Phylogenomic analyses support the bifurcation of ciliates into two major clades that differ in properties of nuclear division

• Published in: Molecular phylogenetics and evolution 2014-01, Vol.70, p.240-243
• Main Authors: Gao, Feng, Katz, Laura A.
• Format: Article
• Language: English
• Subjects: Cell Nucleus Division; Ciliophora; Ciliophora - classification; Ciliophora - cytology; Ciliophora - genetics; DNA, Ribosomal - genetics; Genomics; Intramacronucleata; Likelihood Functions; Macronucleus; Phylogenomic analysis; Phylogeny; Postciliodesmatophora; Sequence Analysis, DNA
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2013.10.001

[Display omitted] •A taxon-rich phylogenomic strategy was used to assess the evolutionary relationships within ciliates.•537 taxa combined with a moderate number of proteins were accessed from GenBank and recently released transcriptome data.•Full data matrix as well as six submatrices were analyzed to assess the impact of taxon sampling and missing data.•The multigene phylogenies support the bifurcation of ciliates into two major clades as suggested by SSU-rDNA. Ciliates are a diverse assemblage of eukaryotes that have been the source of many discoveries including self-splicing RNAs, telomeres and trans-splicing. While analyses of ciliate morphology have given rise to robust hypotheses on relatively shallow level relationships, the deeper evolutionary history of ciliates is largely unknown. This is in part because studies to date have focused on only a single locus, small subunit ribosomal DNA (SSU-rDNA). In the present study, we use a taxon-rich strategy based on multiple loci from GenBank and recently completed transcriptomes to assess deep phylogenetic relationships among ciliates. Our phylogenomic data set includes up to 537 taxa, all of which have been sampled for SSU-rDNA and a subset of which have LSU-rDNA and up to 7 protein-coding sequences. Analyses of these data support the bifurcation of ciliates as suggested by SSU-rDNA, with one major clade defined by having somatic macronuclei that divide with intranuclear microtubules (Intramacronucleata) and the other clade containing lineages that either divide their macronuclei with microtubules external to the macronucleus or are unable to divide their macronuclei (Postciliodesmatophora). These multigene phylogenies provide a robust framework for interpreting the evolution of innovations across the ciliate tree of life.