellomycetes_malasseziomycetes_ustilaginomycotina.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25737592}
}
@Article{Wang2015b,
Title = {{Phylogenetic classification of yeasts and related taxa within Pucciniomycotina.}},
Author = {Q.-M. Wang and A. M. Yurkov and M. G{\"o}ker and H. T. Lumbsch and S. D. Leavitt and M. Groenewald and B. Theelen and X.-Z. Liu and T. Boekhout and F.-Y. Bai},
Journal = {Stud. Mycol.},
Year = {2015},
Pages = {149 - 189},
Volume = {81},
Abstract = {As stated, revised in later paper Zhao et al., 2017},
Doi = {10.1016/j.simyco.2015.12.002},
File = {wang2015_pucciniomycotina.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22679595}
}
@Article{Wang2008b,
Title = {{Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae.}},
Author = {X. Wang and D. V. Lavrov},
Journal = {PLoS ONE},
Year = {2008},
Number = {7},
Pages = {e2723},
Volume = {3},
Abstract = {Mt DNA: Hexa + Hydra; Homoscler || other Demospongia},
Doi = {10.1371/journal.pone.0002723},
File = {wang2008.pdf}
}
@Article{Wang2007a,
Title = {{Mitochondrial Genome of the Homoscleromorph \textit{Oscarella carmela} (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals}},
Author = {X. Wang and D. V. Lavrov},
Journal = {Mol. Biol. and Evolution},
Year = {2007},
Number = {2},
Pages = {363--373},
Volume = {24},
Abstract = {Homoscleromorpha mt genome close to Demospongia but very complex},
File = {webster2007.pdf}
}
@Article{Wang2016,
Title = {{Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China.}},
Author = {X. Wang and X. Liu and J. Z. Groenewald},
Journal = {Antonie Van Leeuwenhoek},
Year = {2016},
Abstract = {As stated},
Doi = {10.1007/s10482-016-0779-1},
File = {wang2016_neocallimastigomycota.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27734254}
}
@Article{Wang1998,
Title = {{A molecular systematic study of \textit{Cathaya}, a relic genus of the Pinaceae in China}},
Author = {X.-Q. Wang and Y. Han and D.-Y. Hong},
Journal = {Pl. Syst. Evol.},
Year = {1998},
Number = {3--4},
Pages = {165--172},
Volume = {213}
}
@Article{Wang2008,
Title = {{Phylogeny of Dinoflagellate Plastid Genes Recently Transferred to the Nucleus Supports a Common Ancestry with Red Algal Plastid Genes}},
Author = {Y. Wang and S. Joly and D. Morse},
Journal = {J. Mol. Evol.},
Year = {2008},
Number = {2},
Pages = {175--184},
Volume = {66},
Abstract = {Red-algae plastids (incl. peridinin dino plastids) occured once},
Doi = {10.1007/s00239-008-9070-z},
File = {wang2008.pdf}
}
@Article{Wang2014a,
Title = {{The molecular symplesiomorphies shared by the stem groups of metazoan evolution: Can sites as few as 1% have a significant impact on recognizing the phylogenetic position of myzostomida?}},
Author = {Y. Wang and Q. Xie},
Journal = {J. Mol. Evol.},
Year = {2014},
Number = {1--2},
Pages = {63--74},
Volume = {79},
Abstract = {Myzost basal among Acoela and Nemertoderrm},
Doi = {10.1007/s00239-014-9635-y},
File = {wang2014_myzostomida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25128981}
}
@Article{Wang2004,
Title = {{A New Permian Gnetalean Cone as Fossil Evidence for Supporting Current Molecular Phylogeny}},
Author = {Z.-Q. Wang},
Journal = {Ann. Bot.},
Year = {2004},
Pages = {281--288},
Volume = {94}
}
@Article{Wanninger2009,
Title = {{Shaping the Things to Come: Ontogeny of Lophotrochozoan Neuromuscular Systems and the Tetraneuralia Concept}},
Author = {A. Wanninger},
Journal = {Biol. Bull.},
Year = {2009},
Pages = {293--306},
Volume = {216},
Abstract = {Tetraneuralia: Entoprocta + Mollusca},
File = {wanninger2009_tetraneuralia.pdf}
}
@Article{Wanninger2008,
Title = {{Comparative lophotrochozoan neurogenesis and larval neuroanatomy: Recent advances from previously neglected taxa}},
Author = {A. Wanninger},
Journal = {Acta Biologica Hungarica},
Year = {2008},
Pages = {127--136},
Volume = {59},
Abstract = {Sipuncula + Annelida (including Echiura); Entoprocta + Mollusca; Lophophorata unclear},
Doi = {10.1556/ABiol.59.2008.Suppl.21},
File = {wanninger2008.txt}
}
@Article{Wanninger2005,
Title = {{Immunocytochemistry of the Nervous System and the Musculature of the Chordoid Larva of \textit{Symbion pandora} (Cycliophora)}},
Author = {A. Wanninger},
Journal = {J. Morphol.},
Year = {2005},
Pages = {237--243},
Volume = {265},
Abstract = {~ Rotifera},
File = {wanninger2005.pdf}
}
@Article{Ward2016,
Title = {{A new phylogeny and environmental DNA insight into paramyxids: An increasingly important but enigmatic clade of protistan parasites of marine invertebrates.}},
Author = {G. M. Ward and M. Bennett and K. Bateman and G. D. Stentiford and R. Kerr and S. W. Feist and S. T. Williams and C. Berney and D. Bass},
Journal = {Int. J. Parasitol.},
Year = {2016},
Number = {10},
Pages = {605 - 619},
Volume = {46},
Abstract = {Marteilia basal},
Doi = {10.1016/j.ijpara.2016.04.010},
File = {ward2016_paramyxids.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27354180}
}
@Article{Ward2018a,
Title = {{Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free- living Giant Amoebae}},
Author = {G. M. Ward and S. Neuhauser and R. Groben and S. Ciaghi and C. Berney and S. Romac and D. Bass},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2018},
Abstract = {Exactly as stated: ENDO-2 and ENDO-3 env groups},
Doi = {10.1111/jeu.12501},
File = {ward2018_gromia_endo_envir_haplosp.pdf}
}
@Article{Ward2018,
Title = {{Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer.}},
Author = {L. M. Ward and J. Hemp and P. M. Shih and S. E. McGlynn and W. W. Fischer},
Journal = {Front Microbiol},
Year = {2018},
Pages = {260},
Volume = {9},
Abstract = {Mostly about Anaerolineae},
Doi = {10.3389/fmicb.2018.00260},
File = {ward2018_thermofonsia_cf_anaerolineae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/27095192}
}
@Article{Ward2009,
Title = {{Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils}},
Author = {N. L. Ward and J. F. Challacombe and P. H. Janssen and B. Henrissat and P. M. Coutinho and M. Wu and G. Xie and D. H. Haft and M. Sait and J. Badger and R. D. Barabote and B. Bradley and T. S. Brettin and L. M. Brinkac and D. Bruce and T. Creasy and S. C. Daugherty and T. M. Davidsen and R. T. DeBoy and J. C. Detter and R. J. Dodson and A. S. Durkin and A. Ganapathy and M. Gwinn-Giglio and C. S. Han and H. Khouri and H. Kiss and S. P. Kothari and R. Madupu and K. E. Nelson and W. C. Nelson and I. Paulsen and K. Penn and Q. Ren and M. J. Rosovitz and J. D. Selengut and S. Shrivastava and S. A. Sullivan and R. Tapia and L. S. Thompson and K. L. Watkins and Q. Yang and C. Yu and N. Zafar and L. Zhou and C. R. Kuske},
Journal = {Appl. Environ. Microbiol.},
Year = {2009},
Number = {7},
Pages = {2046--2056},
Volume = {75},
Abstract = {May be sister to Proteob, esp. delta},
Doi = {10.1128/AEM.02294-08},
File = {ward2009_acidobacteria.pdf}
}
@Article{Watanabe2009,
Title = {{Cnidarians and the evolutionary origin of the nervous system}},
Author = {H. Watanabe and T. Fujisawa and T. W. Holstein},
Journal = {Develop. Growth Differ.},
Year = {2009},
Pages = {167--183},
Volume = {51},
Abstract = {Complicated, comparable with bilaterians; some genes expressed near the mouth},
Doi = {10.1111/j.1440-169X.2009.01103.x},
File = {watanabe2009_cnidaria_nervous_syst.pdf}
}
@Article{Watanabe2015,
Title = {{Limnochorda pilosa gen. Nov., Sp. Nov., A moderately thermophilic, facultative anaerobic pleomorphic bacterium and proposal of Limnochordaceae fam. Nov., Limnochordales ord. Nov. And Limnochordia classis nov. In the phylum Firmicutes.}},
Author = {M. Watanabe and H. Kojima and M. Fukui},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2015},
Abstract = {(Thermoaerobacter + Sulfobacillus || Caldinitratiruptor + Symbiobacterium || Limnochordia) || (Bacilli || Thermolithobacteria || Clostridia + Thermoanaerobacterales + Syntrophomonadaceae etc. + Negativicutes + OPB54)},
Doi = {10.1099/ijs.0.000267},
File = {watanabe2015_limnochordia_firmicutes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25896353}
}
@Article{Watkins1999,
Title = {{Partial Sequence of a Sponge Mitochondrial Genome Reveals Sequence Similarity to Cnidaria in Cytochrome Oxidase Subunit {II} and the Large Ribosomal {RNA} Subunit}},
Author = {R. F. Watkins and A. T. Beckenbach},
Journal = {J. Mol. Evol.},
Year = {1999},
Pages = {542--554},
Volume = {48}
}
@Article{Weatherby2010,
Title = {{Surface and Flagella Morphology of the Motile Form of Chromera velia Revealed by Field-Emission Scanning Electron Microscopy}},
Author = {K. Weatherby and S. Murray and D. Carter and J. Slapeta},
Journal = {Protist},
Year = {2010},
Doi = {10.1016/j.protis.2010.02.003},
File = {weatherby2010_chromera_surface.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20643581}
}
@Article{Weber2012,
Title = {{Phylogenetic analysis of endoparasitic Acanthocephala based on mitochondrial genomes suggests secondary loss of sense organs}},
Author = {M. Weber and R. W.-F. Alexandra and L. Podsiadlowski and A. Witek and O. S. Ralph and L. Sug{\'a}r and H. Herlyn and T. Hankeln},
Journal = {Molecular Phylogenetics and Evolution},
Year = {2012},
Abstract = {Monogodonta || Bdelloidea || Acanth},
Doi = {10.1016/j.ympev.2012.09.017},
File = {weber2012_acanthocephala.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2012.09.017}
}
@Article{Weber2009,
Title = {{Recent Developments in the Molecular Taxonomy of Fungi}},
Author = {R. W. S. Weber},
Journal = {Science},
Year = {2009},
Pages = {1--15},
Volume = {15},
Abstract = {Review},
Booktitle = {{The Mycota. Physiology and genetics}},
File = {weber2009_fungal_taxonomy.pdf}
}
@Article{Webster2004,
