J. M. Alfaro-lucas, M. Shimabukuro, G. D. Ferreira, H. Kitazato, Y. Fujiwara et al., Bone-eating Osedax worms (Annelida: Siboglinidae) regulate biodiversity of deep-sea whale-fall communities, Deep Sea Research Part II: Topical Studies in Oceanography, pp.4-12, 2017.

F. Alvarez, T. M. Iliffe, and J. L. Villalobos, New species of the genus Typhlatya (Decapoda: Atyidae) from anchialine caves in Mexico, the Bahamas, and Honduras, Journal of Crustacean Biology, vol.25, issue.1, pp.81-94, 2005.

M. C. Alvaro, R. Barnich, M. V. Modica, A. Barco, M. Oliverio et al., Phylogenetic relationships and phylogeography in Antarctic symbiotic polyxenous polychaetes, XXXIII SCAR Biennial Meetings and Open Science Conference, 2014.

D. J. Amon, Bone-eating worms and wood-eating bivalves: characterising the ecology of deep-sea organic falls from multiple ocean basins, 2013.

S. T. Ayhong, J. K. Lowy, M. Alonso, R. N. Bamber, G. A. Boxshall et al., Crustacea. In Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness, pp.165-191, 2011.

L. Aznar-cormano, J. Brisset, T. Chan, L. Corbari, N. Puillandre et al., An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods, Genetica, vol.143, issue.2, pp.195-205, 2015.

J. A. Baeza, Observations on the sexual system and the natural history of the semi-terrestrial shrimp Merguia rhizophorae (Rathbun, 1900): Protandry in a semi-terrestrial shrimp, Invertebrate Biology, vol.129, issue.3, pp.266-276, 2010.

P. A. Bain, A. L. Gregg, and A. Kumar, De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water, BMC Genomics, issue.1, p.17, 2016.

M. Ballenghien, N. Faivre, and N. Galtier, Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions, BMC Biology, issue.1, p.15, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01815358

S. Bank, M. Sann, C. Mayer, K. Meusemann, A. Donath et al., Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae), Molecular Phylogenetics and Evolution, issue.116, pp.213-226, 2017.

,

V. Barriel and P. Tassy, Rooting with multiple outgroups: consensus versus parsimony, Cladistics, vol.14, issue.2, pp.193-200, 1998.

M. G. Bentley and A. A. Pacey, Physiological and environmental control of reproduction in polychaetes, 1992.

M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz et al., MITOS: Improved de novo metazoan mitochondrial genome annotation, Molecular Phylogenetics and Evolution, vol.69, issue.2, pp.313-319, 2013.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2120, 2014.

E. Bonnivard, O. Catrice, J. Ravaux, S. C. Brown, and D. Higuet, Survey of genome size in 28 hydrothermal vent species covering 10 families, Genome, vol.52, issue.6, pp.524-536, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00856109

J. Borner, P. Rehm, R. O. Schill, I. Ebersberger, and T. Burmester, A transcriptome approach to ecdysozoan phylogeny, Molecular Phylogenetics and Evolution, issue.80, pp.79-87, 2014.

C. E. Braby, G. W. Rouse, S. B. Johnson, W. J. Jones, and R. C. Vrijenhoek, Bathymetric and temporal variation among Osedax boneworms and associated megafauna on whale-falls in Monterey Bay, California. Deep Sea Research Part I: Oceanographic Research Papers, vol.54, issue.10, pp.1773-1791, 2007.

,

H. D. Bracken, A. Toon, D. L. Felder, J. W. Martin, M. Finley et al.,

K. A. Crandall, The decapod tree of life: compiling the data and moving toward a consensus of decapod evolution, Arthropod Systematics & Phylogeny, vol.67, issue.1, pp.99-116, 2009.

H. D. Bracken, S. De-grave, and D. L. Felder, Phylogeny of the infraorder Caridea based on mitochondrial and nuclear genes (Crustacea: Decapoda). Decapod crustacean phylogenetics, vol.28, pp.1-305, 2009.

H. D. Bracken, S. De-grave, A. Toon, D. L. Felder, and K. A. Crandall, Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda), Zoologica Scripta, vol.39, issue.2, pp.198-212, 2010.

M. J. Brasier, H. Wiklund, L. Neal, R. Jeffreys, K. Linse et al., DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes, Royal Society Open Science, issue.11, p.3, 2016.

T. A. Britayev, Life cycle of the symbiotic scaleworm Arctonoe vittata (Polychaeta: Polynoidae), Systematics, Biology and Morphology of World Polychaeta. Proceedings of the Second International Polychaeta Conference. Ophelia Supplement, vol.5, pp.305-312, 1991.

T. A. Britayev, J. Gil, A. Altuna, M. Calvo, and D. Martin, New symbiotic associations involving polynoids (Polychaeta, Polynoidae) from Atlantic waters, with redescriptions of Parahololepidella greeffi (Augener, 1918) and Gorgoniapolynoe caeciliae (Fauvel, 1913). Memoirs of the National Museum Victoria 71, pp.27-43, 2014.

A. Brösing, S. Richter, and G. Scholtz, Phylogenetic analysis of the Brachyura (Crustacea, Decapoda) based on characters of the foregut with establishment of a new taxon, Journal of Zoological Systematics and Evolutionary Research, vol.45, issue.1, pp.20-32, 2007.

J. S. Buckeridge, A new coral inhabiting barnacle of the genus Chionelasmus (Cirripedia, Balanomorpha) from, vol.20, pp.167-176, 1998.

F. M. Calabrese, D. L. Balacco, R. Preste, M. A. Diroma, R. Forino et al., NumtS colonization in mammalian genomes, Scientific Reports, vol.7, issue.1, 2017.

C. M. Carr, S. M. Hardy, T. M. Brown, T. A. Macdonald, and P. D. Hebert, A Tri-Oceanic Perspective: DNA Barcoding Reveals Geographic Structure and Cryptic Diversity in Canadian Polychaetes, PLoS ONE, vol.6, issue.7, 2011.

