title: First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.
abstract: Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.
authors.affiliation: Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic. Electronic address: mistrpanek@seznam.cz.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Pánek
authors.affiliation: Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic; Centre for Epidemiology and Microbiology, National Institute of Public Health, Srobarova 48, 100 42 Prague, Czech Republic.
authors.forename: Eliška
authors.initials: E
authors.lastname: Zadrobílková
authors.affiliation: Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic.
authors.forename: Giselle
authors.initials: G
authors.lastname: Walker
authors.affiliation: Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Brown
authors.affiliation: School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.
authors.forename: Eleni
authors.initials: E
authors.lastname: Gentekaki
authors.affiliation: Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Miluše
authors.initials: M
authors.lastname: Hroudová
authors.affiliation: Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Seungho
authors.initials: S
authors.lastname: Kang
authors.affiliation: Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Roger
authors.affiliation: Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Alexander K
authors.initials: AK
authors.lastname: Tice
authors.affiliation: Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Čestmír
authors.initials: Č
authors.lastname: Vlček
authors.affiliation: Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic.
authors.forename: Ivan
authors.initials: I
authors.lastname: Čepička
mesh_terms: D056896:Archamoebae / Q000145:classification* / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics; D008928:Mitochondria / Q000378:metabolism; D005810:Multigene Family / Q000235:genetics*; D009586:Nitrogen Fixation / Q000235:genetics; D010802:Phylogeny; D013431:Sulfates / Q000378:metabolism
chemical_list: D013431:Sulfates
keywords: Classification; Conosa; Evolution of parasitism; Flagellar apparatus; Nitrogen fixation system; Pelobiontida