Title = {{Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments}},
Author = {G. Webster and R. J. Parkes and J. C. Fry and A. J. Weightman},
Journal = {Appl. Environ. Microbiol.},
Year = {2004},
Number = {9},
Pages = {5708--5713},
Volume = {70},
Abstract = {OP9, JS1 ~ Firmicutes},
File = {webster2004_js1_op9.pdf}
}
@Article{Weekers1997,
Title = {{Phylogenetic position of \textit{Psalteriomonas lanterna} deduced from the {SSU} r{DNA} sequence}},
Author = {P. H. Weekers and J. Kleyn and G. D. Vogels},
Journal = {J. Euk. Microbiol.},
Year = {1997},
Number = {5},
Pages = {467--470},
Volume = {44}
}
@Article{Weigert2016,
Title = {{Current status of annelid phylogeny}},
Author = {A. Weigert and C. Bleidorn},
Journal = {Org Divers Evol},
Year = {2016},
Abstract = {Most annelid diversity is comprised in two reciprocal monophyletic groups, Sedentaria and Errantia, which are named after the predominant life style of their members. Errantia include Aciculata (Phyllodocida + Eunicida) and Protodriliformia, which is a taxon of interstitial polychaetes. Sedentaria comprise most of the polychaete families formerly classified as Canalipalpata or Scolecida, as well as the Clitellata. Six taxa branch as a basal grade outside of this major radiation: Oweniidae, Magelonidae, Chaetopteridae, Sipuncula, Amphinomida, and Lobatocerebrum. Oweniidae and Magelonidae form a monophyletic group which we name Palaeoannelida, which constitutes the sister taxon of the remaining annelids.},
Doi = {10.1007/s13127-016-0265-7},
File = {weigert2016_annelid_phylogeny.pdf}
}
@Article{Weigert2015,
Title = {{Evolution of mitochondrial gene order in Annelida.}},
Author = {A. Weigert and A. Golombek and M. Gerth and F. Schwarz and T. H. Struck and C. Bleidorn},
Journal = {Mol. Phylogenet. Evol.},
Year = {2015},
Number = {Pt--A},
Pages = {196--206},
Volume = {94},
Abstract = {Myzostomida in},
Doi = {10.1016/j.ympev.2015.08.008},
File = {weigert2015_annelida_gene_order.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26299879}
}
@Article{Weigert2014,
Title = {{Illuminating the base of the annelid tree using transcriptomics}},
Author = {A. Weigert and C. Helm and M. Meyer and B. Nickel and D. Arendt and Bernhard and T. H. Struck},
Journal = {Mol. Biol. Evol.},
Year = {2014},
Abstract = {Oweniidae + Magelonidae || Chaetopteridae || Amphinomidae + Sipuncula || Myzostomida, Errantia [Nereis], Sedentaria [Siboglinum] incl. Echiura and Clitellata [Limbricus]},
File = {weigert2014_annelida.pdf}
}
@Article{Weir2001,
Title = {{Molecular data support the Laboulbeniales as a separate class of Ascomycota, Laboulbeniomycetes}},
Author = {A. Weir and M. Blackwell},
Journal = {Mycol. Res.},
Year = {2001},
Number = {10},
Pages = {1182--1190},
Volume = {105},
Abstract = {|| Sordariomycetes},
Doi = {10.1016/S0953-7562(08},
File = {weir2001.pdf}
}
@Article{Weiss2000,
Title = {{Molecular phylogeny and diagnostic approaches to microsporidia.}},
Author = {L. M. Weiss},
Journal = {Contrib. Microbiol.},
Year = {2000},
Pages = {209--235},
Volume = {6}
}
@Article{Weiss1999,
Title = {{Microsporidian molecular phylogeny: the fungal connection.}},
Author = {L. M. Weiss and T. D. Edlind and C. R. Vossbrinck and T. Hashimoto},
Journal = {J. Euk. Microbiol.},
Year = {1999},
Number = {5},
Pages = {17--18},
Volume = {46}
}
@Article{Welch2005,
Title = {{Bayesian and maximum likelihood analyses of rotifer-acanthocephalan relationships}},
Author = {D. B. M. Welch},
Journal = {Hydrobiologia},
Year = {2005},
Pages = {47--54},
Volume = {546},
Abstract = {Seisonidea || Acanth || Bdell + Monogo},
File = {welch2005.pdf}
}
@Article{Wenderoth1999,
Title = {{The taxonomic position of \textit{Chlamydomyxa labyrinthuloides}}},
Author = {K. Wenderoth and J. Marquardt and M. Fraunholz and Yves van de Peer and J. Wastl and U.-G. Maier},
Journal = {Eur. J. Phycol.},
Year = {1999},
Pages = {97--108},
Volume = {34}
}
@Article{Wennberg2008,
Title = {{Early embryonic development of the priapulid worm Priapulus caudatus}},
Author = {S. A. Wennberg and R. Janssen and G. E. Budd},
Journal = {Evol. Devel.},
Year = {2008},
Pages = {326--338},
Volume = {10},
Abstract = {No similarities with other Scalidomorpha, Nematoidea, Tard., but some with Onych., Myriap. and Crustacea},
File = {wennberg2008.pdf}
}
@Article{Wetherbee2019,
Title = {{The golden paradox - a new heterokont lineage with chloroplasts surrounded by two membranes.}},
Author = {R. Wetherbee and C. J. Jackson and S. I. Repetti and L. A. Clementson and J. F. Costa and A. van de Meene and S. Crawford and H. Verbruggen},
Journal = {J. Phycol.},
Year = {2019},
Number = {2},
Pages = {257 - 278},
Volume = {55},
Abstract = {Raphido || Phaeo || Chrysoparadoxa | Schizocladia | Aurearena + Phaeothamniales | Chrysomerophyceae | Xanthophyceae => 3 classes, Xan. s.a.},
Doi = {10.1111/jpy.12822},
File = {wetherbee2018_chrysoparadoxa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30536815}
}
@Article{WeyFabrizius2014,
Title = {{Transcriptome data reveal Syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage.}},
Author = {A. R. Wey-Fabrizius and H. Herlyn and B. Rieger and D. Rosenkranz and A. Witek and D. B. M. Welch and I. Ebersberger and T. Hankeln},
Journal = {PLoS ONE},
Year = {2014},
Number = {2},
Pages = {e88618},
Volume = {9},
Abstract = {Gnathostom + Syndermata},
Doi = {10.1371/journal.pone.0088618},
File = {wei-fabrizius2014_gnathifera.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21423652}
}
@Article{WeyFabrizius2012,
Title = {{Platyzoan mitochondrial genomes}},
Author = {A. R. Wey-Fabrizius and L. Podsiadlowski and H. Herlyn and T. Hankeln},
Journal = {Molecular Phylogenetics and Evolution},
Year = {2012},
Abstract = {Review of data only},
Doi = {10.1016/j.ympev.2012.12.015},
File = {wey_fabrizius2012_platyzoa_mt_genomes.pdf},
ISSN = {1055-7903},
Url = {http://dx.doi.org/10.1016/j.ympev.2012.12.015}
}
@Article{Wheeler2009,
Title = {{The deep evolution of metazoan microRNAs}},
Author = {B. M. Wheeler and A. M. Heimberg and V. N. Moy and E. A. Sperling and T. W. Holstein and S. Heber and K. J. Peterson},
Journal = {Evol. Devel.},
Year = {2009},
Pages = {50--68},
Volume = {1},
Abstract = {+33 miRNA for Nephrozoa},
Doi = {10.1111/j.1525-142X.2008.00302.x},
File = {wheeler2009_microrna_evol.pdf}
}
@Article{Wheeler2000,
Title = {{Molecular Phylogenetic Reconstructions of the Marchantioid Liverwort Radiation}},
Author = {John A. Wheeler},
Journal = {Bryologist},
Year = {2000},
Pages = {314--333},
Volume = {103}
}
@Article{Whelan2015,
Title = {{Error, signal, and the placement of Ctenophora sister to all other animals.}},
Author = {N. V. Whelan and K. M. Kocot and L. L. Moroz and K. M. Halanych},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2015},
Number = {18},
Pages = {5773--5778},
Volume = {112},
Abstract = {Ctenoph || Spong || Trich || Cnidaria strongly supported},
Doi = {10.1073/pnas.1503453112},
File = {whelan2015_ctenophora.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/12079646}
}
@Article{White2007,
Title = {{Phylogeny of the Zygomycota based on nuclear ribosomal sequence data}},
Author = {M. M. White and T. Y. James and K. O. Donnell and M. J. Cafaro and Y. Tanabe and J. Sugiyama},
Journal = {Mycologia},
Year = {2007},
Pages = {872--884},
Volume = {98},
Abstract = {Kickxellomycetes (incl. Basidiobolaceae, Harpellales, Asellariales), Mucoromycetes (incl. Endogonales, Mortierellales)}
}
@Article{White2018,
Title = {{New species and emendations of Orphella: Taxonomic and phylogenetic reassessment of the genus to establish the Orphellales, for stonefly gut fungi with a twist.}},
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Doi = {10.1128/JB.01480-09},
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}
@Article{Wu2011,
Title = {{Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny}},
Author = {C.-S. Wu and Y.-N. Wang and C.-Y. Hsu and C.-P. Lin and S.-M. Chaw},
Journal = {Genome biology and evolution},
Year = {2011},
Abstract = {Angiosperms sister to rest, gtetopsida unclear},
Doi = {10.1093/gbe/evr095},
File = {wu2011_gymnosperm_cpdna_phyl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21933779}
}
@Article{Wu2009,
Title = {{A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.}},
Author = {D. Wu and P. Hugenholtz and K. Mavromatis and R. Pukall and E. Dalin and N. N. Ivanova and V. Kunin and L. Goodwin and M. Wu and B. J. Tindall and S. D. Hooper and A. Pati and A. Lykidis and S. Spring and I. J. Anderson and P. D'haeseleer and A. Zemla and M. Singer and A. Lapidus and M. Nolan and A. Copeland and C. Han and F. Chen and J.-F. Cheng and S. Lucas and C. Kerfeld and E. Lang and S. Gronow and P. Chain and D. Bruce and E. M. Rubin and N. C. Kyrpides and H.-P. Klenk and J. A. Eisen},
Journal = {Nature},
Year = {2009},
Number = {7276},
Pages = {1056 - 1060},
Volume = {462},
Abstract = {Deino || Thermot || Synerg; then Fuso || Mycopl || Firmi || Actino || Chloroph + Cyano vs. Spiro || Plancto + Bacteroid || (Elusi || Aquif || Epsil) + (Deferri || Acido || Delta and other proteob.)},
Doi = {10.1038/nature08656},
File = {wu2009_bacterial_genomic_enc.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20033048}
}
@Article{Wu1999,
Title = {{Core Histones of the Amitochondriate Protist, \textit{Giardia lamblia}}},
Author = {G. Wu and A. G. Mcarthur and A. Fiser and A. Ali and M. L. Sogin and M. Mueller},
Journal = {Mol. Biol. Evol.},
Year = {1999},
Number = {8},
Pages = {1156--1163},
Volume = {17}
}
@Article{Wu2009a,
Title = {{Unexpected dynamic gene family evolution in algal actins}},
Author = {M. Wu and J. M. Comeron and H. S. Yoon and D. Bhattacharya},