C. M. Cavanaugh, S. L. Gardiner, M. L. Jones, H. W. Jannasch, and J. B. Waterbury, Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts, Science, pp.340-342, 1981.

D. J. Colgan, W. F. Ponder, E. Beacham, and J. M. Macaranas, Molecular phylogenetic studies of Gastropoda based on six gene segments representing coding or non-coding and mitochondrial or nuclear DNA, Molluscan Research, vol.23, pp.123-148, 2003.

F. A. Chace and D. E. Brown, A new polychelate shrimp from the Great Barrier Reef of Australia and its bearing on the family Bresiliidae (Crustacea: Decapoda: Caridea), Proceedings of the Biological Society of Washington, vol.91, issue.3, pp.756-766, 1978.

F. A. Chace, On the classification of the Caridea (Decapoda), Crustaceana, vol.63, issue.1, pp.70-80, 1992.

B. K. Chan, L. Corbari, P. A. Rodriguez-moreno, and L. M. Tsang, Molecular phylogeny of the lower acorn barnacle families (Bathylasmatidae, Chionelasmatidae, Pachylasmatidae and Waikalasmatidae) (Cirripedia: Balanomorpha) with evidence for revisions in family classification, Zoological Journal of the Linnean Society, vol.180, issue.3, pp.542-555, 2017.

T. Chan, H. C. Lei, C. P. Li, and K. H. Chu, Phylogenetic analysis using rDNA reveals polyphyly of Oplophoridae (Decapoda: Caridea), Invertebrate Systematics, vol.24, issue.2, p.172, 2010.

P. Chevaldonné, D. Jollivet, R. A. Feldman, D. Desbruyères, R. A. Lutz et al., Commensal scaleworms of the genus Branchipolynoe (Polychaeta: Polynoidae) at deep-sea hydrothermal vents and cold seeps, Cahier de Bioogie Marine, vol.39, issue.3, pp.347-350, 1998.

M. L. Christoffersen, Phylogenetic relationships between Oplophoridae, Atyidae, Pasiphaeidae, Alvinocarididae fam. n., Bresiliidae, Psalidopodidae and Disciadidae (Crustacea Caridea Atyoidea), Boletim de Zoologia, vol.10, issue.10, pp.273-281, 1986.

A. Clarke, Egg size and egg composition in polar shrimps (Caridea; Decapoda), Journal of Experimental Marine Biology and Ecology, vol.168, issue.2, pp.189-203, 1993.

K. Clarke, Y. Yang, R. Marsh, L. Xie, and Z. K. &-k, Comparative analysis of de novo transcriptome assembly, Science China Life Sciences, vol.56, issue.2, pp.156-162, 2013.

A. Colaço, F. Dehairs, and D. Desbruyères, Nutritional relations of deep-sea hydrothermal fields at the Mid-Atlantic Ridge: a stable isotope approach, Deep Sea Research Part I: Oceanographic Research Papers, vol.49, pp.395-412, 2002.

J. B. Corliss, J. Dymond, L. I. Gordon, J. M. Edmond, R. P. Von-herzen et al., Submarine thermal sprirngs on the galapagos rift, Science, issue.4385, pp.1073-1083, 1979.

R. Von-cosel and K. Olu, Gigantism in Mytilidae. A new Bathymodiolus from cold seep areas on the Barbados accretionary prism. Comptes Rendus de l'Académie des Sciences-Series III-Sciences de la Vie, vol.321, pp.655-663, 1998.

C. D. D'acoz and S. De-grave, A new genus and species of large-bodied caridean shrimp from the Crozet Islands, Southern Ocean (Crustacea, Decapoda, Lipkiidae) with a checklist of Antarctic and sub-Antarctic shrimps, Zootaxa, vol.4392, issue.2, p.201, 2018.

H. Dahms, L. Tseng, and J. Hwang, Are vent crab behavioral preferences adaptations for habitat choice?, PloS one, vol.12, issue.9, p.182649, 2017.

J. M. Daly, The maturation and breeding biology of Harmothoe imbricata (Polychaeta: Polynoidae), Marine Biology, vol.12, issue.1, pp.53-66, 1972.

S. De-grave and M. K. Moosa, A new species of the enigmatic shrimp genus Pseudocheles (Decapoda: Bresiliidae) from Sulawesi (Indonesia), with the designation of a new family Pseudochelidae, Crustacean Research, vol.33, pp.1-9, 2004.

S. De-grave, Y. Cai, and A. Anker, Global diversity of shrimps (Crustacea: Decapoda: Caridea) in freshwater, Hydrobiologia, vol.595, issue.1, pp.287-293, 2008.

N. De-grave, D. Pentcheff, and S. T. Ahyong, A classification of living and fossil genera of decapod crustaceans, Raffles Bulletin of Zoology, pp.1-109, 2009.

S. De-grave, T. Y. Chan, and K. H. Chu, On the Systematic Position of Galatheacaris abyssalis (Decapoda: Galatheacaridoidea), Journal of Crustacean Biology, vol.30, issue.3, pp.521-527, 2010.

S. De-grave and C. H. Fransen, Carideorum catalogus: the recent species of the dendrobranchiate, stenopodidean, procarididean and caridean shrimps (Crustacea: Decapoda), Zoologische Mededelingen, issue.9, 2011.

S. De-grave and L. Y. Goulding, Comparative morphology of the pereiopod 1 carpo-propodal (P1-CP) antennal flagellar grooming brush in caridean shrimps (Crustacea, Decapoda), Zoologischer Anzeiger -A Journal of Comparative Zoology, vol.250, issue.4, pp.280-301, 2011.

S. De-grave, C. P. Li, L. M. Tsang, K. H. Chu, and T. Chan, Unweaving hippolytoid systematics (Crustacea, Decapoda, Hippolytidae): resurrection of several families, Zoologica Scripta, vol.43, issue.5, pp.496-507, 2014.

D. Desbruyères, A. M. Alayse-danet, and S. Ohta, Deep-sea hydrothermal communities in Southwestern Pacific back-arc basins (the North Fiji and Lau Basins): Composition, microdistribution and food web, Marine Geology, vol.116, issue.1-2, pp.227-242, 1994.

