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Pisani}, title = {{Sponges are not Eumetazoans: Complete mitochondrial genome support for a sister group relationship between Porifera and the other animals}}, 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, 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}, title = {{MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda}}, 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, author = {J. del Campo and R. Massana}, title = {{Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys}}, journal = {Protist}, year = {2011}, volume = {49}, pages = {14}, 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, author = {F. Campo-Paysaa and F. Marletaz and V. Laudet and M. Schubert}, title = {{Retinoic acid signaling in development: Tissue-specific functions and evolutionary origins}}, journal = {genesis}, year = {2008}, volume = {46}, pages = {640--656}, abstract = {standard hypothesis}, doi = {10.1002/dvg.20444}, file = {campo-paysaa2008.pdf} } @ARTICLE{CampoPaysaa2011, author = {F. Campo-Paysaa and M. Se and M. Schubert}, title = {{MicroRNA complements in deuterostomes: Origin and evolution of microRNAs}}, journal = {EVOLUTION \& DEVELOPMENT}, year = {2011}, volume = {1}, pages = {15--27}, 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} } @ARTICLE{Campos1998, author = {A. Campos and M. P. Cummings and J. L. Reyes and J. P. Laclette}, title = {{Phylogenetic Relationships of Platyhelminthes Based on 18{S} Ribosomal Gene Sequences}}, journal = {Mol. Phyl. Evol.}, year = {1998}, volume = {10}, pages = {1--10}, number = {1} } @ARTICLE{Canning2000a, author = {E. U. Canning and A. Curry and S. W. Feist and M. Longshaw and B. Okamura}, title = {{A New Class and Order of Myxozoans to Accommodate Parasites of Bryozoans with Ultrastructural Observations on Tetracapsula bryosalmonae (PKX Organism)}}, journal = {J. Euk. Microbiol.}, year = {2000}, volume = {47}, pages = {456--468}, number = {5} } @ARTICLE{Canning2007, author = {E. U. Canning and A. Curry and S. L. L. Hill and B. Okamura}, title = {{Ultrastructure of \textit{Buddenbrockia allmani} n. sp. (Myxozoa, Malacosporea), a Parasite of Lophopus crystallinus (Bryozoa, Phylactolaemata)}}, journal = {J. Euk. Microbiol.}, year = {2007}, volume = {54}, pages = {247--262}, number = {3}, abstract = {Tetracapsuloides and Buddenbrockia are separate; vermifom stage in not known for new species}, file = {canning2007.pdf} } @ARTICLE{Canning2008, author = {E. U. Canning and A. Curry and B. Okamura}, 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}}, journal = {Folia Parasitologica}, year = {2008}, volume = {255}, pages = {241--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} } @ARTICLE{Cannon2009, author = {J. T. Cannon and A. L. Rychel and H. Eccleston and K. M. Halanych and B. J. Swalla}, title = {{Molecular Phylogeny of Hemichordata, with Updated Status of Deep-Sea Enteropneusts}}, journal = {Mol. Phylogenet. Evol.}, year = {In press}, abstract = {Enteropn. paraphyletic}, doi = {10.1016/j.ympev.2009.03.027}, file = {cannon2009_hemichordata.pdf} } @ARTICLE{Cantino2007, author = {P. D. Cantino and J. A. Doyle and S. W. Graham and W. S. Judd and R. G. Olmstead and D. E. Soltis and P. S. Soltis and M. J. Donoghue}, title = {{Towards a phylogenetic nomenclature of Tracheophyta}}, journal = {Taxon}, year = {2007}, volume = {2007}, pages = {822--846}, number = {2}, abstract = {PhyloCode names}, file = {cantino2007.pdf} } @ARTICLE{Cao1994, author = {Y. Cao and J. Adachi and M. Hasegawa}, title = {{Eutherian phylogeny as inferred from mitochondrial DNA sequence data.}}, journal = {Jap. J. Gen.}, year = {1994}, volume = {69}, pages = {455--472}, number = {5} } @ARTICLE{Carafa2005, author = {A. Carafa and J. G. Duckett and J. P. Knox and R. Ligrone}, title = {{Distribution of cell-wall xylans in bryophytes and tracheophytes: new insights into basal interrelationships of land plants}}, journal = {New Phytol.}, year = {2005}, volume = {168}, pages = {231--240}, abstract = {Anthoc || Pterid}, file = {carafa2005.pdf} } @ARTICLE{Carapelli2007, author = {A. Carapelli and P. Li and F. Nardi and E. van der Wath and F. Frati}, title = {{Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea}}, journal = {BMC Evol. Biol.}, year = {2007}, volume = {7}, pages = {1--13}, number = {S8}, abstract = {mt genomes: Coll || Diplu || (Decap + Cephaloc) + Insecta }, file = {carapelli2007.pdf} } @ARTICLE{Carnegie2003, author = {R. B. Carnegie and G. R. Meyer and J. Blackbourn and N. Cochennec-Laureau and F. C. J. Berthe and S. M. Bower}, title = {{Molecular detection of the oyster parasite Mikrocytos mackini, and a preliminary phylogenetic analysis}}, journal = {Diseases of Aquatic Organisms}, year = {2003}, volume = {54}, pages = {219--227}, abstract = {Mikrocytos mackini !~ any amitoch. protists}, file = {carnegie2003.pdf}, url = {www.int-res.com} } @ARTICLE{Caron1999, author = {D. A. Caron and R. L. Lim and M. R. Dennett and R. J. Cast}, title = {{Molecular phylogenetic analysis of the heterothophic chrysophyte genus \textit{Paraphysomonas} (Chrysophyceae), and the design of RNA-targeted oligonucteotide probes for two species}}, journal = {J. Phycol.}, year = {1999}, volume = {35}, pages = {824--837} } @ARTICLE{Carr2008, author = {M. Carr and B. S. Leadbeater and R. Hassan and M. Nelson and S. L. Baldauf}, title = {{Molecular phylogeny of choanoflagellates, the sister group to Metazoa}}, journal = {Proc. Natl. Acad. Sci. USA}, year = {2008}, volume = {105}, pages = {16641--16646}, number = {43}, 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, author = {S. Carranza and J. Baguna and M. Riutort}, title = {{Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences.}}, journal = {Mol. Biol. Evol.}, year = {1997}, volume = {14}, pages = {485--497} } @ARTICLE{Cartwright2007, author = {P. Cartwright and A. Collins}, title = {{Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages}}, journal = {Integr. Comp. Biol.