Journal = {Mol Biol Evol},
Year = {2009},
Number = {2},
Pages = {249--253},
Volume = {26},
Abstract = {As stated},
Doi = {10.1093/molbev/msn263},
File = {wu2009_algal_actins.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19008527}
}
@Article{Wu2009b,
Title = {{Phylogenetic analyses of complete mitochondrial genome of Urechis unicinctus (Echiura) support that echiurans are derived annelids}},
Author = {Z. Wu and X. Shen and M. Sun and J. Ren and Y. Wang and Y. Huang and B. Liu},
Journal = {Mol. Phylogenet. Evol.},
Year = {In press},
Abstract = {~ Clitellata, but sampling low},
Doi = {10.1016/j.ympev.2009.03.009},
File = {wu2009_echiura.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19306935}
}
@Article{Wylezich2014,
Title = {{Dracomyxa pallida gen. Et sp. Nov.: A New Giant Freshwater Foraminifer, with Remarks on the Taxon Reticulomyxidae (emend.)}},
Author = {C. Wylezich and D. Kaufmann and M. Marcuse and N. Hulsmann},
Journal = {Protist},
Year = {2014},
Abstract = {Reticulomyxa, Haplomyxa, Dracomyxa, Wobo},
Doi = {10.1016/j.protis.2014.10.004},
File = {wyzelich2014_dracomyxa_reticulomyxidae.pdf},
ISSN = {1434-4610},
Url = {http://dx.doi.org/10.1016/j.protis.2014.10.004}
}
@Article{Xi2013,
Title = {{Phylogenomics and coalescent analyses resolve extant seed plant relationships.}},
Author = {Z. Xi and J. S. Rest and C. C. Davis},
Journal = {PLoS ONE},
Year = {2013},
Number = {11},
Pages = {e80870},
Volume = {8},
Abstract = {Gnet: nuclear gnepine, plastid gnecup},
Doi = {10.1371/journal.pone.0080870},
File = {xi2013_seed_plants.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/18227120}
}
@Article{Xiao2000,
Title = {{Molecular Characterization of Myxozoan Parasites from Lake Sasajewun, Algonquin Park, Ontario, by Riboprinting}},
Author = {C. Xiao and S. S. Desser},
Journal = {J. Euk. Microbiol.},
Year = {2000},
Number = {1},
Pages = {85--89},
Volume = {47}
}
@Article{Xiao2008,
Title = {{On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota}},
Author = {S. Xiao and M. Laflamme},
Journal = {Trends Ecol. Evol.},
Year = {2009},
Number = {1},
Pages = {31--40},
Volume = {24},
Abstract = {Vendobionts sister to sponges?},
Doi = {10.1016/j.tree.2008.07.015},
File = {xiao2008.pdf}
}
@Article{Xie2021,
Title = {{Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes}},
Author = {R. Xie and Y. Wang and D. Huang and J. Hou and L. Li and H. Hu and X. Zhao and F. Wang},
Journal = {SCIENCE CHINA Life Sciences},
Year = {2021},
Abstract = {Many new names, see review in Da Cunha et al., 2022},
Doi = {10.1007/s11427-021-1969-6},
File = {xie2021_expanded_asgard_archaea.pdf}
}
@Article{Xie2021a,
Title = {{Expanded Asgard archaea shed new light on the origin of eukaryotes and support a 2-domain tree of life}},
Author = {R. Xie and Y. Wang and D. Huang and J. Hou and L. Li and H. Hu and X. Zhao and F. Wang},
Journal = {bioRxiv},
Year = {2021},
Abstract = {Tyrarchaeota, Sigynarchaeota, Hoderarchaeota, Freyrarchaeota, Balderarchaeota (but this is only a preprint)},
Doi = {10.1101/2021.02.04.429862;},
File = {xie2021_expanded_asgard_archaea.pdf}
}
@Article{Xiong1998,
Title = {{Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from \textit{Heliobacillus mobilis}}},
Author = {J. Xiong and K. Inoue and C. E. Bauer},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {1998},
Pages = {14851--14856},
Volume = {95}
}
@Article{Xiong2008,
Title = {{Molecular Phylogeny of Collembola Inferred from Ribosomal RNA Genes}},
Author = {Y. Xiong and Y. Gao and W.-y. Yin and Y.-x. Luan},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {3},
Pages = {728--735},
Volume = {49},
Abstract = {Symphypleona sister to others},
Doi = {10.1016/j.ympev.2008.09.007},
File = {xiong2008.pdf}
}
@Article{Xu2006,
Title = {{Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms}},
Author = {L. Xu and H. Chen and R. Zhang and X. Hu and Z. Zhang and Z. W. Luo},
Journal = {Life Sci.},
Year = {2006},
Pages = {44--121},
Volume = {12},
Abstract = {Arch+Bact},
File = {l_xu2006.pdf}
}
@Article{Yabe2009,
Title = {{Thermosporothrix hazakensis gen. Nov., Sp. Nov., Isolated from compost and description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria}},
Author = {S. Yabe and Y. Aiba and Y. Sakai and M. Hazaka and A. Yokota},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {In press},
Abstract = {As stated},
Doi = {10.1099/ijs.0.018069-0},
File = {yabe2009_ktedonobacteria.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19767365}
}
@Article{Yabe2010,
Title = {{Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from geothermal fallen leaves and a description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria.}},
Author = {S. Yabe and Y. Aiba and Y. Sakai and M. Hazaka and A. Yokota},
Journal = {International journal of systematic and evolutionary microbiology},
Year = {2010},
Abstract = {As stated},
Doi = {10.1099/ijs.0.024877-0},
File = {yabe2010_thermogemmatispora_ktedonob.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20495028}
}
@Article{Yabuki2011,
Title = {{Microheliella maris (Microhelida ord. n.), An Ultrastructurally Highly Distinctive New Axopodial Protist Species and Genus, and the Unity of Phylum Heliozoa.}},
Author = {A. Yabuki and E. E. Chao and K.-I. Ishida and T. Cavalier-Smith},
Journal = {Protist},
Year = {2011},
Abstract = {Microhelida ~ Centrohelea},
Doi = {10.1016/j.protis.2011.10.001},
File = {yabuki2011_microhelida.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22153838}
}
@Article{Yabuki2013,
Title = {{Fine Structure of Telonema subtilis Griessmann, 1913: A Flagellate with a Unique Cytoskeletal Structure Among Eukaryotes}},
Author = {A. Yabuki and W. Eikrem and K. Takishita and D. J. Patterson},
Journal = {Protist},
Year = {2013},
Pages = {556--569},
Volume = {164},
Abstract = {Some resemblances with (among others) Katabl. and Helioz.},
Doi = {10.1016/j.protis.2013.04.004},
File = {yabuki2013_telonema_utrastructure.djvu}
}
@Article{Yabuki2010,
Title = {{Palpitomonas bilix gen. et sp. nov.: A Novel Deep-branching Heterotroph Possibly Related to Archaeplastida or Hacrobia}},
Author = {A. Yabuki and Y. Inagaki and K.-I. Ishida},
Journal = {Protist},
Year = {2010},
Abstract = {Diphylleia ~ Accyro-Apuso; Palpitomonas || Picobili || Crypto},
Doi = {10.1016/j.protis.2010.03.001},
File = {yabuki2010_palpitomonas.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20418156}
}
@Article{Yabuki2018,
Title = {{An Orphan Protist Quadricilia rotundata Finally Finds Its Phylogenetic Home in Cercozoa}},
Author = {A. Yabuki and K.-i. Ishida},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2018},
Abstract = {~ Clautriavia (Monadofilosa)},
Doi = {10.1111/jeu.12502},
File = {yabuki2018_quadricilia_cercoz.pdf}
}
@Conference{Yabuki2008,
Title = {{Palpitomonas bilix gen. et sp. nov., a novel protist related to cryptoiphytes}},
Author = {A. Yabuki and K.-i. Ishida},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {YPF602 was an independent lineage that was closely related to the cryptophytes. We concluded that the strain YPF602 should be treated as a novel protist and named it Palpitomonas bilix gen. et sp. nov. The present study also indicates that the cryptophyte/haptophyte clade may contain more diverse members},
File = {yabuki2008.txt}
}
@Article{Yabuki2011a,
Title = {{Mataza hastifera n. G., N. Sp.: A Possible New Lineage in the Thecofilosea (Cercozoa)}},
Author = {A. Yabuki and K.-I. Ishida},
Journal = {J. Eukaryot. Microbiol.},
Year = {2011},
Abstract = {~ Thecofilosea},
Doi = {10.1111/j.1550-7408.2010.00524.x},
File = {yabuki2011_mazara.pdf}
}
@Article{Yabuki2012,
Title = {{Rigifila ramosa n. Gen., N. Sp., A Filose Apusozoan with a Distinctive Pellicle, is Related to Micronuclearia.}},
Author = {A. Yabuki and K.-I. Ishida and T. Cavalier-Smith},
Journal = {Protist},
Year = {2012},
Abstract = {Rigifila is the closest known relative of Micronuclearia: Rigifilida within the existing class Hilomonadea. Rigifilida groups weakly with Collodictyon (Diphyllatea). Discocelis and Planomonadida form new class (unpublished)},
Doi = {10.1016/j.protis.2012.04.005},
File = {yabiki2012_rigifila_apusozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22682062}
}
@Article{Yabuki2014,
Title = {{Palpitomonas bilix represents a basal cryptist lineage: Insight into the character evolution in Cryptista.}},
Author = {A. Yabuki and R. Kamikawa and S. A. Ishikawa and M. Kolisko and E. Kim and A. S. Tanabe and K. Kume and K.-i. Ishida and Y. Inagki},
Journal = {Sci Rep},
Year = {2014},
Pages = {4641},
Volume = {4},
Abstract = {(Palpit || Leucocr || Crypt) || Telo + Hapt || Archepl; Thecamonas + Opist; Malawi +? Collod},
Doi = {10.1038/srep04641},
File = {yabuki2014_palpitomonas_cryptista.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21551060}
}
@Article{Yabuki2011b,
Title = {{Tsukubamonas globosa n. gen., n. sp., a novel Excavate Flagellate Possibly Holding a Key for the Early Evolution in Discoba}},
Author = {A. Yabuki and T. Nakayama and N. Yubuki and T. Hashimoto and K.-I. Ishida and Y. Inagaki},
Journal = {J. Eukaryot. Microbiol.},
Year = {2011},
Number = {181},
Pages = {1--13},
Volume = {1999},
Abstract = {Not in any Discoba clade},
Doi = {10.1111/j.1550-7408.2011.00552.x},
File = {yabuki2011_tsukubamonas.pdf}
}
@Article{Yamada2008,
Title = {{AINTEGUMENTA homolog expression in Gnetum (gymnosperms) and implications for the evolution of ovulate axes in seed plants}},
Author = {T. Yamada and Y. Hirayama and R. Imaichi and M. Kato},
Journal = {Evolution and Development},
Year = {2008},
Number = {3},
