title: Phylogeny, evolution, and taxonomy of vannellid amoebae.
abstract: We sequenced 18S rRNA genes from 21 vannellid amoebae (Amoebozoa; Vannellidae), including nearly all available type cultures, and performed a comprehensive phylogenetic analysis for 57 Vannellidae sequences. The results show that species of Vannella and Platyamoeba are completely mixed and do not form distinct clades. Several very closely related species pairs exist, each with a Vannella and a Platyamoeba species differing in only a few nucleotides. Therefore, presence (Vannella) or absence (Platyamoeba) of glycostyles in the cell surface coat is an invalid generic distinction; the genera must be merged. As Vannella has priority, we formally transferred Platyamoeba species into Vannella, except for the non-vannellid P. stenopodia, here renamed Stenamoeba stenopodia gen. n. comb. n. and transferred to the family Thecamoebidae. Our trees show that Vannella glycostyles were probably easily and repeatedly evolutionarily lost. We have established a new genus Ripella, with distinct morphology and sequence signatures for Vannella platypodia and morphologically similar species that form a clearly separate clade, very distant from other Vannellidae. Vannellids form four well-separated single-genus clades: Vannella sensu stricto, Ripella, Clydonella, and Lingulamoeba. Species of the revised genus Vannella comprise four closely related, well-supported subclades: one marine and three freshwater. Here, we provide an illustrated checklist for all 40 known Vannellidae species.
authors.affiliation: Faculty of Biology and Soil Sciences, St. Petersburg State University, Universitetskaja nab. 7/9, 199034 St. Petersburg, Russia. polychaos@mail.ru
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Smirnov
authors.forename: Elena S
authors.initials: ES
authors.lastname: Nassonova
authors.forename: Ema
authors.initials: E
authors.lastname: Chao
authors.forename: Thomas
authors.initials: T
authors.lastname: Cavalier-Smith
mesh_terms: D000656:Amoeba / Q000145:classification* / Q000166:cytology / Q000235:genetics* / Q000648:ultrastructure; D000818:Animals; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D046529:Microscopy, Electron, Transmission; D008858:Microscopy, Phase-Contrast; D008969:Molecular Sequence Data; D015388:Organelles / Q000648:ultrastructure; D010802:Phylogeny; D016053:RNA, Protozoan / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D016053:RNA, Protozoan; D012337:RNA, Ribosomal, 18S