}, year = {2007}, volume = {47}, pages = {744--751}, number = {5}, file = {cartwright2007.pdf} } @ARTICLE{Caspers1997, author = {G.-J. Caspers and D. U. de Weerd and J. Wattel and W. W. de Jong}, title = {{Crystallin Sequences Support a Galliform-Anseriform Clade}}, journal = {Mol. Phyl. Evol.}, year = {1997}, volume = {7}, pages = {185--188}, number = {2} } @ARTICLE{Cassens2000, author = {I. Cassens and S. Vicario and V. G. Waddell and H. Balchowsky and Daniel van Belle and W. Dings: and C. Fans: and R. S. L. Mohanp: and P. C. Simoes-Lopes and R. Bastida and A. Meyer and M. J. Stanhope and M. C. Milinkovitch}, title = {{Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages}}, journal = {Proc. Natl. Acad. Sci. USA}, year = {2000}, volume = {97}, pages = {11343--11347}, number = {21} } @ARTICLE{Castresana1999, author = {J. Castresana and D. Moreira}, title = {{Respiratory Chains in the Last Common Ancestor of Living Organisms}}, journal = {J. Mol. Evol.}, year = {1999}, volume = {49}, pages = {453--460} } @ARTICLE{Cavaletti2006, author = {L. Cavaletti and P. Monciardini and R. Bamonte and P. Schumann and M. Rohde and M. Sosio and S. Donadio}, title = {{New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil}}, journal = {Environ. Microbiol.}, year = {2006}, volume = {72}, pages = {4360--4369}, number = {6}, abstract = {Ktedobacteria, ~ Chloroflexi}, file = {cavaletti2006.pdf} } @INCOLLECTION{Cavalier-Smith2007, author = {Th. Cavalier-Smith}, title = {{Evolution and relationships of algae: major branches of the tree of life}}, booktitle = {Unravelling the algae: the past, present and future of algae systematics. The Systematic Association special volume series 75}, publisher = {CRC Press}, year = {2007}, editor = {J. Brodie and J. Lewis}, pages = {21--56}, address = {London}, 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, author = {T. Cavalier-Smith}, title = {{Classification of Percolozoa}}, booktitle = {Endocytobiol. V}, publisher = {Tuebingen University Press}, year = {1993}, editor = {H. Ishikawa and M. Ishida and S. Sato}, pages = {399--406}, address = {Tuebingen}, journal = {Endocytobiol.} } @ARTICLE{Cavalier1996/97, author = {T. Cavalier-Smith}, title = {{Amoeboflagellates and Mitochondrial Cristae in Eukaryote Evolution: Megasystematics of the New Protozoan Subkingdoms Eozoa and Neozoa}}, journal = {Arch. Protistenkd.}, year = {1996/97}, volume = {147}, pages = {237--258} } @ARTICLE{CavalierSmith2010, author = {T. Cavalier-Smith}, title = {{Deep phylogeny, ancestral groups and the four ages of life}}, journal = {Philos. Trans. R. Soc. Lond., B, Biol. Sci.}, year = {2010}, volume = {365}, pages = {111 - 132}, number = {1537}, 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, author = {T. Cavalier-Smith}, title = {{Origin of the cell nucleus, mitosis and sex: Roles of intracellular coevolution}}, journal = {Biology direct}, year = {2010}, volume = {5}, pages = {7}, number = {1}, 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, author = {T. Cavalier-Smith}, title = {{Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree}}, 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, author = {T. Cavalier-Smith}, title = {{Predation and eukaryote cell origins: A coevolutionary perspective.}}, journal = {Int. J. Biochem. Cell Biol.}, year = {2009}, volume = {41}, pages = {307--322}, abstract = {Same scheme with Negibacteria etc.}, doi = {10.1016/j.biocel.2008.10.002}, file = {cavalier-smith2009.pdf} } @ARTICLE{CavalierSmith2009b, author = {Th. Cavalier-Smith}, title = {{Megaphylogeny, Cell Body Plans, Adaptive Zones: Causes and Timing of Eukaryote Basal Radiations}}, journal = {J. Euk. Micriobiol.}, year = {2009}, volume = {56}, pages = {26--33}, 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, author = {T. Cavalier-Smith}, title = {{Rooting the tree of life by transition analyses}}, journal = {Biology Direct}, year = {2006}, volume = {1}, pages = {1--83}, number = {19}, abstract = {new bacterial classification}, file = {cavalier-smith2006.pdf} } @ARTICLE{CavalierSmith2006c, author = {T. Cavalier-Smith}, title = {{Cell evolution and Earth history: stasis and revolution}}, journal = {Phil. Trans. R. Soc. B}, year = {2006}, volume = {361(1470)}, pages = {969--1006}, file = {cavalier-smith2006c.pdf} } @ARTICLE{CavalierSmith2004, author = {T. Cavalier-Smith}, title = {{Only six kingdoms of life}}, journal = {Proc. R. Soc. B}, year = {2004}, volume = {271}, pages = {1251--1262}, file = {cavalier-smith2004a.pdf}, keywords = {pr1} } @ARTICLE{CavalierSmith2003a, author = {T. Cavalier-Smith}, title = {{The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa}}, journal = {Int. J. Syst. Evol. Microbiol.}, year = {2003}, volume = {53}, pages = {1741--1758}, file = {cavalier-smith2003c.pdf} } @ARTICLE{CavalierSmith2003c, author = {T. Cavalier-Smith}, title = {{Protist phylogeny and the high-level classification of Protozoa}}, journal = {Eur. J. Protistol.}, year = {2003}, volume = {39}, pages = {338--348}, 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, author = {T. Cavalier-Smith}, title = {{The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa}}, journal = {Int. J. Syst. Evol. Microbiol.}, year = {2002}, volume = {52}, pages = {297--354} } @ARTICLE{Cavalier-Smith2002b, author = {T. Cavalier-Smith}, title = {{The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification}}, journal = {Int. J. Syst. Evol. Microbiol.}, year = {2002}, volume = {52}, pages = {7--76} } @INCOLLECTION{Cavalier-Smith2000, author = {T. Cavalier-Smith}, title = {{Flagellate megaevolution: the basis for eukaryote diversification}}, booktitle = {The Flagellates: Unity, Diversity and Evolution}, publisher = {Chapman and Hall}, year = {2000}, pages = {361--390}, address = {London} } @ARTICLE{Cavalier1999, author = {T. Cavalier-Smith}, title = {{Principles of Protein and Lipid Targeting in Secondary Symbiogenesis: Euglenoid, Dinoflagellate, and Sporozoan Plastid Origins and the Eukaryote Family Tree}}, journal = {J. Euk. Microbiol.