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Data from: A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes

<p>Alvinellid worms are a family of endemic and closely related species from deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, sister group to the Ampharetidae, occupy a wide range of ecological niches, some of which include the most thermotolerant marine animals described to date such as the Pompeii worm <em>Alvinella pompejana</em>, and other species living at much lower temperatures such as<em> Paralvinella grasslei </em>or <em>Paralvinella pandorae</em>. The phylogeny of this family has not yet been studied extensively. It is, however, a complex case with conflicting molecular phylogenies, the main question being the monophyletic or polyphyletic character of the genus Paralvinella. We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets. The study is based on the assembly of several hundred transcripts for 11 of the 14 species described or in description. The results obtained by the most popular phylogenetic inference models (gene concatenation and maximum likelihood, or coalescent-based methods from gene trees) are compared, and an attempt is made to use sequence insertion and deletion information to evaluate and strengthen our choice over the different phylogenies using a newly-developed maximum likelihood method. Although our study does not allow to definitively assert the phylogeny of the Alvinellidae (three species are still missing), we propose to support the initial hypothesis of the monophyly of the Paralvinella proposed by Desbruy`eres and Laubier on the basis of the morphology of the species, in which the species Paralvinella pandorae and Paralvinella unidentata are basal in the genus Paralvinella and grouped together within the subgenus nautalvinella. Following a clock calibration, the radiation of the Alvinellidae, dated between 55 and 78 Myr, took place very rapidly, resulting in high rates of incomplete lineage sorting between the first ancestors and probable gene transfers between the Alvinella, Nautalvinella and the rest of the Paralvinella lineages.</p>