title: A transcriptome approach to ecdysozoan phylogeny.
abstract: The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns.
authors.affiliation: Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany.
authors.forename: Janus
authors.initials: J
authors.lastname: Borner
authors.affiliation: Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Rehm
authors.affiliation: Zoology, Biological Institute, University of Stuttgart, Germany.
authors.forename: Ralph O
authors.initials: RO
authors.lastname: Schill
authors.affiliation: Department for Applied Bioinformatics, University of Frankfurt, Institute for Cell Biology and Neuroscience, Germany.
authors.forename: Ingo
authors.initials: I
authors.lastname: Ebersberger
authors.affiliation: Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany. Electronic address: thorsten.burmester@uni-hamburg.de.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Burmester
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D020224:Expressed Sequence Tags; D054643:INDEL Mutation; D007448:Invertebrates / Q000145:classification* / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Bayesian analyses; Ecdysozoa; Indel; Next generation sequencing; Phylogenomics