}, year = {1999}, volume = {46}, pages = {347--366}, number = {4} } @ARTICLE{Cavalier1998, author = {T. Cavalier-Smith}, title = {{A revised six-kingdom system of life}}, journal = {Biol. Rev.}, year = {1998}, volume = {73}, pages = {203--266}, number = {2}, keywords = {pr1} } @ARTICLE{Cavalier1996, author = {T. Cavalier-Smith}, title = {{Cryptomonad nuclear and nucleomorph 18S rRNA phylogeny}}, journal = {Eur. J. Phycol.}, year = {1996}, volume = {31}, pages = {315--328}, number = {4} } @ARTICLE{Cavalier1995, author = {T. Cavalier-Smith}, title = {{Zooflagellate phylogeny and classification}}, journal = {Tsitologiya}, year = {1995}, volume = {37}, pages = {1010--1029}, number = {11} } @ARTICLE{Cavalier1993, author = {T. Cavalier-Smith}, title = {{The protozoan phylum Opalozoa}}, journal = {J. Euk. Microbiol.}, year = {1993}, volume = {40}, pages = {609--615}, number = {5} } @ARTICLE{Cavalier1993a, author = {T. Cavalier-Smith}, title = {{Kingdom Protozoa and its 18 phyla}}, journal = {Microbiol. Mol. Biol. Rev.}, year = {1993}, volume = {57}, pages = {953--994} } @ARTICLE{Cavalier1987, author = {T. Cavalier-Smith}, title = {{ Eukaryotes with no mitochondria}}, journal = {Nature}, year = {1987}, volume = {326}, pages = {332--333}, number = {6111} } @ARTICLE{Cavalier1996b, author = {T. Cavalier-Smith and M.T.E.P. Allsop and E.E. Chao and N. Boury-Esnault and J. Vacelet}, title = {{Sponge phylogeny, animal monophyly, and the origin of the nervous system: 18S RNA evidence}}, journal = {Can. J. Zool.}, year = {1996}, volume = {74}, pages = {2031--2045} } @ARTICLE{Cavalier1994, author = {T. Cavalier-Smith and M. T. Allsopp and E. E. Chao}, title = {{Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic?}}, journal = {Proc. Natl. Acad. Sci. USA}, year = {1994}, volume = {91}, pages = {11368--11372}, number = {24} } @ARTICLE{Cavalier1996c, author = {T. Cavalier-Smith and M. T. P. Allsopp}, title = {{Corallochytrium, an Enigmatic Non-flagellate Protozoan Related to Choanoflagellates}}, journal = {Eur. J. Protistol.}, year = {1996}, volume = {32}, pages = {306--310} } @ARTICLE{Cavalier1996/97a, author = {T. Cavalier-Smith and E. E. Chao}, title = {{Sarcomonad Ribosomal RNA Sequences, Rhizopod Phylogeny, and the Origin of Euglyphid Amoebae}}, journal = {Arch. Protistenkd.}, year = {1996/97}, volume = {147}, pages = {227--236} } @ARTICLE{CavalierSmith2012b, author = {T. Cavalier-Smith and E. E. Chao}, title = {{Oxnerella micra sp. N . (Oxnerellidae fam. N.), A Tiny Naked Centrohelid, and the Diversity and Evolution of Heliozoa}}, 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, author = {T. Cavalier-Smith and E. E. Chao}, title = {{Phylogeny and Evolution of Apusomonadida (Protozoa: Apusozoa): New Genera and Species}}, 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, author = {T. Cavalier-Smith and E. E. Chao}, title = {{Protalveolate phylogeny and systematics and the origins of Sporozoa and dinoflagellates (phylum Myzozoa nom. nov.)}}, journal = {Eur. J. Protistol.}, year = {2004}, volume = {40}, pages = {185--212}, 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, author = {T. Cavalier-Smith and E. E. Chao}, title = {{\textit{Hyperamoeba} rRNA Phylogeny and the Classification of the Phylum Amoebozoa}}, journal = {J. Euk. Microbiol.}, year = {1998}, volume = {45}, pages = {1--8} } @ARTICLE{Cavalier1996a, author = {T. Cavalier-Smith and E. E. Chao}, title = {{Molecular phylogeny of the free-living archezoan \textit{Trepomonas agilis} and the nature of the first eukaryote}}, journal = {J. Mol. Evol.}, year = {1996}, volume = {43}, pages = {551--562}, number = {6} } @ARTICLE{Cavalier1995a, author = {T. Cavalier-Smith and E. E. Chao}, title = {{The opalozoan \textit{Apuzomonas} is related to the common ancestor of animals, fungi and choanoflagellates}}, journal = {Proc. R. Soc. B}, year = {1995}, volume = {261}, pages = {1--6} } @ARTICLE{CavalierSmith2008b, author = {T. Cavalier-Smith and E. E. Chao and A. Stechmann and B. Oates and S. Nikolaev}, title = {{Planomonadida ord. nov. (Apusozoa): Ultrastructural Affinity with Micronuclearia podoventralis and Deep Divergences within Planomonas gen. nov.}}, journal = {Protist}, year = {2008}, volume = {159}, pages = {535--562}, number = {4}, 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{CavalierSmith2006, author = {T. Cavalier-Smith and E. E.-Y. Chao}, title = {{Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista)}}, journal = {J. Mol. Evol.}, year = {2006}, volume = {62}, pages = {388--420}, 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, author = {T. Cavalier-Smith and E. E.-Y. Chao}, title = {{Molecular Phylogeny of Centrohelid Heliozoa, a Novel Lineage of Bikont Eukaryotes That Arose by Ciliary Loss}}, journal = {J. Mol. Evol.}, year = {2003}, volume = {56}, pages = {387--396}, abstract = {Centroh || Hapto}, doi = {10.1007/s00239-002-2409-y}, file = {cavalier-smith2003a.pdf} } @ARTICLE{CavalierSmith2003b, author = {T. Cavalier-Smith and E. E.-Y. Chao}, title = {{Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution}}, journal = {J. Mol. Evol.}, year = {2003}, volume = {56}, pages = {540--563}, abstract = {Ministeria || Choano, Demosp+Hexac ! Calcisp, Paramyx -> Ascetosp, Radiol + Foram = Retaria}, doi = {10.1007/s00239-002-2424-z}, file = {cavalier-smith2003b.pdf} } @ARTICLE{CavalierSmith2003d, author = {T. Cavalier-Smith and E. E.-Y. Chao}, title = {{Phylogeny and Classification of Phylum Cercozoa (Protozoa)}}, journal = {Protist}, year = {2003}, volume = {154}, pages = {341--358}, abstract = {Metopion || Chlorarachn. (incl. in Cerco); Thecofilosea: Testofilosida \& Cryomonadida; 5.8 Filosa \& Endomyxa; Commation \& Vampyrellida -- Protista i.s.}, file = {cavalier-smith2003d.pdf} } @ARTICLE{CavalierSmith2004a, author = {T. Cavalier-Smith and E. E.-Y. Chao and B. Oates}, title = {{Molecular phylogeny of Amoebozoa and the evolutionary signifcance of the unikont Phalansterium}}, journal = {Eur. J. Protistol.