title: Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data.
abstract: Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree.
authors.affiliation: Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil. Electronic address: noemi.mfernandes@gmail.com.
authors.forename: Noemi M
authors.initials: NM
authors.lastname: Fernandes
authors.affiliation: Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil; Laboratório de Biologia Molecular "Francisco Mauro Salzano", Instituto de Ciências Biológicas, Universidade Federal do Pará, Brazil.
authors.forename: Thiago da Silva
authors.initials: Tda S
authors.lastname: Paiva
authors.affiliation: Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Brazil.
authors.forename: Inácio D
authors.initials: ID
authors.lastname: da Silva-Neto
authors.affiliation: Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Schlegel
authors.affiliation: Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil. Electronic address: guerra@biologia.ufrj.br.
authors.forename: Carlos G
authors.initials: CG
authors.lastname: Schrago
mesh_terms: D001499:Bayes Theorem; D016798:Ciliophora / Q000145:classification* / Q000166:cytology* / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers; D010802:Phylogeny; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014404:Tubulin / Q000235:genetics
chemical_list: D004275:DNA, Ribosomal; D005819:Genetic Markers; D012337:RNA, Ribosomal, 18S; D014404:Tubulin; D003576:Electron Transport Complex IV
keywords: 18S-rDNA; 28S-rDNA gene; Alpha-tubulin; COI; Coalescence; Heterotrichea; ITS1-5.8S-ITS2 region