Pages = {280--287},
Volume = {10},
Abstract = {Outer integument of Arabidopsis ~ bracts of Gnetum ~ ovuliferous scale of Pinus},
File = {yamada2008.pdf}
}
@Article{Yamada2006,
Title = {{\textit{Anaerolinea thermolimosa} sp. nov., \textit{Levilinea saccharolytica} gen. nov., sp. nov. and \textit{Leptolinea tardivitalis} gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi.}},
Author = {T. Yamada and Y. Sekiguchi and S. Hanada and H. Imachi and A. Ohashi and H. Harada and Y. Kamagata},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2006},
Number = {6},
Pages = {1331--1340},
Volume = {56},
Abstract = {Chloroflexi: Thermomicrobia, Chloroflexi, Dehalococcoidetes, Anaerolineae},
File = {yamada2006.pdf}
}
@Article{Yamaguchi2009,
Title = {{Phylogeny and taxonomy of the Raphidophyceae (Heterokontophyta) and Chlorinimonas sublosa gen. et sp. nov., a new marine sand-dwelling raphidophyte}},
Author = {H. Yamaguchi and T. Nakayama and A. Murakami and I. Inouye},
Journal = {J. Plant Res.},
Year = {2009},
Abstract = {8 genera},
Doi = {10.1007/s10265-009-0281-1},
File = {yamaguchi2009_raphidophyceae_phyl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19946727}
}
@Article{Yamasaki2015,
Title = {{Phylogenetic position of Loricifera inferred from nearly complete 18S and 28S rRNA gene sequences}},
Author = {H. Yamasaki},
Journal = {Zoological Letters},
Year = {2015},
Pages = {2--6},
Volume = {1},
Abstract = {Priap + Kino || Nematomorpha + Nematoda || Loric || Panarthropoda},
Doi = {10.1186/s40851-015-0017-0},
File = {yamasaki2015_loricifera.pdf},
ISSN = {2056-306X},
Url = {http://dx.doi.org/10.1186/s40851-015-0017-0}
}
@Article{Yamasaki2013,
Title = {{Molecular phylogeny of kinorhynchs.}},
Author = {H. Yamasaki and S. F. Hiruta and H. Kajihara},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Number = {2},
Pages = {303--310},
Volume = {67},
Abstract = {As stated},
Doi = {10.1016/j.ympev.2013.02.016},
File = {yamasaki2013_kinorhyncha.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23454469}
}
@Article{Yan2012,
Title = {{Nearly complete mitochondrial genome of Polyascus gregaria and the phylogenetic relationships among maxillopodans.}},
Author = {J. Yan and J. Zhou and P. Li and H. Sun and K. Zhou},
Journal = {Molecular biology reports},
Year = {2012},
Abstract = {Copepoda + Cirripedia, Branchiura and Pentastomida unclear},
Doi = {10.1007/s11033-012-1573-4},
File = {yan2012_maxillopoda.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22311049}
}
@Article{Yang1999a,
Title = {{The Structure and Evolution of the Ribosomal Proteins Encoded in the spc Operon of the Archaeon (Crenarchaeota) \textit{Sulfolobus acidocaldarius}}},
Author = {D. Yang and I. Kusser and A. K. E. Koepke and B. F. Koop and A. T. Matheson},
Journal = {Mol. Phyl. Evol.},
Year = {1999},
Number = {2},
Pages = {177--185},
Volume = {12}
}
@Article{Yang2011,
Title = {{Supermatrix Data Highlight the Phylogenetic Relationships of Photosynthetic Stramenopiles}},
Author = {E. C. Yang and G. H. Boo and H. J. Kim and S. M. Cho and S. M. Boo and R. A. Andersen and H. S. Yoon},
Journal = {Protist},
Year = {2011},
Abstract = {SI: Raphid || Chrysome | Xantho || Phaeoth + Aureare || Schizocl || Phaeoph; SII: Ping || Eust || Synchr, Chrys, Synur; SIII: Bolid + Bacill || Dict + Pelag},
Doi = {10.1016/j.protis.2011.08.001},
File = {yang2011_stramenopiles.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22001261}
}
@Article{Yang2015,
Title = {{Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae.}},
Author = {E. C. Yang and K. M. Kim and S. Y. Kim and J. Lee and G. H. Boo and J.-H. Lee and W. A. Nelson and G. Yi and W. E. Schmidt and S. Fredericq and S. M. Boo and D. Bhattacharya and H. S. Yoon},
Journal = {Genome Biol Evol},
Year = {2015},
Number = {8},
Pages = {2394--2406},
Volume = {7},
Abstract = {As stated},
Doi = {10.1093/gbe/evv147},
File = {yang2015_red_algae.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/10860957}
}
@Article{Yang2016,
Title = {{Fuxianhuiid ventral nerve cord and early nervous system evolution in Panarthropoda.}},
Author = {J. Yang and J. Ortega-Hern{\'a}ndez and N. J. Butterfield and Y. Liu and G. S. Boyan and J.-B. Hou and T. Lan and X.-G. Zhang},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2016},
Abstract = {Cycloneuralia -> Panarthropoda},
Doi = {10.1073/pnas.1522434113},
File = {yang2016_panarthropoda_neur_syst.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26933218}
}
@Article{Yang2005,
Title = {{Phylogeny determined by protein domain content}},
Author = {S. Yang and R. F. Doolittle and P. E. Bourne},
Journal = {Proc. Natl. Acad. Sci. USA},
Year = {2005},
Number = {2},
Pages = {373--378},
Volume = {102},
Abstract = {Chla ~ Planct, Bacteroidetes ~ Chlorobi, Fus, Therm, Spir ~ Firm, Deino ~ Proteo},
File = {yang2005.pdf}
}
@Article{Yang2017a,
Title = {{Protognetaceae: A new gnetoid macrofossil family from the Jurassic of northeastern China}},
Author = {Y. Yang},
Journal = {Perspectives in Plant Ecology, Evolution and Systematics},
Year = {2017},
Abstract = {As stated},
Doi = {10.1016/j.ppees.2017.08.001},
File = {yang2017_protognetaceae.pdf},
ISSN = {1433-8319},
Url = {http://dx.doi.org/10.1016/j.ppees.2017.08.001}
}
@Article{Yang2022,
Title = {{Recent advances on phylogenomics of gymnosperms and an updated classification}},
Author = {Y. Yang and D. K. Ferguson and B. Liu and K.-S. Mao and L.-M. Gao and S. Zhang and T. Wan and K. Rushforth and Z.-X. Zhang},
Journal = {Plant Diversity},
Year = {2022},
Abstract = {Cycadopsida, Ginkgoopsida, and Pinopsida},
Doi = {10.1016/j.pld.2022.05.003},
File = {yang2022_gymnosperms.pdf}
}
@Article{Yang2015a,
Title = {{Parallel evolution of leaf morphology in gnetophytes}},
Author = {Y. Yang and L. Lin and D. K. Ferguson},
Journal = {Org Divers Evol},
Year = {2015},
Abstract = {Fossil Ephedra multinervia},
Doi = {10.1007/s13127-015-0226-6},
File = {yang2015_ephedra_multinervia_gnet_leaves.pdf}
}
@Article{Yang2017,
Title = {{A new gnetalean macrofossil from the Early Cretaceous and its evolutionary significance}},
Author = {Y. Yang and L.-B. Lin and D. K. Ferguson and S.-Z. Zhang and T. Wan},
Journal = {Cretaceous Research},
Year = {2017},
Abstract = {Some characters intermediate between Gnerales genara},
Doi = {10.1016/j.cretres.2017.02.007},
File = {yang2017_liaoningia_gnetales.pdf},
ISSN = {0195-6671},
Url = {http://dx.doi.org/10.1016/j.cretres.2017.02.007}
}
@Article{Yazaki2022,
Title = {{The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include Microheliella maris}},
Author = {E. Yazaki and A. Yabuki and A. Imaizumi and K. Kume and T. Hashimoto and Y. Inagaki},
Journal = {Open Biology},
Year = {2022},
Abstract = {(((Microheliella || Palpitom. + Crypt.) || (Glauco + Chloro || Pico + Rhodoph, Rhodel)) || (Ancoracysta || Hemimast + Centrohelea)) || (Hapto + Telon || SAR)},
Doi = {10.1098/rsob.210376},
File = {yazaki2022_microheliella_archaeplastida_eukaryotes.pdf}
}
@Article{Yeoh2016,
Title = {{Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.}},
Author = {Y. K. Yeoh and Y. Sekiguchi and D. H. Parks and P. Hugenholtz},
Journal = {Mol. Biol. Evol.},
Year = {2016},
Number = {4},
Pages = {915--927},
Volume = {33},
Abstract = {Patescibacteria || Phylum Dependentiae (TM6): classis Babeliae, Babelia massiliensis},
Doi = {10.1093/molbev/msv281},
File = {yeoh2015_tm6_dependentiae.pdf}
}
@Article{Yilmaz2015,
Title = {{Expanding the World of Marine Bacterial and Archaeal Clades.}},
Author = {P. Yilmaz and P. Yarza and J. Z. Rapp and F. O. Gl{\"o}ckner},
Journal = {Front Microbiol},
Year = {2015},
Pages = {1524},
Volume = {6},
Abstract = {Review},
Doi = {10.3389/fmicb.2015.01524},
File = {yilmaz2016_marine_bact_archaean_clades.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26779174}
}
@Article{YinLong2012,
Title = {{Evolution of the life cycle in land plants}},
Author = {Q. I. U. Yin-Long and A. B. Taylor and H. A. McManus},
Journal = {Journal of Systematics and Evolution},
Year = {2012},
Number = {3},
Pages = {171--194},
Volume = {50},
Abstract = {Propagation of sexual determination},
Doi = {10.1111/j.1759-6831.2012.00188.x},
File = {qiu2012_evol_life_cycle_land_plants.pdf}
}
@Article{Yokobori2008,
Title = {{Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: Implications for lophotrochozoan phylogeny}},
Author = {S.-i. Yokobori and T. Iseto and S. Asakawa and T. Sasaki and N. Shimizu and A. Yamagishi and T. Oshima and E. Hirose},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {2},
Pages = {612--628},
Volume = {47},
Abstract = {mt gene organisation: Kampt + Moll + Nemert + Phoron; Brachiop + ( Echiur + Annel )},
File = {yokobori2008.pdf}
}
@Article{Yokouchi2022,
Title = {{Description of an Enigmatic Alveolate, Platyproteum noduliferae n. Sp., And Reconstruction of its Flagellar Apparatus}},
Author = {K. Yokouchi and D. Iritani and L. K. Hian and P. Y. Heng and T. Horiguchi and K. C. Wakeman},
Journal = {Protist},
Year = {2022},
Abstract = {Gregarine-like but sister to all alveolates, next to chromerids},
Doi = {10.1016/j.protis.2022.125878},
File = {yokouchi2022_platyproteum_filipodium_digyalum_sister_to_chromerids.pdf}
}
@Article{Yonezawa2010,
Title = {{Was the universal common ancestry proved?}},
Author = {T. Yonezawa and M. Hasegawa},
Journal = {Nature},
Year = {2010},
Pages = {E9},
Volume = {468},
Abstract = {No},
Doi = {10.1038/nature09482},
File = {yonesawa2010_theobald_uca.pdf},
ISSN = {0028-0836}
}
@Article{Yoon2006,
Title = {{Defining the major lineages of red algae (Rhodophyta)}},
Author = {H. S. Yoon},
Journal = {J. Phycol.},
Year = {2006},
Number = {2006},