}, year = {2004}, volume = {40}, pages = {21--48} } @ARTICLE{CavalierSmith2007, author = {T. Cavalier-Smith and S. von der Heyden}, title = {{Molecular phylogeny, scale evolution and taxonomy of centrohelid Heliozoa}}, journal = {Mol. Phyl. 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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, author = {W. Foissner and H. O. Blatterer and I. Foissner}, title = {{The Hemimastigophora (\textit{Hemimastix amphikineta} nov. gen., nov. spec.), a new protozoan phylum from Gondwanian soils}}, journal = {Eur. J. Protistol.}, year = {1988}, volume = {23}, pages = {361--383} } @ARTICLE{Foissner1993, author = {W. Foissner and I. Foissner}, title = {{The Hemimastigophora, remarkable heterotrophic flagellates possibly related to euglenoid protists}}, journal = {Proc. Germ. Zool. 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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, author = {A. Gruhl and I. Wegener and T. Bartolomaeus}, title = {{Ultrastructure of the body cavities in Phylactolaemata (Bryozoa}}, journal = {J. Morphol.}, year = {2009}, volume = {270}, pages = {306--318}, number = {3}, 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} } @INCOLLECTION{Grygier1983, author = {M. J. 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Whitman}, title = {{Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes}}, 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, author = {W. Ludwig and H.-P. Klenk}, title = {{Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systematics}}, booktitle = {Bergey's Manual of Systematic Bacteriology}, publisher = {Springer-Verlag}, year = {2001}, editor = {D. R. 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Yoder}, title = {{Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction}}, journal = {Molecular Phylogenetics and Evolution}, 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}, file = {mallatt2009_metazoa_complete_rna.djvu} } @ARTICLE{Mallatt2006, author = {J. Mallatt and G. Giribet}, title = {{Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch}}, journal = {Mol. Phyl. Evol.}, year = {2006}, volume = {40}, pages = {772--794}, number = {2006}, abstract = {Scalidophora+Nematoidea || Tardigrada + Onychophora || Chelic (inc. 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Shultz}, title = {{Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin}}, journal = {Mol. Phyl. Evol.}, year = {2004}, volume = {31}, pages = {178--191}, abstract = {Priap || Nematoida || Tard.+Onych. || Pycn+Chel+Myriap || Pancrust., incl. Hexapoda}, file = {mallatt2004.pdf} } @ARTICLE{Mamkaev2008, author = {Y. Mamkaev}, title = {{Nervous System of the Vestimentifera: Comparative Anatomy and Phylogenetic Considerations}}, journal = {J. Morphol.}, year = {2008}, volume = {269}, pages = {1456--1500}, number = {12}, abstract = {However, the pogonophoran body plan is clearly original with an evident hiatus between them and the polychaetes. These peculiarities characterize the Pogonophora as a taxon of high rank (Type or Subtype)}, doi = {10.1002/jmor.10683}, file = {mamkaev2008.txt} } @ARTICLE{Mannen1999, author = {H. Mannen and S. S.-L. 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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, 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}, 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}}, 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, author = {Y. Marcy and C. 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Phylogeny and Classification of the Pedinophyceae (Viridiplantae) Revealed by Molecular Phylogenetic Analyses of Complete Nuclear and Plastid-encoded rRNA Operons.}}, 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, author = {B. Marin and M. Melkonian}, title = {{Molecular Phylogeny and Classification of the Mamiellophyceae class. Nov. 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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}, file = {mayer2010_onychophora_growth_patterns.txt} } @ARTICLE{Mayer2009b, author = {G. Mayer and N. N. Tait}, title = {{Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda}}, journal = {Zool. J. Linn. Soc.}, year = {In press}, 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}, doi = {10.1111/j.1096-3642.2009.00523.x}, file = {mayer2009_oocytes_arthtopoda.pdf} } @ARTICLE{Mayer2009, author = {G. Mayer and P. M. 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Mylnikov}, title = {New data about morphology and life cycle of athalamic amoebae ({P}rotista, {A}thalamida)}, journal = {Zool. Zhurn.}, year = {1996}, volume = {75}, pages = {1283--1293}, number = {9}, note = {(In Russian)}, annote = {xerox} } @ARTICLE{Mikrjukov1995, author = {K. Mikrjukov and A. Mylnikov}, title = {{Fine structure of an unusual rhizopod, \textit{Penardia cometa}, containing extrusomes and kinetosomes}}, journal = {Eur. J. Protistol.}, year = {1995}, volume = {31}, pages = {90--96} } @ARTICLE{Millanes2011, author = {A. M. Millanes and P. Diederich and S. Ekman and M. Wedin}, title = {{Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)}}, 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, author = {G. S. Min and S. H. Kim and W. Kim}, title = {{Molecular phylogeny of arthropods and their relatives: polyphyletic origin of arthropodization.}}, journal = {Mol Cells}, year = {1998}, volume = {8}, pages = {75--83}, number = {1} } @ARTICLE{Min2009, author = {G.-S. Min and J.-K. Park}, title = {{Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata).}}, journal = {BMC Genomics}, year = {2009}, volume = {10}, pages = {533}, 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, author = {D. P. Mindell and M. D. Sorenson and D. E. Dimcheff and M. Hasegawa and J. C. Ast and T. Yuri}, title = {{Interordinal relationships of birds and other reptiles bases on whole mitochondrial genomes}}, journal = {Syst. Biol.}, year = {1999}, volume = {48}, pages = {138--152}, number = {1} } @ARTICLE{Minelli2010, author = {A. Minelli}, title = {{The origins of larval forms: What the data indicate, and what they don't.