D. Desbruyères, M. Segonzac, and M. Bright, Handbook of Deep-Sea Hydrothermal Vent Fauna (Second compl. rev. ed), 2006.

R. E. Ditter, A. M. Goebel, and R. B. Erdman, First Record of the anchialine shrimp Parhippolyte sterreri (Decapoda, Barbouriidae) from San Salvador Island, Bahamas, with observations on Barbouria cubensis, Marine Biodiversity Records, vol.8, 2015.

D. Reis, M. Thawornwattana, Y. Angelis, K. Telford, M. J. Donoghue et al., Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales, Current Biology, vol.25, issue.22, pp.2939-2950, 2015.

J. J. Doyle and J. L. Doyle, A rapid procedure for DNA purification from small quantities of fresh leaf tissue, Phytochemical Bulletin, vol.19, pp.11-15, 1987.

N. Dubilier, C. Bergin, and C. Lott, Symbiotic diversity in marine animals: the art of harnessing chemosynthesis, Nature Reviews Microbiology, vol.6, issue.10, pp.725-740, 2008.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.

K. Fauchald, The polychaete worms. Definitions and keys to the orders, families and genera, Natural History Museum of Los Angeles Country, vol.28, pp.1-190, 1977.

H. Felbeck, Chemoautotrophic potential of the hydrothermal vent tube worm, Riftia pachyptila Jones (Vestimentifera). Science, 213(4505), pp.336-338, 1981.

O. Folmer, M. Blak, W. Hoej, and R. Vrijenhoek, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Molecular Marine Biology and Biotechnology, vol.3, issue.5, pp.294-299, 1994.

E. Forbes, Report on the Mollusca and Radiata of the Aegean Sea, and on their distribution, considered as bearing on geology, Report of the British Association for the Avancement of Science for 1843, pp.129-193, 1844.

J. Forest, Un groupement injustifie: la superfamille des Bresilioidea. Remarques critiques sur les statuts des familles réunies sous ce nom (Crustacea Decapoda Caridea), Bulletin de Museum National d'Histoire Naturelle, issue.3, pp.869-888, 1977.

J. Forest and P. Cals, Une deuxième espèce du genre Bresilia Caïman, B. corsicana sp. nov. Comparaison avec B. atlantica Caïman (Crustacea Decapoda Bresiliidae), pp.549-565, 1977.

H. M. Fox, Haemoglobin in crustacea, Nature, vol.164, issue.4158, p.59, 1949.

C. W. Fuller, L. R. Middendorf, S. A. Benner, G. M. Church, T. Harris et al., The challenges of sequencing by synthesis, Nature Biotechnology, vol.27, issue.11, pp.1013-1023, 2009.

,

S. M. Gaudron, S. Lefebvre, A. N. Jorge, F. Gaill, and F. Pradillon, Spatial and temporal variations in food web structure from newly-opened habitat at hydrothermal vents, Marine environmental research, issue.77, pp.129-140, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00806893

S. M. Gaudron, S. Hourdez, and K. Olu, Aspects on gametogenesis, fertilization and embryogenesis of two deep-sea polychaetes from Eastern Atlantic cold seeps. Deep Sea Research Part I: Oceanographic Research Papers, pp.59-68, 2017.

E. Gaya, S. Fernández-brime, R. Vargas, R. F. Lachlan, C. Gueidan et al., The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift, Proceedings of the National Academy of Sciences, vol.112, issue.37, pp.11600-11605, 2015.

G. Consortium, J. C. Havird, and S. R. Santos, Genomic Resources Notes accepted 1, vol.14, pp.1322-1322, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02630738

A. G. Glover, E. Goetze, T. G. Dahlgren, and C. R. Smith, Morphology, reproductive biology and genetic structure of the whale-fall and hydrothermal vent specialist, Bathykurila guaymasensis Pettibone, 1989 (Annelida: Polynoidae), Marine Ecology, issue.26, pp.223-234, 2005.

S. K. Goffredi, V. J. Orphan, G. W. Rouse, L. Jahnke, T. Embaye et al., Evolutionary innovation: a bone-eating marine symbiosis, Environmental Microbiology, vol.7, issue.9, pp.1369-1378, 2005.

S. K. Goffredi, S. Johnson, V. Tunnicliffe, D. Caress, D. Clague et al., Hydrothermal vent fields discovered in the southern Gulf of California clarify role of habitat in augmenting regional diversity, Proceedings of the Royal Society B: Biological Sciences, vol.284, 1859.

B. C. Gonzalez, A. Martínez, E. Borda, T. M. Iliffe, D. Eibye-jacobsen et al., Phylogeny and systematics of Aphroditiformia, Cladistics, vol.34, issue.3, pp.225-259, 2017.

B. C. Gonzalez, H. C. Petersen, M. Di-domenico, A. Martínez, M. Armenteros et al.,

K. &-worsaae, Phylogeny and biogeography of the scaleless scale worm Pisione (Sigalionidae, Annelida), Ecology and evolution, vol.7, issue.9, pp.2894-2915, 2017.

B. C. Gonzalez, K. Worsaae, D. Fontaneto, and A. Martínez, Anophthalmia and elongation of body appendages in cave scale worms (Annelida: Aphroditiformia), Zoologica Scripta, vol.47, issue.1, pp.106-121, 2017.

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.29, issue.7, pp.644-652, 2011.

T. Guggolz, L. Lins, K. Meißner, and A. Brandt, Biodiversity and distribution of polynoid and spionid polychaetes (Annelida) in the Vema Fracture Zone, tropical North Atlantic, Deep Sea Research Part II: Topical Studies in Oceanography, pp.54-63, 2018.

D. Guinot, L. A. Hurtado, and R. Vrijenhoek, New genus and species of brachyuran crab from the southern East Pacific Rise (Crustacea Decapoda Brachyura Bythograeidae), Comptes Rendu des Biologie, vol.325, issue.11, pp.1143-1152, 2002.