Pages = {482--492},
Volume = {42},
Abstract = {Cyanidio, Compsopogono, (Stylonemato, Porphyridio, Rhodello), Bangio, Florideo (brackets mine) },
File = {yoon2006.pdf}
}
@Article{Yoon2008,
Title = {{Broadly sampled multigene trees of eukaryotes}},
Author = {H. S. Yoon and J. Grant and Y. I. Tekle and M. Wu and B. C. Chaon and J. C. Cole and J. M. Logsdon Jr and D. J. Patterson and D. Bhattacharya and L. A. Katz},
Journal = {BMC Evol. Biol.},
Year = {2008},
Number = {14},
Pages = {1--12},
Volume = {8},
Abstract = {105 taxa/4 genes: (Fungi, Anim., Choano), Ancyro || Exc1 [Andalucia, Streblomastix, Archem]|| Amoebozoa || Rhodo + Foram || Exc2 [Malaw., Jacob., Heter. + Stephan.] || Glauco || Crypto || Viridi || Hapto || Cerco + Stramenop || Alveo},
Doi = {10.1186/1471-2148-8-14},
File = {yoon2008.pdf}
}
@Article{Yoon2009,
Title = {{A single origin of the photosynthetic organelle in different Paulinella lineages}},
Author = {H. S. Yoon and T. Nakayama and A. Reyes-Prieto and R. A. Andersen and S. M. Boo and K.-I. Ishida and D. Bhattacharya},
Journal = {BMC Evol. Biol.},
Year = {2009},
Pages = {98},
Volume = {9},
Abstract = {As stated},
Doi = {10.1186/1471-2148-9-98},
File = {yoon2009_paulinella_chlor_orig.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19439085}
}
@Article{Yoon2014,
Title = {{Algisphaera agarilytica gen. Nov., Sp. Nov., A novel representative of the class Phycisphaerae within the phylum Planctomycetes isolated from a marine alga.}},
Author = {J. Yoon and J.-H. Jang and H. Kasai},
Journal = {Antonie Van Leeuwenhoek},
Year = {2014},
Number = {2},
Pages = {317--324},
Volume = {105},
Abstract = {Planctomycetia m. incl. Phycisphaereae},
Doi = {10.1007/s10482-013-0076-1},
File = {yoon2014_algisphaera_phycisphaerae_planctomycetes.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24264814}
}
@Article{Yoon2008b,
Title = {{Description of \textit{Persicirhabdus sediminis} gen. nov., sp. nov., \textit{Roseibacillus ishigakijimensis} gen. nov., sp. nov., \textit{Roseibacillus} ponti sp. nov., \textit{Roseibacillus persicicus} sp. nov., \textit{Luteolibacter pohnpeiensis} gen. nov., sp. nov. and \textit{Luteolibacter algae} sp. nov., six marine members of the phylum ``Verrucomicrobia'', and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae}},
Author = {J. Yoon and Y. Matsuo and K. Adachi and M. Nozawa and S. Matsuda and H. Kasai and A. Yokota},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2008},
Pages = {998--1007},
Volume = {58},
Abstract = {Opitutae (#4) || clone LD19 || #3 (clones) || Spartobacteria (#2) || Verrumicrobia s.str. (#1)},
Doi = {10.1099/ijs.0.65520--0},
File = {yoon2008.pdf}
}
@Article{Yoshida2017,
Title = {{Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.}},
Author = {Y. Yoshida and G. Koutsovoulos and D. R. Laetsch and L. Stevens and S. Kumar and D. D. Horikawa and K. Ishino and S. Komine and T. Kunieda and M. Tomita and M. Blaxter and K. Arakawa},
Journal = {PLoS Biol.},
Year = {2017},
Number = {7},
Pages = {e2002266},
Volume = {15},
Abstract = {Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.},
Doi = {10.1371/journal.pbio.2002266},
File = {yoshida2017_tardigrada.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/25516281}
}
@Article{Yoshii2006,
Title = {{Diversity and evolution of photosynthetic antenna systems in green plants}},
Author = {Y. Yoshii},
Journal = {Phycol. Res.},
Year = {2006},
Pages = {220--229},
Volume = {54},
Abstract = {siphonaxantin -> lutein},
File = {yoshii2006.pdf}
}
@Article{Yoshii2003,
Title = {{Photosynthetic pigment composition in the primitive green alga Mesostigma viride (Prasinophyceae): Phylogenetic and evolutionary implications}},
Author = {Y. Yoshii and S. Takaichi and T. Maoka and I. Inouye},
Journal = {Science},
Year = {2003},
Pages = {570--576},
Volume = {39},
Abstract = {Nothing exiting :)},
File = {youshii2003_mesostigma_pigments.pdf}
}
@Article{Yoshikawa2011,
Title = {{Isolation and characterization of Parmales (Heterokonta ??? Heterokontophyta ??? Stramenopiles) from the Oyashio region, western north Pacific}},
Author = {S. Yoshikawa and M. Kamiya and K. Ohki and S. Takaichi},
Journal = {J. Phycol.},
Year = {2011},
Pages = {144--151},
Volume = {47},
Abstract = {~ Bolidophyceae},
Doi = {10.1111/j.1529-8817.2010.00926.x},
File = {ichinomyia2011_parmales.pdf}
}
@Article{Youssef2012,
Title = {{Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone Spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach.}},
Author = {N. Youssef and B. L. Steidley and M. S. Elshahed},
Journal = {Appl. Environ. Microbiol.},
Year = {2012},
Number = {8},
Pages = {2677--2688},
Volume = {78},
Abstract = {ZDP1, 4, 5 and ZDP 2, 3 outstand},
Doi = {10.1128/AEM.00002-12},
File = {youssef2012_zodletone_spring_ok_new_phyla.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22307312}
}
@Article{Youssef2011,
Title = {{Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).}},
Author = {N. H. Youssef and P. C. Blainey and S. R. Quake and M. S. Elshahed},
Journal = {Appl. Environ. Microbiol.},
Year = {2011},
Number = {21},
Pages = {7804--7814},
Volume = {77},
Abstract = {~ Firmicutes, nearest environmental is TM7},
Doi = {10.1128/AEM.06059-11},
File = {youssef2011_op11_partial_genome.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21908640}
}
@Article{Yu2005,
Title = {{Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment}},
Author = {Z. G. Yu and L. Q. Zhou and V. V. Anh and K. H. Chu and S. C. Long and J. Q. Deng},
Journal = {J. Mol. Evol.},
Year = {2005},
Pages = {538--545},
Volume = {60}
}
@Article{Yuasa2006,
Title = {{Phylogenetic position of the small solitary phaeodarians (Radiolaria) based on 18S rDNA sequences by single cell PCR analysis}},
Author = {T. Yuasa and O. Takahashi and J. K. Dolven and S. Mayama and A. Matsuoka and D. Honda and K. R. Bjorklund},
Journal = {Mar. Micropaleontology},
Year = {2006},
Pages = {104--114},
Volume = {59},
Abstract = {Phaeodarea monophyletic and sister to Silicofilosea},
File = {yuaza2006.pdf}
}
@Article{Yuasa2005,
Title = {{Phylogenetic analyses of the polycystine Radiolaria based on the 18s rDNA sequences of the Spumellarida and the Nassellarida}},
Author = {T. Yuasa and O. Takahashi and D. Honda and S. Mayama},
Journal = {Eur. J. Protistol.},
Year = {2005},
Number = {2005},
Pages = {287--298},
Volume = {41},
File = {yuasa2005.pdf}
}
@Article{Yubuki2009,
Title = {{Ultrastructure and molecular phylogeny of Calkinsia aureus: cellular identity of a novel clade of deep-sea euglenozoans with epibiotic bacteria}},
Author = {N. Yubuki and V. P. Edgcomb and J. M. Bernhard and B. S. Leander},
Journal = {BMC Microbiol.},
Year = {2009},
Number = {1},
Pages = {16},
Volume = {9},
Abstract = {Bacteriov. eugl. (Notosolenus, Petalomonas) || Diplon || other Eugl. || Symbiontida (Calkinsia, Postgaardi and envir.) || Kinetoplast.; Hemimast. may be eugl.},
Doi = {10.1186/1471-2180-9-16},
File = {yubuki2009_calkinsia.djvu},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19173734}
}
@Conference{Yubuki2008b,
Title = {{Cellular identity of a diverse group of deep sea, anoxic euglenozoans with epibiotic bacteria: Ultrastructure and molecular phylogeny of Calkinsia areaus from the Santa Barbara Basin (California, USA)}},
Author = {N. Yubuki and V. P. Edgcomb and J. M. Bernhard and B. S. Leander},
Booktitle = {{Protist 2008 Conference. 21-26 July 2008. Dalhouse University, Halifax, Nova Scotia, Canada. Abstracts}},
Year = {2008},
Abstract = {some characters present in Calkinsia were like those found in Postgaardi, but none of the features were synapomorphic for any of the main euglenozoan subclades. Phylogenetic analyses using 18S rDNA demonstrated that Calkinsia clustered strongly with several environmental sequences derived from anoxic sediments and formed a fourth euglenozoan subclade, tentatively named the "Symbiontida".},
File = {yubuki2008.txt}
}
@Article{Yubuki2007,
Title = {{Ultrastructure and ribosomal RNA phylogeny of the free-living heterotrophic flagellate dysnectes brevis n. gen., n. sp., a new member of the Fornicata}},
Author = {N. Yubuki and Y. Inagaki and T. Nakayama and I. Inouye},
Journal = {J. Euk. Microbiol.},
Year = {2007},
Number = {2},
Pages = {191--200},
Volume = {54},
Abstract = {Dysnectes || Carpedieomonas || Retort || Diplo},
File = {yubuki2007.pdf}
}
@Article{Yubuki2008a,
Title = {{Ultrastructure and molecular phylogeny of \textit{Stephanopogon minuta}: An enigmatic microeukaryote from marine interstitial environments}},
Author = {N. Yubuki and B. S. Leander},
Journal = {Eur. J. Protistol.},
Year = {2008},
Number = {4},
Pages = {241--253},
Volume = {44},
Abstract = {Heterolobosea, SSU RNA: Heteramoeba group || Naegleria + Pleurostomum || Acrasis || Percolomonas + Stephanopogon || Valkampfia + Tetramitus},
Doi = {doi:10.1016/j.ejop.2007.12.001},
File = {yubuki2008.pdf}
}
@Article{Yubuki2010,
Title = {{Ultrastructure and Molecular Phylogenetic Position of a Novel Phagotrophic Stramenopile from Low Oxygen Environments: Rictus lutensis gen. Et sp. Nov. (Bicosoecida, incertae sedis).}},
Author = {N. Yubuki and B. S. Leander and J. D. Silberman},
Journal = {Protist},
Year = {2010},
Number = {2},
Pages = {264 - 278},
Volume = {161},
Abstract = {MAST 1, 2 ~ Oo; MAST 3, 12 ~ Opal; MAST 4, 6, 7, 8, 9, 11 ~ Labyr},
Doi = {10.1016/j.protis.2009.10.004},
File = {yubuki2009_riktus.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20034852}
}
@Article{Yubuki2011,
Title = {{Comparative ultrastructure of the Symbiontida (Euglenozoa)}},
Author = {N. Yubuki and A. Simpson and B. S. Leander},
Journal = {J. Phycol.},
