title: Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic.
abstract: The phylum Ciliophora is one of the most broadly studied protozoan lineages. The era of molecular investigation has brought forth a major ongoing debate: is the subclass Peritrichia Stein, 1859 monophyletic? Numerous analyses mostly using the small subunit (SSU) rRNA gene have failed to recover the Mobilida and Sessilida, the two peritrich orders, as sister clades. Here we have sequenced five peritrich species - three sessilids and two mobilids. We constructed a supermatrix of 158 genes and 44,696 characters for 24 ciliate species, and as outgroup taxa, nine species from the Apicomplexa and four from the Dinophyceae. Our analyses using both maximum likelihood and Bayesian methods recover a monophyletic class Oligohymenophorea and two robust clades within it. The first clade is a monophyletic Peritrichia with the orders Sessilida and Mobilida maximally supported as sister clades. The second oligohymenophorean clade includes species of the subclasses Scuticociliatia and Hymenostomatia, which are sister clades. Our analyses resolve a long-standing debate in ciliate molecular phylogenetics and provide support for the classical view that the morphological features of the two peritrich orders Mobilida and Sessilida arose by descent from the same common ancestor and are not the result of convergence.
authors.affiliation: School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand. Electronic address: Gentekaki.ele@mfu.ac.th.
authors.forename: Eleni
authors.initials: E
authors.lastname: Gentekaki
authors.affiliation: Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada.
authors.forename: Martin
authors.initials: M
authors.lastname: Kolisko
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan 430072, PR China.
authors.forename: Yingchun
authors.initials: Y
authors.lastname: Gong
authors.affiliation: Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
authors.forename: Denis
authors.initials: D
authors.lastname: Lynn
mesh_terms: D005075:Biological Evolution; D016798:Ciliophora / Q000145:classification* / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D016802:Oligohymenophorea / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D012335:RNA, Ribosomal; D004247:DNA
keywords: Ciliophora; Mobilida; Peritrichia; Phylogenomics; Sessilida