D. Guinot, M. Tavares, and P. Castro, Significance of the sexual openings and supplementary structures on the phylogeny of brachyuran crabs (Crustacea, Decapoda, Brachyura), with new nomina for higher-ranked podotreme taxa, Zootaxa, vol.3665, issue.1, 2013.

D. Guinot and M. Segonzac, A review of the brachyuran deep-sea vent community of the western Pacific, with two new species of Austinograea Hessler & Martin, 1989 (Crustacea, Decapoda, Brachyura, Bythograeidae) from the Lau and North Fiji Back-Arc Basins, Zoosystema, vol.40, issue.1, pp.1-36, 2018.

C. W. Hart and R. B. Manning, Two New Shrimps (Procarididae and Agostocarididae, New Family) from Marine Caves of the Western North Atlantic, Journal of Crustacean Biology, vol.6, issue.3, p.408, 1986.

J. C. Havird and S. R. Santos, Developmental Transcriptomics of the Hawaiian Anchialine Shrimp Halocaridina rubra Holthuis, Crustacea: Atyidae). Integrative and Comparative Biology, vol.56, pp.1170-1182, 1963.

P. D. Hebert, A. Cywinska, and S. L. Ball, Biological identifications through DNA barcodes, Proceedings of the Royal Society of London B: Biological Sciences, vol.270, pp.313-321, 1512.

S. Herrera, H. Watanabe, and T. M. Shank, Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents, Molecular Ecology, vol.24, issue.3, pp.673-689, 2015.

D. M. Hillis and M. T. Dixon, Ribosomal DNA: molecular evolution and phylogenetic inference. The Quarterly review of biology, vol.66, pp.411-453, 1991.

D. D. Hinsinger, R. Debruyne, M. Thomas, G. P. Denys, M. Mennesson et al., Fishing for barcodes in the Torrent: from COI to complete mitogenomes on NGS platforms, DNA Barcodes, issue.1, p.3, 2015.
URL : https://hal.archives-ouvertes.fr/mnhn-02309917

P. W. Holland, A. Hacker, and N. A. Williams, A molecular analysis of the phylogenetic affinities of Saccoglossus cambrensis Brambell & Cole (Hemichordata), Philosophical Transactions of the Royal Society B, vol.332, pp.185-189, 1264.

S. Hourdez and C. Jouin-toulmond, Functional anatomy of the respiratory system of Branchipolynoe species (Polychaeta, Polynoidae), commensal with Bathymodiolus species (Bivalvia, Mytilidae) from deep-sea hydrothermal vents, Zoomorphology, vol.118, issue.4, pp.225-233, 1998.

S. Hourdez and F. H. Lallier, Adaptations to hypoxia in hydrothermal-vent and cold-seep invertebrates, Reviews in Environmental Science and Bio/Technology, vol.6, issue.1-3, pp.143-159, 2007.

S. Hourdez, F. H. Lallier, V. Martin-jézéquel, R. E. Weber, and A. Toulmond, Characterization and functional properties of the extracellular coelomic hemoglobins from the deep-sea, hydrothermal vent scaleworm Branchipolynoe symmytilida, Proteins: Structure, Function, and Bioinformatics, vol.34, issue.4, pp.435-442, 1999.

S. Hourdez, J. Lamontagne, P. Peterson, R. Weber, and C. Fisher, Hemoglobin from a deep-sea hydrothermal-vent copepod, The Biological Bulletin, vol.199, issue.2, pp.95-99, 2000.

S. Hourdez and R. Weber, Molecular and functional adaptations in deep-sea hemoglobins, Journal of Inorganic Biochemistry, vol.99, issue.1, pp.130-141, 2005.

S. Hourdez, L. A. Frederick, A. Schernecke, and C. R. Fisher, Functional respiratory anatomy of a deep-sea orbiniid polychaete from the Brine Pool NR-1 in the Gulf of Mexico, Invertebrate Biology, vol.120, issue.1, pp.29-40, 2001.

H. Hourdez, Life at extremes: Environments, organisms, and strategies for survival, pp.438-453, 2012.

X. Huang and A. Madan, CAP3: A DNA sequence assembly program, Genome research, vol.9, issue.9, pp.868-877, 1999.

A. F. Hugall, T. D. O'hara, S. Hunjan, R. Nilsen, and A. Moussalli, An exon-capture system for the entire class Ophiuroidea, Molecular biology and evolution, vol.33, issue.1, pp.281-294, 2015.

C. A. Hutchison, DNA sequencing: bench to bedside and beyond, Nucleic Acids Research, vol.35, issue.18, pp.6227-6237, 2007.

M. Imajima, Deep-sea benthic polychaetous annelids from around Nansei Islands, National Science Museum Monographs, issue.29, pp.37-99, 2005.

P. Ioannidis, F. A. Simao, R. M. Waterhouse, M. Manni, M. Seppey et al., Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders, Genome Biology and Evolution, 2017.

M. L. Jaramillo, F. Guzman, C. L. Paese, R. Margis, E. M. Nazari et al., Exploring developmental gene toolkit and associated pathways in a potential new model crustacean using transcriptomic analysis, Development Genes and Evolution, vol.226, issue.5, pp.325-337, 2016.

M. S. Jeng, N. K. Ng, and P. K. Ng, Feeding behaviour: hydrothermal vent crabs feast on sea 'snow', Nature, vol.432, issue.7020, p.969, 2004.

D. Jollivet, A. Empis, M. C. Baker, S. Hourdez, T. Comtet et al., Reproductive biology, sexual dimorphism, and population structure of the deep sea hydrothermal vent scale-worm, Branchipolynoe seepensis (Polychaeta: Polynoidae), Journal of the Marine Biological Association of the United Kingdom, vol.80, issue.1, pp.55-68, 2000.

C. Jouin-toulmond, F. Zal, and S. Hourdez, Genital apparatus and ultrastructure of the spermatozoa in Alvinella pompejana (Annelida: Polychaeta), Cahiers de Biologie Marine, issue.2, 1997.

M. L. Jones, Riftia pachyptila, new genus, new species, the vestimentiferan from the Galapagos Rift geothermal vents (Pogonophora), Proceedings of the National Academy of Sciences, pp.1295-1313, 1981.