}}, journal = {Bioessays}, year = {2010}, volume = {32}, number = {1}, 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}}, publisher = {Cambridge University Press}, year = {2003}, author = {A. Minelli}, pages = {1--323}, address = {Cambridge}, isbn = {0521808510} } @CONFERENCE{Minge2008, 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}, title = {{Evolutionary position of breviate amoebae illuminates the primary eukaryote divergence}}, 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, 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}, title = {{Evolutionary position of breviate amoebae and the primary eukaryote divergence}}, 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, author = {Ju. Minichev and Ja. I. Starobogatov}, title = {Subclasses of gastropods and their phylogeny}, journal = {Zool. Zhurn.}, year = {1979}, volume = {58}, pages = {293--305}, number = {3}, note = {(In Russian)}, abstract = {sistematika, Gastropoda, Mollusca} } @INCOLLECTION{Minichev1975, author = {Ju. Minichev and Ja. I. Starobogatov}, title = {About phylogenetic relations inside molluscan phylum}, booktitle = {The condition of exploration degree of living world}, publisher = {Institute of Palaeontology}, year = {1975}, pages = {205--276}, address = {Moscow}, note = {(In Russian)}, abstract = {sistematika, Mollusca} } @ARTICLE{Miquelis2000, author = {A. Miquelis and J. F. Martin and E. W. Carson and G. Brun and A. Gilles}, title = {{Performance of 18S rDNA helix E23 for phylogenetic relationships within and between the Rotifera-Acanthocephala clades.}}, journal = {C. R. Acad. Sci. III}, year = {2000}, volume = {323}, pages = {925--941}, number = {10} } @ARTICLE{Mirabdullaev1994, author = {I. M. Mirabdullaev}, title = {{About origin and placement of fungi in the scassification of living things}}, journal = {Uspekhi sovremennoj biologii}, year = {1994}, volume = {114}, pages = {30--41}, number = {1} } @ARTICLE{Mirabdullaev1989, author = {I. M. Mirabdullaev}, title = {The problems of classification of living things on the level of kingdoms}, journal = {Zhurn. Obshch. Biol.}, year = {1989}, volume = {50}, pages = {725--736}, number = {6}, note = {(In Russian)}, annote = {xerox} } @ARTICLE{Mirabdullaev1988, author = {I. M. Mirabdullaev}, title = {Taxonomic placement and the origin of archebacteria}, journal = {Izv. Akademii Nauk (Ser. biol.)}, year = {1988}, volume = {2}, pages = {175--185}, note = {(In Russian)} } @CONFERENCE{Mirabdullaev1987, author = {I. M. Mirabdullaev}, title = {About perestroika of the classification of living organisms}, booktitle = {Actual questions of science and technics development in Usbekistan}, year = {1987}, pages = {73}, note = {(In Russian)} } @ARTICLE{Mirabdullaev1985, author = {I. M. Mirabdullaev}, title = {The evolution of chloroplasts and origin of cyanobacteria}, journal = {Zhurn. Obshch. Biol.}, year = {1985}, volume = {46}, pages = {483--490}, number = {4}, note = {(In Russian)}, abstract = {evoljucija, Bacteria, Protista}, annote = {xerox} } @ARTICLE{Miroshnichenko2003, author = {M. L. Miroshnichenko and N. A. Kostrikina and N. A. Chernyh and N. V. Pimenov and T. P. Tourova and A. N. Antipov and S. Spring and E. Stackebrandt and E. A. Bonch-Osmolovskaya}, title = {{\textit{Caldithrix abyssi} gen. nov., sp. nov., a nitratereducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage}}, journal = {Int. J. Syst. Evol. Microbiol.}, year = {2003}, volume = {53}, pages = {323--329}, abstract = {ML-5 and Calditrix ~ Deferribacteres, Nitrospira, Thermodesulfovibrio}, file = {miroshnichenko2003.pdf} } @ARTICLE{Miroshnichenko2009, author = {M. L. Miroshnichenko and A. V. Lebedinsky and N. A. Chernyh and T. P. Tourova and T. V. Kolganova and S. Spring and E. A. Bonch-Osmolovskaya}, title = {{Caldimicrobium rimae gen. Nov., Sp. Nov., An extremely thermophilic, facultatively lithoautotrophic, anaerobic bacterium from the Uzon Caldera, Kamchatka}}, journal = {Int. J. Syst. Evol. Microbiol.}, year = {2009}, volume = {59}, pages = {1040--044}, number = {5}, abstract = {Member of Thermodesulfobacteria, deeply branched G- lineage (maybe more or less close from Desulfurobacteriaceae)}, doi = {10.1099/ijs.0.006072-0}, file = {miroshnichenko2009_caldimicribium.pdf}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19406789} } @ARTICLE{Mishler1984, author = {B. D. Mishler and S. P. Churchill}, title = {{A cladistic approach to the phylogeny of the ``Bryophytes''}}, journal = {Brittonia}, year = {1984}, volume = {36}, pages = {406--424} } @INCOLLECTION{Mishler2008, author = {B. D. Mishler and D. G. Kelch}, title = {{Phylogenomics and early land plant evolution}}, booktitle = {Bryophyte Biology}, publisher = {Oxford University Press}, year = {2008}, editor = {B. Goffinet and A. J. Shaw}, pages = {173--197}, address = {Cambridge}, abstract = {Chloroplast genomes, presence/absence of whole-gene characters: typical tree} } @ARTICLE{Miskin1999, author = {I. P. Miskin and P. Farrimond and I. M. Head}, title = {{Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR}}, journal = {Microbiology}, year = {1999}, volume = {145}, pages = {1977--1987}, abstract = {OP5 ~ Verru, Plancto}, file = {miskin1999_op5.pdf} } @ARTICLE{Misof2007, author = {B. Misof and O. Niehuis and I. Bischoff and A. Rickert and D. Erpenbeck and A. Staniczek}, title = {{Towards an 18S phylogeny of hexapods: Accounting for group-specific character covariance in optimized mixed nucleotide/doublet models}}, journal = {Zoology}, year = {2007}, volume = {110}, pages = {409--429}, number = {5}, abstract = {Coll + (Prot+Dipl) + Ectogn}, file = {misof2007.pdf} } @ARTICLE{Miyashita2003, author = {H. Miyashita and H. Ikemoto and N. Kurano and S. Miyachi and M. Chihara}, title = {{\textit{Acaryochloris marina} gen. et sp. nov. (Cyanobacteria), an oxygenic photosynthetic prokaryote containing chlorophyll d as a major pigment}}, journal = {J. Phycol.