Year = {2011},
Number = {47},
Pages = {S1--S98},
Abstract = {Postgaardi, Calkinsia, Bihospites -- all Symbiontida},
Doi = {10.1111/j.1529-8817.2011.01050.x},
File = {yubuki2011_symbiontida.pdf}
}
@Article{Yubuki2013,
Title = {{Comprehensive Ultrastructure of Kipferlia bialata Provides Evidence for Character Evolution within the Fornicata (Excavata)}},
Author = {N. Yubuki and A. G. B. Simpson and B. S. Leander},
Journal = {Protist},
Year = {2013},
Abstract = {Carpediemonas-like (incl. "Retortamonads") || Diplomonads},
Doi = {10.1016/j.protis.2013.02.002},
File = {yubuki2013_kipferlia_carpediemonad.djvu},
Url = {http://dx.doi.org/10.1016/j.protis.2013.02.002}
}
@Article{Yubuki2012,
Title = {{Reconstruction of the feeding apparatus in Postgaardi mariagerensis provides evidence for character evolution within the Symbiontida (Euglenozoa).}},
Author = {N. Yubuki and A. G. B. Simpson and B. S. Leander},
Journal = {Eur. J. Protistol.},
Year = {2012},
Abstract = {Bihospites || Calkinsia || Postgaardi + environmental},
Doi = {10.1016/j.ejop.2012.07.001},
File = {yubuki2012_postgaardi.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22925570}
}
@Article{Yubuki2016,
Title = {{Ultrastructure and Molecular Phylogeny of Iotanema spirale gen. Nov. Et sp. Nov., A New Lineage of Endobiotic Fornicata with Strikingly Simplified Ultrastructure}},
Author = {N. Yubuki and E. Zadrob{\'i}lkov{\'a} and I. {\v{C}}epi{\v{c}}ka},
Journal = {Journal of Eukaryotic Microbiology},
Year = {2016},
Abstract = {Eopharyngea is caviomonads, diplo, and mixture of multiple smaller groups including two parts of retortamonads},
Doi = {10.1111/jeu.12376-4829},
File = {yubuki2016_iotanema_fornicata.pdf}
}
@Article{Yurkov2016,
Title = {{Yeast diversity and species recovery rates from beech forest soils}},
Author = {A. M. Yurkov and T. Wehde and J. Federici and A. M. Sch{\"a}fer and M. Ebinghaus and S. Lotze-Engelhard and M. Mittelbach and R. Prior and C. Richter and O. R{\"o}hl and D. Begerow},
Journal = {Mycological Progress},
Year = {2016},
Pages = {1503 - 1510},
Volume = {3},
Abstract = {Chernovia ~ Wallemiomycetes},
Doi = {10.1007/s11557-016-1206-8},
File = {yurkov2016_chernovia_wallemiomycetes.pdf},
Url = {www.biodiversity-}
}
@Article{Yutin2013,
Title = {{Pandoraviruses are highly derived phycodnaviruses.}},
Author = {N. Yutin and E. V. Koonin},
Journal = {Biol. Direct},
Year = {2013},
Number = {1},
Pages = {25},
Volume = {8},
Abstract = {As stated},
Doi = {10.1186/1745-6150-8-25},
File = {yutin2013_pandoraviruses_are_phycodnaviruses.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24148757}
}
@Article{Yutin2012,
Title = {{Archaeal origin of tubulin.}},
Author = {N. Yutin and E. V. Koonin},
Journal = {Biol. Direct},
Year = {2012},
Pages = {10},
Volume = {7},
Abstract = {As stated},
Doi = {10.1186/1745-6150-7-10},
File = {yutin2012_tubulin_archaea.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22458654}
}
@Article{Yutin2008,
Title = {{The deep archaeal roots of eukaryotes}},
Author = {N. Yutin and K. S. Makarova and S. L. Mekhedov and Y. I. Wolf and E. V. Koonin},
Journal = {Mol. Biol. Evol.},
Year = {2008},
Number = {8},
Pages = {1619--1630},
Volume = {25},
Abstract = {Eukar || Cren + Eury, part of genes <- LGT},
File = {yutin2008.pdf}
}
@Article{Yutin2009,
Title = {{The origins of phagocytosis and eukaryogenesis}},
Author = {N. Yutin and M. Y. Wolf and Y. I. Wolf and E. V. Koonin},
Journal = {Biol Direct},
Year = {2009},
Pages = {9},
Volume = {4},
Abstract = {Euk actins in Crenach and Korarch; Euk sister to Archaea or eocyte hypothesis is true},
Doi = {10.1186/1745-6150-4-9},
File = {yutin2009_eukaryogenesis.pdf},
Keywords = {pr1},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19245710}
}
@Article{Zaballos2006,
Title = {{Comparison of prokaryotic diversity at two offshore oceanic locations reveals a different microbiota in the Mediterranean Sea}},
Author = {M. Zaballos and A. Lopez-Lopez and L. Ovreas and S. G. Bartual and G. D'Auria and J. C. Alba and B. Legault and R. Pushker and F. L. Daee and F. Rodrguez-Valera},
Journal = {FEMS Microbiol. Ecol.},
Year = {2006},
Pages = {389--405},
Volume = {56},
Abstract = {(Fibrobacter, Acidobacteria)},
File = {zaballos2006.pdf}
}
@Article{Zadrobilkova2015,
Title = {{Morphological and Molecular Evidence Support a Close Relationship Between the Free-living Archamoebae Mastigella and Pelomyxa}},
Author = {E. Zadrob{\'i}lkov{\'a} and G. Walker and I. Cepicka},
Journal = {Protist},
Year = {2015},
Pages = {14--41},
Volume = {166},
Abstract = {As stated},
Doi = {10.1016/j.protis.2014.11},
File = {zadrobilkova2015_mastigella_pelomyxa.djvu}
}
@Article{Zalar2005,
Title = {{Taxonomy and phylogeny of the xerophilic genus \textit{Wallemia} (Wallemiomycetes and Wallemiales, cl. et ord. nov.)}},
Author = {P. Zalar and G. S. de Hoog and H.-J. Schroers and J. M. Frank and N. Gunde-Cimerman},
Journal = {Antonie van Leeuwenhoek},
Year = {2005},
Pages = {311--328},
Volume = {87},
Abstract = {Wallemiomycetes basal to Basidiomycetes},
File = {zalar2005.pdf}
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@Article{Zamora2012,
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Journal = {Proc. Biol. Sci.},
Year = {2012},
Number = {1727},
Pages = {293--298},
Volume = {279},
Abstract = {Ancestral diversity},
Doi = {10.1098/rspb.2011.0777},
File = {zamora2012_fossil_echinoderms.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/21653588}
}
@Article{Zantke2008,
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Year = {2008},
Number = {12},
Pages = {1456--1500},
Volume = {269},
Abstract = {some similarities to the nervous system of Cycloneuralia support a phylogenetic position of Tardigrada outside an Onychophora/Euarthropoda clade},
Doi = {10.1002/jmor.10683},
File = {zantke2008.txt}
}
@Article{Zardoya1998,
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@Article{ZarembaNiedzwiedzka2017,
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Author = {K. Zaremba-Niedzwiedzka and E. F. Caceres and J. H. Saw and D. B{\"a}ckstr{\"o}m and L. Juzokaite and E. Vancaester and K. W. Seitz and K. Anantharaman and P. Starnawski and K. U. Kjeldsen and M. B. Stott and T. Nunoura and J. F. Banfield and A. Schramm and B. J. Baker and A. Spang and T. J. G. Ettema},
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Abstract = {TACK and Asgard archaea: Odinarchaeotes | Lokiarchaeotes | Thorarchaeotes | Heimdallarchaeotes + Eukarya},
Doi = {10.1038/nature21031},
File = {zaremba_niedzwiedzka2016_asgard_archaea.pdf},
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Abstract = {Palmophyllum + Verdigellas (Palmophyllales): ?~ Prasinococcophyceae},
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File = {zechmann2010_palmophyllales.pdf}
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Volume = {83},
Abstract = {Thaliacea embedded in Ascidiae; Appendiculariae are long-branch so maybe separate taxon (also Hox support)},
File = {zeng2005.pdf}
}
@Book{Zerov1972,
Title = {The outline of phylogeny of non-vascular plants},
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Abstract = {sistematika, Protista}
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Title = {{Phylogenetic relationships between the Acantharea and the Polycystinea: A molecular perspective on Haeckel's Radiolaria}},
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}
@Article{Zgurski2008,
Title = {{How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set}},
Author = {J. M. Zgurski and H. S. Rai and Q. M. Fai and D. J. Bogler and J. Francisco-Ortega and S. W. Graham},
Journal = {Mol. Phyl. Evol.},
Year = {2008},
Number = {3},
Pages = {1232--1237},
Volume = {47},
Abstract = {Plastid genes: Cycas || Dioon || others},
Doi = {10.1016/j.ympev.2008.03.002},
File = {zgurski2008.pdf}
}
@Article{Zhang2007,
Title = {{A Three-Gene Dinoflagellate Phylogeny Suggests Monophyly of Prorocentrales and a Basal Position for Amphidinium and Heterocapsa}},
Author = {H. Zhang and D. Bhattacharya and S. Lin},
Journal = {J. Mol. Evol.},
Year = {2007},
Pages = {463--474},
Volume = {65},
Abstract = {Oxyrrhis || all (incl. Noctiluca)},
File = {zhang2007.pdf}
}
@Article{Zhang2011a,
Title = {{Spliced Leader RNAs, Mitochondrial Gene Frameshifts and Multi-Protein Phylogeny Expand Support for the Genus Perkinsus as a Unique Group of Alveolates}},
Author = {H. Zhang and D. A. Campbell and N. R. Sturm and C. F. Dungan and S. Lin},
Journal = {Proteins},
Year = {2011},
Number = {4781196},
Pages = {2011},
Volume = {24},
Abstract = {Poor},
Doi = {10.1371/journal.pone.0019933},
File = {zhang2011_perkinsozoa.pdf}
}
@Article{Zhang2003,
Title = {{\textit{Gemmatimonas aurantiaca} gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.}},
Author = {H. Zhang and Y. Sekiguchi and S. Hanada and P. Hugenholtz and H. Kim and Y. Kamagata and K. Nakamura},
Journal = {Int. J. Syst. Evol. Microbiol.},
Year = {2003},
Pages = {1155--1163},
Volume = {53}
}
@Article{Zhang2012,
Title = {{Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses.}},
Author = {Q. Zhang and A. Simpson and W. Song},
Journal = {Proc. Biol. Sci.},
Year = {2012},
Number = {1738},
Pages = {2625--2635},
Volume = {279},
Abstract = {Cyclotrichium and Paraspathidium are not Litostomatea; Protocruzia in Spiro},
Doi = {10.1098/rspb.2011.2688},
File = {zhang2012_ciliophora.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/14530136}
}
@Article{Zhang2015,
Title = {{Marine Isolates of Trimastix marina Form a Plesiomorphic Deep-branching Lineage within Preaxostyla, Separate from Other Known Trimastigids (Paratrimastix n. Gen.).}},