M. L. Jones, On the Vestimentifera, new phylum: six new species, and other taxa, from hydrothermal vents and elsewhere, Biol Soc Wash Bull, issue.6, pp.117-158, 1985.

M. L. Jones and S. L. Gardiner, Evidence for a transient digestive tract in Vestimentifera, Proc. Biol. Soc. Wash, issue.101, pp.423-433, 1988.

P. A. Jumars, K. M. Dorgan, and S. M. Lindsay, Diet of worms emended: an update of polychaete feeding guilds, Annual Review of Marine Science, vol.7, issue.1, pp.497-520, 2015.

R. Kawahara-miki, K. Wada, N. Azuma, and S. Chiba, Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing, PLoS ONE, vol.6, issue.10, 2011.

M. Kearse, R. Moir, A. Wilson, S. Stones-havas, M. Cheung et al., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, issue.12, pp.1647-1649, 2012.

V. C. Kenk, B. Wilson, and R. , A new mussel (Bivalvia, Mytilidae) from hydrothermal vents in the Galapagos Rift zone, Malacologia, issue.26, pp.253-271, 1985.

N. Kenny, Y. Sin, X. Shen, Q. Zhe, W. Wang et al., Genomic Sequence and Experimental Tractability of a New Decapod Shrimp Model, Neocaridina denticulata, Marine Drugs, vol.12, issue.3, pp.1419-1437, 2014.

S. Kim, K. Y. Lee, and S. Ju, Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding, Molecular Ecology Resources, vol.13, issue.5, pp.781-787, 2013.

S. Kim, H. S. Kim, and S. Ju, Mitochondrial genome of the hydrothermal vent crab Austinograea alayseae (Crustacea: Bythograeidae): genetic differences between individuals from Tofua Arc and Manus Basin, Mitochondrial DNA, vol.25, issue.4, pp.251-252, 2014.

S. Kim, J. Moon, and S. Ju, Complete mitochondrial genome of the blind vent crab Gandalfus puia (Crustacea: Bythograeidae) from the Tonga Arc, Mitochondrial DNA, pp.1-2, 2015.

,

S. Kojima, T. Hashimoto, M. Hasegawa, S. Murata, S. Ohta et al., Close phylogenetic relationship between vestimentifera (tube worms) and annelida revealed by the amino acid sequence of elongation factor-l?, Journal of Molecular Evolution, vol.37, issue.1, pp.66-70, 1993.

T. Komai, L. Menot, and M. Segonzac, New records of caridean shrimp (Crustacea: Decapoda) from hydrothermally influenced fields off Futuna Island, Southwest Pacific, with description of a new species assigned to the genus Alvinocaridinides Komai &amp, 2016.

C. , Alvinocarididae), Zootaxa, vol.4098, issue.2, p.298

T. Komai and M. Segonzac, Review of the hydrothermal vent shrimp genus Mirocaris, redescription of M. fortunata and reassessment of the taxonomic status of the family Alvinocarididae (Crustacea: Decapoda: Caridea), Cahiers de Biologie Marine, vol.44, issue.2, pp.199-215, 2003.

P. K. Koonjul, W. F. Brandt, G. G. Lindsey, and J. M. Farrant, Inclusion of polyvinylpyrrolidone in the polymerase chain reaction reverses the inhibitory effects of polyphenolic contamination of RNA, Nucleic acids research, vol.27, issue.3, pp.915-916, 1999.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.

V. Leignel, M. Cibois, B. Moreau, and B. Chénais, Identification of new subgroup of HSP70 in Bythograeidae (hydrothermal crabs) and Xanthidae, Gene, vol.396, issue.1, pp.84-92, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02050286

V. Leignel, L. A. Hurtado, and M. Segonzac, Ecology, adaptation and acclimatisation mechanisms of Bythograeidae Williams, 1980, a unique endemic hydrothermal vent crabs family: current state of knowledge. Marine and Freshwater Research, vol.69, p.1, 2018.

B. Li and C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC bioinformatics, vol.12, issue.1, p.323, 2011.

C. P. Li, S. De-grave, T. Chan, H. C. Lei, and K. H. Chu, Molecular systematics of caridean shrimps based on five nuclear genes: Implications for superfamily classification, Zoologischer Anzeiger -A Journal of Comparative Zoology, vol.250, issue.4, pp.270-279, 2011.

M. Li, R. Schroeder, A. Ko, and M. Stoneking, Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs, Nucleic Acids Research, vol.40, issue.18, p.137, 2012.

Y. Li, K. M. Kocot, N. V. Whelan, S. R. Santos, D. S. Waits et al., Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods, Zoologica Scripta, vol.46, issue.2, pp.200-213, 2017.

Y. Liao, S. De-grave, T. W. Ho, B. H. Ip, L. M. Tsang et al., Molecular phylogeny of Pasiphaeidae (Crustacea, Decapoda, Caridea) reveals systematic incongruence of the current classification, Molecular Phylogenetics and Evolution, vol.115, pp.171-180, 2017.

C. R. Lister, On the thermal balance of a mid-ocean ridge, Geophysical Journal International, vol.26, issue.5, pp.515-535, 1972.

S. Liu, X. Wang, L. Xie, M. Tan, Z. Li et al., Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis, Molecular Ecology Resources, vol.16, issue.2, pp.470-479, 2016.

P. Lonsdale, Clustering of suspension-feeding macrobenthos near abyssal hydrothermal vents at oceanic spreading centers, Deep-Sea Research, vol.24, issue.9, pp.857-863, 1977.

J. V. Lopez, N. Yuhki, R. Masuda, W. Modi, and S. J. Brien, Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat, Journal of Molecular Evolution, vol.39, issue.2, pp.174-190, 1994.

J. Lorion, B. Buge, C. Cruaud, and S. Samadi, New insights into diversity and evolution of deep-sea Mytilidae (Mollusca: Bivalvia), Molecular Phylogenetics and Evolution, vol.57, issue.1, pp.71-83, 2010.

