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.

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

Department of Biological Sciences Mississippi State University Mississippi State MS 39762 USA; Institute for Genomics Biocomputing and Biotechnology Mississippi State University Mississippi State MS 39762 USA

Department of Genomics and Bioinformatics Institute of Molecular Genetics Czech Academy of Sciences Videnska 1083 142 20 Prague 4 Czech Republic

Department of Zoology Faculty of Science Charles University Prague Vinicna 7 128 44 Prague Czech Republic

Department of Zoology Faculty of Science Charles University 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

School of Science Mae Fah Luang University Chiang Rai 57100 Thailand

References provided by Crossref.org

Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti

Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics

The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba

Anaerobic peroxisomes in Mastigamoeba balamuthi

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Between a Pod and a Hard Test: The Deep Evolution of Amoebae