}, year = {2003}, volume = {39}, pages = {1247--1253}, number = {2003}, abstract = {Gloeobacter || other Cyanobacteria}, file = {miyashita2003.pdf} } @ARTICLE{Miyoshi2005, author = {T. Miyoshi and T. Iwatsuki and T. Naganuma}, title = {{Phylogenetic Characterization of 16S rRNA Gene Clones from Deep-Groundwater Microorganisms That Pass through 0.2-Micrometer-Pore-Size Filters}}, journal = {Appl. Environ. Microbiol.}, year = {2005}, volume = {71}, pages = {1084--1088}, number = {2}, abstract = {< 0.2 nm (nanobacteria?) ~ OD1/OP5/SR11/OP11/WS6 group}, file = {miyoshi2005.pdf} } @ARTICLE{Moczydlowska2011, author = {M. Moczydlowska and E. Landing and W. Zang and T. Palacios}, title = {{Proterozoic phytoplankton and timing of Chlorophyte algae origins}}, journal = {Palaeontology}, year = {2011}, volume = {54}, pages = {721--733}, abstract = {Review}, doi = {10.1111/j.1475-4983.2011.01054.x}, file = {moczydlowska2011_chlorophyta_timing.pdf} } @ARTICLE{Moeller2008, author = {O. S. Moeller and J. Olesen and A. Avenant-Oldewage and P. F. Thomsen and H. Glenner}, title = {{First maxillae suction discs in Branchiura (Crustacea): development and evolution in light of the first molecular phylogeny of Branchiura, Pentastomida, and other ``Maxillopoda''}}, journal = {Arthropod Struct. Devel.}, year = {2008}, volume = {37}, pages = {333--346}, number = {4}, abstract = {Cirripedia || Branchiopoda || Ostracoda || (Branchiura + Pentastomida)}, doi = {10.1016/j.asd.2007.12.002}, file = {moeller2008.pdf} } @ARTICLE{Moestrup1991, author = {O. Moestrup}, title = {{Further studies of presumedly primitive green algae, including the description of Pedinophyceae class. nov. and \em{Resultor} gen. nov.}}, journal = {J. Phycol.}, year = {1991}, volume = {27}, pages = {119--133} } @INCOLLECTION{Moestrup2007, author = {O. Moestrup and N. Daugbjerg}, title = {{On dinoflagellate phylogeny and classification}}, booktitle = {Unravelling the algae: the past, present and future of algae systematics. The Systematic Association special volume series 75}, publisher = {CRC Press}, year = {2007}, editor = {J. Brodie and J. Lewis}, pages = {215--230}, address = {London}, abstract = {8 chloroplast types, orders discussed} } @ARTICLE{Moestrup2001, author = {Ojvind Moestrup and Mario Sengco}, title = {{Ultrastructural studies on \textit{Bigelowiella natans}, gen. et sp. nov., a chlorarachniophyte flagellate}}, journal = {J. Phycol.}, year = {2001}, volume = {37}, pages = {624--646} } @ARTICLE{Mondal2008, author = {U. K. Mondal and B. Das and T. C. Ghosh and A. Sen and A. K. Bothra}, title = {{Nucleotide Triplet Based Molecular Phylogeny of Class I and Class II Aminoacyl t-RNA Synthetase in Three Domain of Life Process: Bacteria, Archaea, and Eukarya}}, journal = {J. Biomol. Struct. Dyn.}, year = {2008}, volume = {26}, pages = {321--328}, number = {3}, abstract = {Archaea are different from bact. and eukarya}, file = {mondal2008.txt}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18808198} } @ARTICLE{Mongodin2005, author = {E. F. Mongodin and K. E. Nelson and S. Daugherty and R. T. DeBoy and J. Wister and H. Khouri and J. Weidman and D. A. Walsh and R. T. Papke and G. S. Perez and A. K. Sharma and C. L. Nesb and D. MacLeod and E. Bapteste and W. F. Doolittle and R. L. Charlebois and B. Legault and F. Rodriguez-Valera}, title = {{The genome of \textit{Salinibacter ruber}: Convergence and gene exchange among hyperhalophilic bacteria and archaea}}, journal = {Proc. Natl. Acad. Sci. USA}, year = {2005}, volume = {102}, pages = {18147--18152}, number = {50}, abstract = {Salinibacter is unique}, file = {mongodin2005.pdf} } @ARTICLE{Montagne2010, author = {N. Montagne and Y. Desdevises and D. Soyez and J.-Y. Toullec}, title = {{Molecular evolution of the crustacean hyperglycemic hormone family in ecdysozoans}}, journal = {BMC evolutionary biology}, year = {2010}, volume = {10}, pages = {62}, number = {1}, abstract = {Branchiopoda + Hexapoda, Collembola in}, doi = {10.1186/1471-2148-10-62}, file = {montagne2010_chh_ecdysozoa.pdf}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20184761} } @ARTICLE{Montegut1994, author = {A. E. Montegut-Felkner and R. E. Triemer}, title = {{Phylogeny of \textit{Diplonema ambulator} (Larsen and Patterson). 1. Homologies of the Flagellar Apparatus}}, journal = {Eur. J. Protistol.}, year = {1994}, volume = {30}, pages = {227--237}, number = {2} } @ARTICLE{Monteiro2002, author = {Ana Sara Monteiro and Beth Okamura and Peter W. H. Holland}, title = {{Orphan Worm Finds a Home: \textit{Buddenbrockia} is a Myxozoan}}, journal = {Mol. Biol. Evol.}, year = {2002}, volume = {19}, pages = {968--971} } @ARTICLE{Moore2008, author = {R. B. Moore and M. Oborni and J. Janouskovec and T. Chrudimsky and M. Vancova and D. H. Green and S. W. Wright and N. W. Davies and C. J. S. Bolch and K. Heimann and J. Slapeta and O. Hoegh-Guldberg and J. M. Logsdon Jr and D. A. Carter}, title = {{A photosynthetic alveolate closely related to apicomplexan parasites}}, journal = {Nature}, year = {2008}, volume = {451}, pages = {959--963}, abstract = {((Chromerida: Chromera velia + Colpodellids) || (Grega || (Piro + Haematosp) || Coccid)) || Perkinsids || Noctiluca || other Dinophlagellata}, doi = {10.1038/nature06635}, file = {moore2008.pdf} } @ARTICLE{Moran2007, author = {D. M. Moran and O. R. Anderson and M. R. Dennett and D. A. Caron and R. J. Gast}, title = {{A description of seven Antarctic marine gymnamoebae including a new subspecies, two new species and a new genus: Neoparamoeba aestuarina antarctica n. subsp., Platyamoeba oblongata n. sp., Platyamoeba contorta n. sp. and Vermistella antarctica n. gen. n. sp.}}, journal = {J. Eukaryot. Microbiol.}, year = {2007}, volume = {54}, pages = {169--183}, number = {2}, abstract = {Vermistella incertae sedis, ~? to Mayorella}, doi = {10.1111/j.1550-7408.2007.00249.x}, file = {moran2007.pdf} } @ARTICLE{Moreira2008, author = {D. Moreira and C. Brochier-Armanet}, title = {{Giant viruses, giant chimeras: The multiple evolutionary histories of Mimivirus genes}}, journal = {BMC Evol. Biol.