,

K. Katoh, K. Misawa, K. I. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic acids research, vol.30, issue.14, pp.3059-3066, 2002.

P. Mandon, L. Aznar-cormano, S. Hourdez, and S. Samadi, Assembly of the mitochondrial genome of the hydrothermal vent crab Segonzacia mesatlantica and detection of potential nuclear pseudogenes, Mitochondrial DNA Part B, vol.2, issue.1, pp.291-293, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01550571

G. Marçais and C. Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, vol.27, issue.6, pp.764-770, 2011.

J. Marcus and S. Hourdez, A new species of scale-worm (Polychaeta: Polynoidae) from Axial Volcano, Proceedings of the Biological Society of Washington, vol.115, issue.2, pp.341-349, 2002.

E. J. Márquez, J. C. Hurtado-alarcón, J. P. Isaza, J. F. Alzate, and N. H. Campos, Mitochondrial genome of the Caribbean king crab Damithrax spinosissimus (Lamarck, 1818) (Decapoda: Majidae). Mitochondrial DNA, pp.1-2, 2014.

D. Martin and T. Britayev, Symbiotic Polychaetes: Review of known species, Oceanography and Marine Biology: An Annual Review, vol.36, issue.1, pp.217-340, 1998.

J. W. Martin and T. A. Haney, Decapod crustaceans from hydrothermal vents and cold seeps: a review through, Zoological Journal of the Linnean Society, vol.145, issue.4, pp.445-522, 2005.

J. W. Martin, R. Hessler, and R. , Chorocaris vandoverae, a new genus and species of hydrothermal vent shrimp (Crustacea, Decapoda, Bresiliidae), Contributions in Science, issue.417, pp.1-11, 1990.

J. W. Martin and J. C. Christiansen, A new species of the shrimp genus Chorocaris Martin & Hessler, 1990 (Crustacea: Decapoda: Bresiliidae) from hydrothermal vent fields along the Mid-Atlantic Ridge, Proceedings -Biological Society of Washington, issue.108, pp.220-220, 1995.

M. Mateos, L. A. Hurtado, C. A. Santamaria, V. Leignel, and D. Guinot, Molecular Systematics of the Deep-Sea Hydrothermal Vent Endemic Brachyuran Family Bythograeidae: A Comparison of Three Bayesian Species Tree Methods, PLoS ONE, vol.7, issue.3, 2012.

A. G. Mcarthur and B. F. Koop, Partial 28S rDNA sequences and the antiquity of hydrothermal vent endemic gastropods, Molecular Phylogenetics and Evolution, vol.13, issue.2, pp.255-274, 1999.

A. G. Mcarthur and V. Tunnicliffe, Relics and antiquity revisited in the modern vent fauna, Geological Society, vol.148, issue.1, pp.271-291, 1998.

L. M. Mejía-ortíz, G. Yañez, and M. López-mejía, Anchialocarididae, a new family of anchialine decapods and a new species of the genus Agostocaris from Cozumel Island, Crustaceana, vol.90, issue.4, pp.381-398, 2017.

M. L. Metzker, Emerging technologies in DNA sequencing, Genome research, vol.15, issue.12, pp.1767-1776, 2005.

M. A. Miller, W. Pfeiffer, and T. Schwartz, Creating the CIPRES Science Gateway for inference of large phylogenetic trees, Gateway Computing Environments Workshop (GCE), pp.1-8, 2010.

W. Miller, D. I. Drautz, J. E. Janecka, A. M. Lesk, A. Ratan et al., The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus), Genome Research, vol.19, issue.2, pp.213-220, 2008.

T. Miura, Two new branchiate scale worms (Polynoidae: Polychaeta) from the hydrothermal vent of the Okinawa Trough and the volcanic seamount off Chichijima Island, Proceedings of the Biological Society of Washington, issue.104, pp.166-174, 1991.

T. Miura, Two new scale-worms (Polynoidae: polychaeta) from the Lau back-arc and North Fiji basins, Proceedings of the Biological Society of Washington, issue.107, pp.532-543, 1994.

J. Miyazaki, L. Martins, O. De, Y. Fujita, H. Matsumoto et al., Evolutionary Process of Deep-Sea Bathymodiolus Mussels, PLoS ONE, vol.5, issue.4, 2010.

Y. Moalic, D. Desbruyères, C. M. Duarte, A. F. Rozenfeld, C. Bachraty et al., Biogeography Revisited with Network Theory: Retracing the History of Hydrothermal Vent Communities, Systematic Biology, issue.1, p.127, 2011.

J. Moreton, A. Izquierdo, and R. D. Emes, Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes, Frontiers in Genetics, issue.6, 2016.

A. I. Muir, Generic Characters in the Polynoinae (Annelida, Polychaeta), with Notes on the Higher Classification of Scale-worms (Aphroditacea), British Museum (Natural History), 1982.

L. Neal, H. Wiklund, A. I. Muir, K. Linse, and A. G. Glover, The identity of juvenile Polynoidae (Annelida) in the Southern Ocean revealed by DNA taxonomy, with notes on the status of Herdmanella gracilis Ehlers sensu Augener. Memoirs of Museum Victoria, pp.203-216, 2014.

D. C. Nelson, K. D. Hagen, and D. B. Edwards, The gill symbiont of the hydrothermal vent mussel Bathymodiolus thermophilus is a psychrophilic, chemoautotrophic, sulfur bacterium, Marine Biology, vol.121, issue.3, pp.487-495, 1995.

W. A. Newman, The abyssal hydrothermal vent invertebrate fauna. A glimpse of antiquity?, Bulletin of the Biological Society of Washington, issue.6, pp.231-242, 1985.

P. K. Ng, D. Guinot, and P. J. Davie, Systema Brachyurorum: Part I. An annotated checklist of extant brachyuran crabs of the world, The Raffles Bulletin of Zoology, vol.17, issue.1, pp.1-286, 2008.

E. Norlinder, A. Nygren, H. Wiklund, and F. Pleijel, Phylogeny of scale-worms (Aphroditiformia, Annelida), assessed from 18SrRNA, 28SrRNA, 16SrRNA, mitochondrial cytochrome c oxidase subunit I (COI), and morphology, Molecular Phylogenetics and Evolution, vol.65, issue.2, pp.490-500, 2012.