Author = {Q. Zhang and P. T{\'a}borsk{\'y} and J. D. Silberman and T. P{\'a}nek and I. {\v{C}}epi{\v{c}}ka and A. G. B. Simpson},
Journal = {Protist},
Year = {2015},
Number = {4},
Pages = {468--491},
Volume = {166},
Abstract = {Trimastix || Oxymonadida || Paratrimastix},
Doi = {10.1016/j.protis.2015.07.003},
File = {zhang2015_trimastix.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26312987}
}
@Article{Zhang2014a,
Title = {{Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora).}},
Author = {Q. Zhang and Z. Yi and X. Fan and A. Warren and J. Gong and W. Song},
Journal = {Mol. Phylogenet. Evol.},
Year = {2014},
Pages = {162--170},
Volume = {70},
Abstract = {Discotrichida to Ventrata i.s.; Cyclotrichum and Paraspathidium to Prostomatea},
Doi = {10.1016/j.ympev.2013.09.015},
File = {zhang2013_ciliophora.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24075983}
}
@Article{Zhang2018,
Title = {{A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus.}},
Author = {Q.-L. Zhang and G.-L. Zhang and M.-L. Yuan and Z.-X. Dong and H.-W. Li and J. Guo and F. Wang and X.-Y. Deng and J.-Y. Chen and L.-B. Lin},
Journal = {Front Physiol},
Year = {2018},
Pages = {1833},
Volume = {9},
Abstract = {As stated},
Doi = {10.3389/fphys.2018.01833},
File = {zhang2018_cephalochordata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30618839}
}
@Article{Zhang2022,
Title = {{Genomic insights into versatile lifestyle of three new bacterial candidate phyla}},
Author = {X. Zhang and Z. Liu and W. Xu and J. Pan and Y. Huang and M. Cai and Z. Luo and M. Li},
Journal = {SCIENCE CHINA Life Sciences},
Year = {2022},
Abstract = {Quinglongiota ~ Coatesbacteria; Heilongiota ~ WOR-3; Canglongiota ~ Myxococcota},
Doi = {10.1007/s11427-021-2037-x},
File = {zhang2022_quinglongiota_heilongiota_canglongiota_bact.pdf}
}
@Article{Zhang2000,
Title = {{Phylogeny of Ultra-Rapidly Evolving Dinoflagellate Chloroplast Genes: A Possible Common Origin for Sporozoan and Dinoflagellate Plastids}},
Author = {Z. Zhang and B. R. Green and T. Cavalier-Smith},
Journal = {J. Mol. Evol.},
Year = {2000},
Pages = {26--40},
Volume = {51}
}
@Article{Zhang1999,
Title = {{Single gene circles in dinoflagellate chloroplast genomes.}},
Author = {Z. Zhang and B. R. Green and T. Cavalier-Smith},
Journal = {Nature},
Year = {1999},
Number = {6740},
Pages = {155--159},
Volume = {400}
}
@Article{Zhang2013,
Title = {{A sclerite-bearing stem group entoproct from the early Cambrian and its implications.}},
Author = {Z. Zhang and L. E. Holmer and C. B. Skovsted and G. A. Brock and G. E. Budd and D. Fu and X. Zhang and D. Shu and J. Han and J. Liu and H. Wang and A. Butler and G. Li},
Journal = {Sci Rep},
Year = {2013},
Pages = {1066},
Volume = {3},
Abstract = {Colyledion},
Doi = {10.1038/srep01066},
File = {zhang2013_stem_entoproct.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/19439437}
}
@Article{Zhang2014,
Title = {{An early Cambrian agglutinated tubular lophophorate with brachiopod characters.}},
Author = {Z.-F. Zhang and G.-X. Li and L. E. Holmer and G. A. Brock and U. Balthasar and C. B. Skovsted and D.-J. Fu and X.-L. Zhang and H.-Z. Wang and A. Butler and Z.-L. Zhang and C.-Q. Cao and J. Han and J.-N. Liu and D.-G. Shu},
Journal = {Sci Rep},
Year = {2014},
Pages = {4682},
Volume = {4},
Abstract = {Yuganotheca},
Doi = {10.1038/srep04682},
File = {zhang2014_lophophorata.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23336066}
}
@Article{Zhang2011b,
Title = {{Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness}},
Author = {Z.-Q. Zhang},
Journal = {Zootaxa},
Year = {2011},
Pages = {1--237},
Volume = {3148},
Abstract = {Xenacoelomorpha},
File = {animal_biodiversity_2011_1.pdf},
ISBN = {978-1-86977-849-1}
}
@Article{Zhao2017,
Title = {{A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective}},
Author = {R.-L. Zhao and G.-J. Li and S. Sanchez-Ramirez and M. Stata and Z.-L. Yang and G. Wu and Y.-C. Dai and S.-H. He and B.-K. Cui and J.-L. Zhou and F. Wu and M.-Q. He and J.-M. Moncalvo and K. D. Hyde},
Journal = {Fungal Diversity},
Year = {2017},
Abstract = {Wallemiomycotina; Ustil: Exobas, Ustilago, Malass + Monilie; Pucciniomycotina: Agaricos + Spiculogloeomycetes, Puccinio + Classiculomycetes + Atractiellomycetes, Cystobasidio + Microbotry + Mixio; Agaricomycotina: Agar, Dacry, Tremello},
Doi = {10.1007/s13225-017-0381-5},
File = {zhao2017_basidiomycota.pdf},
ISSN = {1878-9129},
Url = {http://dx.doi.org/10.1007/s13225-017-0381-5}
}
@Article{Zhao2012,
Title = {{Collodictyon --- an ancient lineage in the tree of eukaryotes}},
Author = {S. Zhao and F. Burki and J. Br{\aa{}}te and P. Keeling and D. Klaveness and K. Shalchian-Tabrizi},
Journal = {Molecular Biology and Evolution},
Year = {2012},
Abstract = {Diphylatia: Collodictyon ~ Malawimonas ~ Excavata; Archaeplastida || CCTH (Cry, Centr, Telo, Hapto) || SAR (Strame, Alveo, Rhizar)},
File = {zhao2012_collodictyon.pdf}
}
@Article{Zhao2013,
Title = {{Sulcozoa revealed as a paraphyletic group in mitochondrial phylogenomics.}},
Author = {S. Zhao and K. Shalchian-Tabrizi and D. Klaveness},
Journal = {Mol. Phylogenet. Evol.},
Year = {2013},
Number = {3},
Pages = {462--468},
Volume = {69},
Abstract = {Collodictyon ~ Amoebozoa whereas Thecamonas ~ Opist; Malawimonas unplaced (Euk. root?)},
Doi = {10.1016/j.ympev.2013.08.005},
File = {zhao2013_sulcozoa.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23973893}
}
@Article{Zhao2016,
Title = {{A new method for studying the evolutionary origin of the SAR11 clade marine bacteria.}},
Author = {X. Zhao and X. Wan and R. L. He and S. S.-T. Yau},
Journal = {Mol. Phylogenet. Evol.},
Year = {2016},
Pages = {271--279},
Volume = {98},
Abstract = {In Alphaproteobacteria},
Doi = {10.1016/j.ympev.2016.02.015},
File = {zhao2016_sar11.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26926946}
}
@Article{Zhao2019,
Title = {{Cambrian Sessile, Suspension Feeding Stem-Group Ctenophores and Evolution of the Comb Jelly Body Plan.}},
Author = {Y. Zhao and J. Vinther and L. A. Parry and F. Wei and E. Green and D. Pisani and X. Hou and G. D. Edgecombe and P. Cong},
Journal = {Curr. Biol.},
Year = {2019},
Number = {7},
Pages = {1112 - 1125 - e2},
Volume = {29},
Abstract = {Sessile basal! Then Ctenophores ~ Anthozoa + Medusozoa},
Doi = {10.1016/j.cub.2019.02.036},
File = {zhao2019_dinomischids_sitting_cambrian_ctenophores.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/30905603}
}
@Article{Zheng2007,
Title = {{Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation}},
Author = {J. Zheng and I. B. Rogozin and E. V. Koonin and T. M. Przytycka},
Journal = {Mol. Biol. Evol.},
Year = {2007},
Pages = {1--37},
Volume = {24},
File = {zheng2007.pdf}
}
@InProceedings{Zheng2009,
Title = {{Solaranthus: Flower-like Bisexual Reproductive Organs from the Jurassic in China}},
Author = {S. Zheng and X. Wang},
Booktitle = {{Botany and Mycology 2009. Snowbird, Utah, July 25-29. Abstracts}},
Year = {2009},
Abstract = {As stated},
File = {zheng2009_solaranthus.txt}
}
@Article{Zhong2011,
Title = {{Systematic error in seed plant phylogenomics}},
Author = {B. Zhong and O. Deusch and V. V. Goremykin and D. Penny and P. J. Biggs and R. A. Atherton and S. V. Nikiforova and P. J. Lockhart},
Journal = {Genome biology and evolution},
Year = {2011},
Abstract = {Support for gnepine},
Doi = {10.1093/gbe/evr105},
File = {zhong2011_gnepine.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/22016337}
}
@Article{Zhong2013a,
Title = {{Origin of land plants using the multispecies coalescent model.}},
Author = {B. Zhong and L. Liu and Z. Yan and D. Penny},
Journal = {Trends Plant Sci.},
Year = {2013},
Number = {9},
Pages = {492--495},
Volume = {18},
Abstract = {Chara || Coleoch || Zygn || land plants},
Doi = {10.1016/j.tplants.2013.04.009},
File = {zhong2013_land_plants_zygnem.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/23707196}
}
@Article{Zhong2013,
Title = {{Streptophyte Algae and the Origin of Land Plants Revisited Using Heterogeneous Models with Three New Algal Chloroplast Genomes.}},
Author = {B. Zhong and Z. Xi and V. V. Goremykin and R. Fong and P. A. McLenachan and P. M. Novis and C. C. Davis and D. Penny},
Journal = {Mol. Biol. Evol.},
Year = {2013},
Abstract = {Zygnematales alone, or a clade consisting of Coleochaetales plus Zygnematales, as the closest living relatives of land plants},
Doi = {10.1093/molbev/mst200},
File = {zhong2013_streptophytes_land_plants.txt},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/24136916}
}
@Article{Zhong2010,
Title = {{The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics}},
Author = {B. Zhong and T. Yonezawa and Y. Zhong and M. Hasegawa},
Journal = {Molecular biology and evolution},
Year = {2010},
Abstract = {Unclear},
Doi = {10.1093/molbev/msq170},
File = {zhong2010_gnetales.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20601411}
}
@Article{Zhong2009,
Title = {{Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data}},
Author = {J. Zhong and J. Zhang and E. Mukwaya and Y. Wang},
Journal = {J. Genet. Genomics},
Year = {2009},
Number = {3},
Pages = {151--160},
Volume = {36},
Abstract = {Everything tangled with mtDNA},
Doi = {10.1016/S1673-8527(08)60102-2},
File = {zhong2009_deuterostomes.pdf},
ISSN = {1673-8527},
Url = {http://dx.doi.org/10.1016/S1673-8527(08)60102-2}
}
@Article{Zhou2010,
Title = {{Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants}},
Author = {X. Zhou and Z. Lin and H. Ma},
Journal = {Genome biology},
Year = {2010},
Number = {4},
Pages = {R38},
Volume = {11},
Abstract = {Some duplications found, weak},
Doi = {10.1186/gb-2010-11-4-r38},
