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 Alvinella pompejana, and other species living at much lower temperatures such as Paralvinella grasslei or Paralvinella pandorae. 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.

Alvinellid species were collected during several oceanic cruises from 2004 to 2019 using the N/O L’Atalante and either the ROV Victor6000 or the manned submersible Nautile with the exception of Paralvinella palmiformis which was sampled during the jdfR cruise on Juan de Fuca. Alvinella caudata, Paralvinella grasslei and Paralvinella pandorae irlandei were collected from hydrothermal vents on the EPR à 2,550m depth during the Mescal Oeanographic cruise in 2010. Other alvinellid species and the vent terebellid were sampled on different vent sites of the western Pacific back-arc basins during the Chubacarc 2019 cruise with the tele-manipulated arm of the ROV Victor6000 and brought back to the surface in an insulated basket. Paralvinella hessleri was sampled from Fenway in the Manus basin, Paralvinella fijiensis from Big Papi (Manus Basin) and Tu’i Malila (Lau Basin), Paralvinella unidentata from Fenway (Manus Basin), Paralvinella sp. nov. from the volcano South Su (Manus Basin) and the vent terebellid Terebellidae gen. sp. (not yet described) at Snow Cap (Manus Basin). Finally, Paralvinella mira was sampled from the Wocan vent field in the northwest Indian Ocean on the Carlsberg Ridge by HOV Jialong during the DY38 cruise in March 2017 (Han et al., 2021). Melinna palmata and Neoamphitrite edwardsii, which are shallow-water species, were respectively sampled in the bay of Morlaix and Roscoff, France. Total RNA extraction from flash-frozen tissue were performed with Trizol. RNAseq libraries were produced at Genome Qu ́ebec following a polyA purification of mRNAs, andsequenced using the Novaseq technology.