,

A. Nørrevang, The position of Pogonophora in the phylogenetic system, Journal of Zoological Systematics and Evolutionary Research, vol.8, issue.1, pp.161-172, 1970.

V. Nye, J. Copley, and S. Plouviez, A new species of Rimicaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vent fields on the Mid-Cayman Spreading Centre, Caribbean, Journal of the Marine Biological Association of the United Kingdom, vol.92, issue.5, pp.1057-1072, 2012.

T. D. O'hara, A. F. Hugall, B. Thuy, and A. Moussalli, Phylogenomic Resolution of the Class Ophiuroidea Unlocks a Global Microfossil Record, Current Biology, vol.24, issue.16, pp.1874-1879, 2014.

S. R. Palumbi, Nucleic acids II: the polymerase chain reaction. Molecular systematics, pp.205-247, 1996.

E. Pante, L. Corbari, J. Thubaut, T. Y. Chan, R. Mana et al., Exploration of the deepsea fauna of Papua New Guinea, Oceanography, vol.25, issue.3, pp.214-225, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00873493

E. Pante, J. Abdelkrim, A. Viricel, D. Gey, S. C. France et al., Use of RAD sequencing for delimiting species, Heredity, vol.114, issue.5, p.450, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01064545

A. Perina, A. M. González-tizón, I. F. Meilán, and A. Martínez-lage, De novo transcriptome assembly of shrimp Palaemon serratus, Genomics Data, issue.11, pp.89-91, 2017.

B. Pernet, Reproduction and development of three symbiotic scale worms (Polychaeta: Polynoidae), Invertebrate Biology, vol.119, issue.1, pp.45-57, 2000.

M. H. Pettibone, Revision of the Genus Macellicephala McIntosh and the Subfamily Macellicephalinae Hartmann-SchrAder (Polychaeta: Polynoidae), 1976.

M. H. Pettibone, A new scale worm (Polychaeta: Polynoidae) from the hydrothermal rift-area off western Mexico at 21 N, Proceedings of the Biological Society of Washington, vol.96, issue.3, pp.392-399, 1983.

M. H. Pettibone, A new scale-worm commensal with deep-sea mussels on the Galapagos hydrothermal vent (Polychaeta: Polynoidae), Proceedings of the Biological Society of Washington, pp.226-239, 1984.

M. H. Pettibone, An additional new scale worm (Polychaeta: Polynoidae) from the hydrothermal rift area off western Mexico at 21 N, 1985.

M. H. Pettibone, Additional branchiate scale-worms (Polychaeta: Polynoidae) from Galapagos hydrothermal vent and rift-area off Western Mexico at 21 N, 1985.

M. H. Pettibone, Review of the Iphioninae (Polychaeta: Polynoidae) and Revision of Iphione Cimex Quatrefages, Gattyana Deludens Fauvel and Harmothoe Iphionelloides Johnson (Harmothoinae), 1986.

M. H. Pettibone, Polynoidae and Sigalionidae (Polychaeta) from the Guaymas Basin, with descriptions of two new species, and additional records from hydrothermal vents of the Galapagos Rift, 21 N, and seep-sites in the Gulf of Mexico, 1989.

M. H. Pettibone, Polynoid polychaetes associated with a whale skeleton in the bathyal Santa Catalina Basin, Proceedings of the Biological Society of Washington, vol.106, issue.4, pp.678-688, 1993.

F. Pleijel, T. G. Dahlgren, and G. W. Rouse, Progress in systematics: from Siboglinidae to Pogonophora and Vestimentifera and back to Siboglinidae, Comptes Rendus Biologies, vol.332, issue.2-3, pp.140-148, 2009.

F. Pleijel, U. Jondelius, E. Norlinder, A. Nygren, B. Oxelman et al., Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies, Molecular Phylogenetics and Evolution, vol.48, issue.1, pp.369-371, 2008.

S. Plouviez, A. Jacobson, M. Wu, and C. L. Van-dover, Characterization of vent fauna at the Mid-Cayman Spreading Center, Deep Sea Research Part I: Oceanographic Research Papers, pp.124-133, 2015.

M. Portail, K. Olu, E. Escobar-briones, J. C. Caprais, L. Menot et al., Comparative study of vent and seep macrofaunal communities in the Guaymas Basin, Biogeosciences, vol.12, issue.18, pp.5455-5479, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02559412

J. Projecto-garcia, N. Zorn, D. Jollivet, S. W. Schaeffer, F. H. Lallier et al., Origin and Evolution of the Unique Tetra-Domain Hemoglobin from the Hydrothermal Vent Scale Worm Branchipolynoe, Molecular Biology and Evolution, vol.27, issue.1, pp.143-152, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01250930

J. Projecto-garcia, D. Jollivet, J. Mary, F. H. Lallier, S. W. Schaeffer et al., Selective forces acting during multi-domain protein evolution: the case of multi-domain globins, SpringerPlus, vol.4, issue.1, p.354, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01177910

J. Projecto-garcia, A. Le-port, T. Govindji, D. Jollivet, S. W. Schaeffer et al., Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms, Journal of Molecular Evolution, vol.85, issue.5-6, pp.172-187, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01624983

J. L. Rainford, M. Hofreiter, D. B. Nicholson, and P. J. Mayhew, Phylogenetic Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects, PLoS ONE, vol.9, issue.10, 2014.

A. Rambaut and A. J. Drummond, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007.

A. Ravara, D. Ramos, M. A. Teixeira, F. O. Costa, and M. R. Cunha, Taxonomy, distribution and ecology of the order Phyllodocida (Annelida, Polychaeta) in deep-sea habitats around the Iberian margin, Deep Sea Research Part II: Topical Studies in Oceanography, pp.207-231, 2017.

G. Read and K. Fauchald, World Polychaeta database. Polynoidae Kinberg, 1856. Accessed through: World Register of Marine Species at, pp.2018-2025, 2018.