File = {zhou2010_euk_dupl.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/20370904}
}
@Article{Zhou2017,
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Year = {2017},
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Abstract = {Review},
Doi = {10.1007/s00253-018-8831-x},
File = {zhou2018_two_or_three_domains.pdf},
Url = {https://doi.org/10.1007/s00253-018-8831-x}
}
@Article{Zhuang2012,
Title = {{What an rRNA Secondary Structure Tells about Phylogeny of Fungi in Ascomycota with Emphasis on Evolution of Major Types of Ascus}},
Author = {W.-Y. Zhuang and C.-Y. Liu},
Journal = {PLOS One},
Year = {2012},
Number = {10},
Pages = {e47546},
Volume = {7},
Abstract = {Geoglosso + Leotio},
Doi = {10.1371/journal.pone.0047546},
File = {zhuang2012_ascomycota.pdf},
Url = {www.plosone.org}
}
@Book{Zhukov1990,
Title = {Atlas of freshwater heterotrophic flagellate protozoans},
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Publisher = {Nauka},
Year = {1990},
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Note = {(In Russian)},
Abstract = {sistematika, Protista}
}
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@Article{Zhuravlev2011,
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@Article{Zimek2008,
Title = {{In contrast to the nematode and fruit fly all 9 intron positions of the sea anemone lamin gene are conserved in human lamin genes}},
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Title = {{Phylogenetic position of \textit{Crustomastix stigmatica} sp. nov. and \textit{Dolichomastix tenuilepis} in relation to the Mamiellales (Prasinophyceae, Chlorophyta)}},
Author = {A. Zingone and M. Borra and C. Brunet and G. Forlani and W. H. C. F. Kooistra and G. Procaccini},
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Year = {2002},
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Abstract = {Prasinophyceae VI (Prasinococcus) || I (Pyraminomonadales) || II (Mamiellales) || V (Pseudoscoupfieldiales/Pseudoscourfieldia) || III (Pseud./Nephroselmis) || Ulvo || IV (Chlorodendrales: Tetraselmis, Scherffelia) || Treboux || Chloro, every || unsupp.},
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Title = {{There and Back Again: Parallel Evolution of Cell Coverings in Centrohelid Heliozoans.}},
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Journal = {Protist},
Year = {2016},
Number = {1},
Pages = {51--66},
Volume = {167},
Abstract = {Centroh: Acanthocystida and Pterocystida || Hapt || Microhelida incl. Palpitomonas, Microheliella || Crypt || Telon || Viridipl},
Doi = {10.1016/j.protis.2015.12.002},
File = {zlatogursky2016_centrohelida.pdf},
Url = {http://www.ncbi.nlm.nih.gov/pubmed/26828628}
}
@Article{Zlatogursky2021,
Title = {{The long-time orphan protist Meringosphaera mediterranea Lohmann, 1902 [1903] is a centrohelid heliozoan}},
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Journal = {Eukaryotic Microbiology},
Year = {2021},
Pages = {e12860},
Volume = {68},
Abstract = {As stated, photosynthetic bodies are of yet unknown structure},
Doi = {10.1111/jeu.12860},
File = {zlatogursky2021_meringosphaera_photosynthetic_centrohelid.pdf}
}
@Article{Zoelfel1997,
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@Article{Zrzavy2003,
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@Article{Zrzavy2003a,
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@Article{Zrzavy2001,
Title = {{Myzostomida Are Not Annelids: Molecular and Morphological Support for a Clade of Animals with Anterior Sperm Flagella}},
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@Article{Zrzavy2009,
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Abstract = {Orthonectida after basal annelids; Dicyema separate; Macrodasyida | Chaetonotida || Plathelm.; Gnath || Microgn || Synderm},
Doi = {10.3389/fgene.2019.00443},
File = {zverkov2019_mesozoa.pdf},
Url = {https://www.ncbi.nlm.nih.gov/pubmed/31178892}
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}
@Book{Garrity2005,
Title = {{Bergey's Manual of Systematic Bacteriology: The Proteobacteria (Part C) }},
Editor = {G. Garrity and D. J. Brenner and N. R. Krieg and J. T. Staley and D. R. Boone and P. De Vos and M. Goodfellow and F. A. Rainey and G. M. Garrity and K.-H. Schleifer},
Publisher = {Springer},
Year = {2005},
Address = {New York},
Number = {Part C},
Volume = {2},
ISBN = {0387241450}
}
@Book{Gupta2002,
Title = {{Modern Foraminifera}},
Editor = {B. K. S. Gupta},
Publisher = {Kluwer Academic},
Year = {2002},
Address = {Dordrecht},
ISBN = {1402005989},
Pages = {1--371}
}
@Book{Hirt2004,
Title = {{Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. Systematics Association Special Volume, No. 68}},
Editor = {R. P. Hirt},
Publisher = {CRC},
Year = {2004},
Pages = {1--352}
}
@Book{Origin1979,
Title = {{Origin of major invertebrate groups}},
Editor = {R. P. S. Jefferies and M. R. House},
Publisher = {Academic Press},
Year = {1979},
Address = {London},
Key = {Origin...},
Pages = {1--358}
}
@Book{Jekely2007,
Title = {{Eukaryotic Membranes and Cytoskeleton. Origins and Evolution}},
Editor = {G. Jekely},
Publisher = {Springer},
Year = {2007},
Address = {New York},
ISBN = {978-0-387-74020-1},
Pages = {1--146}
}
@Book{Kaas2006,
Title = {{Evolution of Nervous Systems}},
Editor = {J. H. Kaas},
Publisher = {Academic Press},
Year = {2006},
Address = {London},
Volume = {1--4},
ISBN = {0123925606},
Pages = {1--2000}
}
@Book{Katz2006,
Title = {{Genomics and Evolution of Microbial Eukaryotes}},
Editor = {L. A. Katz and D. Bhattacharya},
Publisher = {Oxford University Press},
Year = {2006},
Address = {Oxford},
ISBN = {0198569742},
Pages = {1--243}
}
@Book{Ainsworth1983,
Title = {{Ainsworth and Bisby's dictionary of the Fungi}},
Editor = {P. M. Kirk and P. F. Cannon and J. C. David and J. A. Stalpers},
Publisher = {CABI},
Year = {2001},
Address = {Kew},
Key = {Ainsworth},
Pages = {445}
}
@Book{Leadbeater2000,
Title = {{The Flagellates: Unity, Diversity and Evolution}},
Editor = {B. S. C. Leadbeater and J. C. Green},
Publisher = {Taylor and Francis},
Year = {2000},
Address = {London},
ISBN = {0748409149},
Pages = {1--401}
}
@Book{Margulis1989,
Title = {{Handbook of protoctista: the structure, cultivation, habitats, and life histories of the eukaryotic microorganisms and their descendants exclusive of animals, plants, and fungi: a guide to the algae, ciliates, foraminifera, sporozoa, water molds, slime molds, and the other protoctists}},
Editor = {L. Margulis and J. Corliss and M. Melkonian and D. J. Chapman},
Publisher = {Jones and Bartlett Publishers},
Year = {1989},
Address = {Boston},
Key = {Handbook...},
Responsible = {L. Margulis}
}
@Article{McLaughlin2014,
Year = {2014},
Volume = {7},
Abstract = {Archaeorhizomycetes ~ Taphrinom; Laboulb ~ Sordar},
Address = {Berlin},
Booktitle = {{Systematics and evolution: The Mycota}},
Editor = {D. J. McLaughlin and J. W. Spatafora},
Publisher = {Springer}
}
@Book{Minelli2008,
Title = {{Evolving Pathways Key. Themes in Evolutionary Developmental Biology}},
Editor = {A. Minelli and G. Fusco},
Publisher = {Cambridge University Press},
Year = {2008},
Address = {Cambridge},
ISBN = {9780521875004},
Pages = {1--426}
}
@Book{Origins1985,
Title = {{The origins and relationships of lower invertebrates}},
Editor = {S. Conway Morris},
Publisher = {Oxford University Press},
Year = {1985},
Address = {Oxford},
Key = {The origins...}
}
@Book{Nash2008,
Title = {{Lichen Biology}},
Editor = {T. H. Nash},
Publisher = {Cambridge University Press},
Year = {2008},
Address = {Cambridge},
ISBN = {9780521871624},
Pages = {1--486}
}
@Book{Parker1982,
Title = {{Synopsis and Classification of Living Organisms}},
Editor = {S. P. Parker},
Publisher = {McGraw Hill},
Year = {1982},
Address = {New York},
Abstract = {Classification down to family level}
}
@Book{Ranker2008,
Title = {{Biology and Evolution of Ferns and Lycophytes}},
Editor = {T. A. Ranker and C. H. Haufler},
Publisher = {Cambridge University Press},
Year = {2008},
Address = {Cambridge},
ISBN = {0521696895},
Pages = {1--500}
}
@Book{Rohde2005,
Title = {{Marine Parasitology}},
Editor = {K. Rohde},
Publisher = {CSIRO PUBLISHING},
Year = {2005},
Address = {Collingwood},
ISBN = {0643090258},
Pages = {1--592}
}
@Book{Marine2015,
Editor = {S. H. S. htsuka,Susumu,Toshinobu and F. Not},
Publisher = {Springer},
Year = {2015},
Abstract = {Review of several groups, including basal Chlorophyta},
Booktitle = {{Marine Protists: Diversity and Dynamics}},
Doi = {10.1111/jse.12180}
}
@Book{Seckbach2007,
Title = {{Origins: Genesis, Evolution and Diversity of Life}},
Editor = {J. Seckbach},
Publisher = {Kluwer Academic},
Year = {2007},
Address = {New York},
ISBN = {1402018134},
Pages = {1--707}
}
@Book{Syvanen2002,
Title = {{Horizontal Gene Transfer}},
Editor = {M. Syvanen and C. I. Kado},
Publisher = {Academic Press},
Year = {2002},
Address = {London},
Edition = {2},
Pages = {1--445}
}
@Book{Tachezy2008,
Title = {{Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes}},
Editor = {J. Tachezy},
Publisher = {Springer},
Year = {2008},
Address = {Berlin},
ISBN = {9783540767329},
Pages = {1--287}
}
@Book{Wagele2014,
Editor = {J. W. B. W{\"a}gele and T. Bartolomaeus},
Publisher = {Walter de Gruyter GmbH},
Year = {2014},
Address = {Berlin},
Booktitle = {{Deep Metazoan Phylogeny: The Backbone of the Tree of Life}}
}
@Book{Speziellezoologie1996,
Title = {{Spezielle Zoologie. Erster Teil: Einzeller und Wirbellose Tiere}},
Editor = {W. Westheide and R. W. Rieger},
Publisher = {Gustav Fisher Verlag},
Year = {1996},
Address = {Stuttgart},
Pages = {909},
Responsible = {W. Westheide, R. Reiger (ed.)}
}