title: A transcriptomic approach to ribbon worm systematics (nemertea): resolving the pilidiophora problem.
abstract: Resolving the deep relationships of ancient animal lineages has proven difficult using standard Sanger-sequencing approaches with a handful of markers. We thus reassess the relatively well-studied phylogeny of the phylum Nemertea (ribbon worms)-for which the targeted gene approaches had resolved many clades but had left key phylogenetic gaps-by using a phylogenomic approach using Illumina-based de novo assembled transcriptomes and automatic orthology prediction methods. The analysis of a concatenated data set of 2,779 genes (411,138 amino acids) with about 78% gene occupancy and a reduced version with 95% gene occupancy, under evolutionary models accounting or not for site-specific amino acid replacement patterns results in a well-supported phylogeny that recovers all major accepted nemertean clades with the monophyly of Heteronemertea, Hoplonemertea, Monostilifera, being well supported. Significantly, all the ambiguous patterns inferred from Sanger-based approaches were resolved, namely the monophyly of Palaeonemertea and Pilidiophora. By testing for possible conflict in the analyzed supermatrix, we observed that concatenation was the best solution, and the results of the analyses should settle prior debates on nemertean phylogeny. The study highlights the importance, feasibility, and completeness of Illumina-based phylogenomic data matrices.
authors.affiliation: Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University soniacsandrade@gmail.com.
authors.forename: Sónia C S
authors.initials: SC
authors.lastname: Andrade
authors.affiliation: Departamento de Entomologia, ESALQ-USP, Piracicaba, São Paulo, Brazil.
authors.forename: Horácio
authors.initials: H
authors.lastname: Montenegro
authors.affiliation: Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Malin
authors.initials: M
authors.lastname: Strand
authors.affiliation: Division of Science and Mathematics, University of Washington, Tacoma.
authors.forename: Megan L
authors.initials: ML
authors.lastname: Schwartz
authors.affiliation: Faculty of Science, Hokkaido University, Sapporo, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kajihara
authors.affiliation: Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC.
authors.forename: Jon L
authors.initials: JL
authors.lastname: Norenburg
authors.affiliation: Department of Biology, Virginia Commonwealth University.
authors.forename: James M
authors.initials: JM
authors.lastname: Turbeville
authors.affiliation: Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Sundberg
authors.affiliation: Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Giribet
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D005796:Genes; D007448:Invertebrates / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome
keywords: Illumina; Neonemertea; Palaeonemertea; Pilidiophora; concatenation; phylogeny; supermatrix