}, year = {2008}, volume = {8}, pages = {12}, abstract = {It is not a fourth domain, huge HGT}, doi = {10.1186/1471-2148-8-12}, file = {moreira2008_mimivirus.pdf} } @ARTICLE{Moreira2007, author = {D. Moreira and S. von der Heyden and D. Bass and P. Lopez-Garcia and E. Chao and T. Cavalier-Smith}, title = {{Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata}}, journal = {Mol. Phyl. Evol.}, year = {2007}, volume = {44}, pages = {255--266}, abstract = {Nuclearia ~ Fung; Capsasp ~ Choano; Apuso ~~ Rhiz; (Hapto+Centroh+Glauc+Crypto) || (Chlor+Rhod); Chrom+Alv; Opisto || Amoe || others; Breviates > Apuso}, file = {moreira2007.pdf} } @ARTICLE{Moreira1998, author = {D. Moreira and P. Lopez-Garcia}, title = {{Symbiosis between methanogenic Archaea and delta-Proteobacteria as the origin of eukaryotes: the syntrophic hypothesis}}, journal = {J. Mol. Evol.}, year = {1998}, volume = {47}, pages = {517--530} } @ARTICLE{Moreno2010, author = {E. Moreno and K. De Mulder and W. Salvenmoser and P. Ladurner and P. Martinez}, title = {{Inferring the ancestral function of the posterior Hox gene within the bilateria: Controlling the maintenance of reproductive structures, the musculature and the nervous system in the acoel flatworm Isodiametra pulchra}}, journal = {Evol. Devel.}, year = {2010}, volume = {3}, pages = {258--266}, abstract = {posterior Hox genes were used to specify and maintain defined anatomical regions within the AP axis of animals since the beginning of bilaterian evolution}, doi = {10.1111/j.1525-142X.2010.00411.x}, file = {moreno2010_acoel_hox.pdf} } @ARTICLE{Moreno2009, author = {E. Moreno and M. Nadal and J. Bagu{\~n}{\`a} and P. Mart{\'i}nez}, title = {{Tracking the origins of the bilaterian Hox patterning system: Insights from the acoel flatworm Symsagittifera roscoffensis}}, journal = {Evol. Dev.}, year = {2009}, volume = {11}, pages = {574--581}, number = {5}, abstract = {Primitive Hox}, doi = {10.1111/j.1525-142X.2009.00363.x}, file = {moreno2009_acoel_hox.pdf}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19754713} } @ARTICLE{Mori2008, author = {K. Mori and M. Sunamura and K. Yanagawa and J.-i. Ishibashi and Y. Miyoshi and T. Iino and K.-I. Suzuki and T. Urabe}, title = {{First cultivation and ecological investigation of a bacterium affiliated with the candidate phylum OP5 from hot springs}}, journal = {Appl. Environ. Microbiol.}, year = {2008}, volume = {74}, pages = {6223--6229}, number = {20}, abstract = {Now in press: Caldisericum exile gen. nov., sp. nov., an anaerobic thermophilic filamentous bacterium of a novel bacterial phylum, Caldiseria phyl. nov. May be close (?) to Proteo and Chloroflexi}, doi = {10.1128/AEM.01351-08}, file = {mori2008_op5.pdf} } @ARTICLE{Mori2009, author = {K. Mori and K. Yamaguchi and Y. Sakiyama and T. Urabe and K.-I. Suzuki}, title = {{Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiseria phyl. nov., Originally called candidate phylum OP5.}}, journal = {Int. J. Syst. Evol. Microbiol.}, year = {2009}, abstract = {Isolated group, maybe close to TM6, Proteo, TG1; OP11 maybe clode to Thermot, TM7 ~ OP10 ~ Chloroflexi (16S only)}, doi = {10.1099/ijs.0.010033-0}, file = {mori2009_caldisericum.pdf}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19628600} } @ARTICLE{Morin2000, author = {L. Morin}, title = {{Long Branch Attraction Effects and the Status of ``Basal Eukaryotes'': Phylogeny and Structural Analysis of the Ribosomal RNA Gene Cluster of the Free-living Diplomonad Trepomonas agilis}}, journal = {J. Euk. Microbiol.}, year = {2000}, volume = {47}, pages = {167--177}, number = {2} } @ARTICLE{Moriya2002, author = {M. Moriya and T. Nakayama and I. Inouye}, title = {{A New Class of the Stramenopiles, Placididea Classis nova: Description of \textit{Placidia cafeteriopsis} gen. et sp. nov.}}, journal = {Protist}, year = {2002}, volume = {153}, pages = {143--156}, abstract = {Placidia || Wobbia; between Protero \& Bicoec}, file = {moriya2002.pdf} } @ARTICLE{Moriya2000, author = {M. Moriya and T. Nakayama and I. Inouye}, title = {{Ultrastructure and 18S rDNA Sequence Analysis of \textit{Wobblia lunata} gen. et sp. nov., a New Heterotrophic Flagellate (Stramenopiles, Incertae Sedis)}}, journal = {Protist}, year = {2000}, volume = {151}, pages = {41--55} } @ARTICLE{Moriya2001, author = {Shigeharu Moriya and Kentaro Tanaka and Moriya Ohkuma and Sumio Sugano and Toshiaki Kudo}, title = {{Diversification of the Microtubule System in the Early Stage of Eukaryote Evolution: Elongation Factor 1alpha and alpha-Tubulin Protein Phylogeny of Termite Symbiotic Oxymonad and Hypermastigote Protists}}, journal = {J. Mol. Evol}, year = {2001}, volume = {52}, pages = {6--16} } @ARTICLE{Morris2007, author = {D. J. Morris and A. Adams}, title = {{Sacculogenesis of \textit{Buddenbrockia plumatellae} (Myxozoa) within heinvertebrate host \textit{Plumatella repens} (Bryozoa) with comments on the evolutionary relationships of theMyxozoa}}, journal = {Int. J. Parasitol.}, year = {2007}, volume = {37}, pages = {1163--1171}, number = {10}, abstract = {Sacculas formed from separate amoeboid cells}, file = {morris2007.pdf} } @ARTICLE{Morris2007a, author = {D. J. Morris and A. Adams}, title = {{Sacculogenesis and sporogony of \textit{Tetracapsuloides bryosalmonae} (Myxozoa: Malacosporea) within the bryozoan host \textit{Fredericella sultana} (Bryozoa: Phylactolaemata)}}, journal = {Parasitol Res}, year = {2007}, volume = {100}, pages = {983--992}, 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} } @INCOLLECTION{Moshkova1989, author = {I. A. Moshkova}, title = {Brown algae~--- Phaeophyta}, booktitle = {Algae: the reference}, publisher = {Naukova Dumka}, year = {1989}, pages = {386--408}, address = {Kiev}, note = {(In Russian)} } @ARTICLE{Mouchaty2000, author = {S. K. Mouchaty and A. Gullberg and A. Janke and U. Arnason}, title = {{The Phylogenetic Position of the Talpidae Within Eutheria Based on Analysis of Complete Mitochondrial Sequences}}, journal = {Mol. Biol. Evol.}, year = {2000}, volume = {17}, pages = {60--67}, number = {1} } @ARTICLE{Moustafa2008, author = {A. Moustafa and and A. Reyes-Prieto and D. Bhattacharya}, title = {{Chlamydiae Has Contributed at Least 55 Genes to Plantae with Predominantly Plastid Functions}}, journal = {PLoS One}, year = {2008}, volume = {3}, pages = {1--9}, number = {5}, abstract = {As stated}, doi = {10.1371/journal.pone.0002205}, file = {moustafa2008.pdf} } @ARTICLE{Mowbrey2009, author = {K. Mowbrey and J. B. Dacks}, title = {{Evolution and diversity of the Golgi body}}, 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, author = {S. E. Mozley-Standridge and P. M. Letcher and J. E. Longcore and D. Porter and D. R. Simmons}, title = {{Cladochytriales~--- a new order in Chytridiomycota}}, journal = {Myc. Res.}, year = {2009}, volume = {113}, pages = {498--507}, number = {4}, 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, author = {Z. Msiska and J. B. Morton}, title = {{Phylogenetic analysis of the Glomeromycota by partial beta-tubulin gene sequences.}}, journal = {Mycorrhiza}, year = {In press}, abstract = {Sister to core Zygo}, doi = {10.1007/s00572-008-0216-z}, file = {msiska2008.pdf} } @ARTICLE{Mueller2008, author = {C. H. G. Mueller and V. Rieger and Y. Perez and N. Hansson and S. Harzsch}, title = {{Neurophylogeny of Chaetognatha: Can Neuroanatomical Characters Shed Light on the Phylogenetic Position of Arrow Worms?}}, journal = {J. Morphol.}, year = {2008}, volume = {269}, pages = {1456--1500}, number = {12}, 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, author = {W. E. G. Mueller and J. Li and H. C. Schroder and L. Qiao and X. Wang}, title = {{The unique skeleton of siliceous sponges (Porifera; Hexactinellida and Demospongiae) that evolved first from the Urmetazoa during the Proterozoic: a review}}, journal = {Biogeosciences}, year = {2007}, volume = {4}, pages = {219--232}, abstract = {Hexact of ediacarian origin; Hexact + Demo || Calcarea || Archaeocyatha}, file = {mueller2007.pdf}, url = {www.biogeosciences.net/4/219/2007/} } @ARTICLE{Muller2010, author = {F. Muller and T. Brissac and N. Le Bris and H. Felbeck and O. Gros}, title = {{First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat}}, journal = {Environ. Microbiol.}, year = {2010}, volume = {12}, pages = {2371 - 2383}, number = {8}, abstract = {(Cenarchaeum || Giganthauma || Nitrosopumilus) || Crenarchaeota}, doi = {10.1111/j.1462-2920.2010.02309.x}, file = {muller2010_giganthauma.pdf} } @ARTICLE{Muller2001, author = {K. M. Muller and M. C. Oliveira and R. G. Sneath and D. Bhattacharya}, title = {{Ribosomal RNA phylogeny of the Bangiophycidae (Rhodophyta) and the origin of secondary plastids}}, journal = {Amer. J. Bot.}, year = {2001}, volume = {88}, pages = {1390--1400} } @ARTICLE{Muona2003, author = {J. Muona}, title = {{Abstracts of the 21st Annual Meeting of the Willi Hennig Society}}, journal = {Cladistics}, year = {2003}, volume = {19}, pages = {148--163}, 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, author = {A. G. Murdock}, title = {{Phylogeny of marattioid ferns (Marattiaceae): Inferring a root in the absence of a closely related outgroup}}, journal = {Amer. J. Bot.}, year = {2008}, volume = {95}, pages = {626--641}, number = {5}, abstract = {Danaea basal, Marattia polyphyletic}, doi = {10.3732/ajb.2007308}, file = {murdock2008.pdf} } @ARTICLE{Murdock2008b, author = {A. G. Murdock}, title = {{A taxonomic revision of the eusporangiate fern family Marattiaceae, with description of a new genus \textit{Ptisana}}}, journal = {Taxon}, year = {2008}, volume = {2008}, pages = {737--755}, number = {3}, abstract = {Angiopteris, Christensenia, Danaea, Eupodium, Marattia, Marattiaceae, Ptisana}, file = {murdock2008.pdf} } @INCOLLECTION{Murphy1995, 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.)}, title = {{Classification And Nomenclature Of Viruses. 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Myl'nikov}, title = {{Ultrastructure of the Marine Predatory Flagellate Metromonas simplex Larsen et Patterson, 1990 (Cercozoa)}}, journal = {BIOLOGY, MORPHOLOGY, AND SYSTEMATICS OF HYDROBIONTS}, year = {1995}, volume = {4}, pages = {105--110}, number = {2}, abstract = {Metromonas ~ Metopion and Cryomonadida}, doi = {10.1134/S1995082911020155}, file = {mylnikova2011_metromonas.pdf} } @ARTICLE{Mylnikov2009, author = {A. P. Mylnikov}, title = {{Ultrastructure and Phylogeny of Colpodellids (Colpodellida, Alveolata)}}, journal = {Biology Bulletin}, year = {2009}, volume = {36}, pages = {582--590}, number = {6}, abstract = {~ CA of sporoz + dinofl}, doi = {10.1134/S1062359009060065}, file = {mylnikov2009_colpodellids.pdf} } @ARTICLE{Mylnikov2008, author = {A. P. Mylnikov and A. A. 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Kawachi}, 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.}}, journal = {Phycologia}, year = {2007}, volume = {46}, pages = {680--697}, number = {6}, abstract = {Mamiellales-Pyraminomon vs. Nephroselmidales-Pycnococc}, doi = {10.2216/04-25.1}, file = {nakayama2007.pdf} } @ARTICLE{Nazina2006, 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}, title = {{Phylogenetic Diversity and Activity of Anaerobic Microorganisms of High-Temperature Horizons of the Dagang Oil Field (P. R. China)}}, journal = {Microbiology}, year = {2006}, volume = {75}, pages = {55--65}, number = {1}, abstract = {Thermotog ~ Clostridia}, file = {nazina2006.pdf} } @ARTICLE{Near2009, author = {T. J. Near}, title = {{Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes}}, 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, author = {T. J. Near and J. R. Garey and S. A. Nadler}, title = {{Phylogenetic Relationships of the Acanthocephala Inferred from 18{S} Ribosomal {DNA} Sequences}}, journal = {Mol. Phyl. Evol.}, year = {1998}, volume = {10}, pages = {287--298}, number = {3} } @ARTICLE{Nechitaylo2009, author = {T. Y. Nechitaylo and K. N. Timmis and P. N. Golyshin}, title = {{``Candidatus Lumbricincola'', a novel lineage of uncultured Mollicutes from earthworms of family Lumbricidae}}, journal = {Environ. 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