D. J. Rees, C. Belzile, H. Glémet, and F. Dufresne, Large genomes among caridean shrimp, Genome, vol.51, issue.2, pp.159-163, 2008.

A. J. Richardson and R. A. Cook, Habitat use by caridean shrimps in lowland rivers, Marine and Freshwater Research, vol.57, issue.7, p.695, 2006.

E. Richly and D. Leister, NUMTs in sequenced eukaryotic genomes, Molecular biology and evolution, vol.21, issue.6, pp.1081-1084, 2004.

M. C. Rivera, R. Jain, J. E. Moore, and J. A. Lake, Genomic evidence for two functionally distinct gene classes, Proceedings of the National Academy of Sciences, vol.95, issue.11, pp.6239-6244, 1998.

G. Robertson, J. Schein, R. Chiu, R. Corbett, M. Field et al., De novo assembly and analysis of RNA-seq data, Nature Methods, vol.7, issue.11, pp.909-912, 2010.

F. Ronquist, M. Teslenko, P. Van-der-mark, D. L. Ayres, A. Darling et al., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, issue.3, pp.539-542, 2012.

G. W. Rouse and K. Fauchald, The articulation of annelids, Zoologica Scripta, vol.24, issue.4, pp.269-301, 1995.

G. W. Rouse and K. Fauchald, Cladistics and polychaetes, Zoologica Scripta, vol.26, issue.2, pp.139-204, 1997.

V. Rousset, F. Pleijel, G. W. Rouse, C. Erséus, and M. E. Siddall, A molecular phylogeny of annelids, Cladistics, vol.23, issue.1, pp.41-63, 2007.

S. Samadi, L. Corbari, J. Lorion, S. Hourdez, and T. Haga, Biodiversity of deep-sea organisms associated with sunken-wood or other organic remains sampled in the tropical Indo-Pacific, Cahiers de Biologie Marine, vol.51, p.459, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01250934

S. Samadi, Evolutionary origins of hydrothermal vents metazoans, BIO Web of Conferences, vol.4, p.7, 2015.

F. Sanger, S. Nicklen, and A. R. Coulson, DNA sequencing with chain-terminating inhibitors, Proceedings of the national academy of sciences, vol.74, pp.5463-5467, 1977.

J. Sarvala, Ecology of Harmothoe sarsi (Malmgren)(Polychaeta, Polynoidae) in the northern Baltic area, Annales Zoologici Fennici. JSTOR, pp.231-309, 1971.

A. F. Sell, Life in the extreme environment at a hydrothermal vent: haemoglobin in a deep-sea copepod, Proceedings of the Royal Society B: Biological Sciences, vol.267, pp.2323-2326, 1459.

N. Serpetti, M. L. Taylor, D. Brennan, D. H. Green, A. D. Rogers et al., Ecological adaptations and commensal evolution of the Polynoidae (Polychaeta) in the Southwest Indian Ocean Ridge: A phylogenetic approach, Deep Sea Research Part II: Topical Studies in Oceanography, pp.273-281, 2017.

T. M. Shank, R. A. Lutz, and R. C. Vrijenhoek, Molecular systematics of shrimp (Decapoda: Bresiliidae) from deepsea hydrothermal vents, I: Enigmatic" small orange" shrimp from the Mid-Atlantic ridge are juvenile Rimicaris exoculata, Molecular marine biology and biotechnology, vol.7, issue.2, pp.88-96, 1998.

H. Shen, A. Braband, and G. Scholtz, Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships, Molecular Phylogenetics and Evolution, vol.66, issue.3, pp.776-789, 2013.

X. Shen, X. Zhou, J. Kominek, C. P. Kurtzman, C. T. Hittinger et al., Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data, Genes, Genomes, Genetics, vol.3, pp.3-116, 2016.

M. A. Shields, A. G. Glover, and H. Wiklund, Polynoid polychaetes of the Mid-Atlantic Ridge and a new holothurian association, Marine Biology Research, vol.9, issue.5-6, pp.547-553, 2013.

J. W. Short, C. L. Humphrey, and T. J. Page, Systematic revision and reappraisal of the Kakaducarididae Bruce (Crustacea : Decapoda : Caridea) with the description of three new species of Leptopalaemon Bruce & Short, Invertebrate Systematics, vol.27, issue.1, p.87, 2013.

F. A. Simão, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, issue.19, pp.3210-3212, 2015.

E. Sjölin, C. Erséus, and M. Källersjö, Phylogeny of Tubificidae (Annelida, Clitellata) based on mitochondrial and nuclear sequence data, Molecular phylogenetics and evolution, vol.35, issue.2, pp.431-441, 2005.

C. R. Smith, A. G. Glover, T. Treude, N. D. Higgs, and D. J. Amon, Whale-Fall Ecosystems: Recent Insights into Ecology, Paleoecology, and Evolution, Annual Review of Marine Science, vol.7, issue.1, pp.571-596, 2015.

H. Song, M. J. Moulton, and M. F. Whiting, Rampant Nuclear Insertion of mtDNA across Diverse Lineages within Orthoptera (Insecta), PLoS ONE, vol.9, issue.10, 2014.

A. J. Southward, E. C. Southward, P. R. Dando, G. H. Rau, H. Felbeck et al., Bacterial symbionts and low 13C/12C ratios in tissues of Pogonophora indicate unusual nutrition and metabolism, Nature, vol.293, issue.5834, p.616, 1981.

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.

J. Sui and X. Li, A new species and new record of deep-sea scale-worms (Polynoidae: Polychaeta) from the Okinawa Trough and the South China Sea, Zootaxa, vol.4238, issue.4, p.562, 2017.

P. Y. Sumida, J. M. Alfaro-lucas, M. Shimabukuro, H. Kitazato, J. A. Perez et al., Deep-sea whale fall fauna from the Atlantic resembles that of the Pacific Ocean, Scientific Reports, vol.6, issue.1, 2016.

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.

M. H. Tan, H. M. Gan, Y. P. Lee, and C. M. Austin, The complete mitogenome of the moon crab Ashtoret lunaris (Forskal, 1775), (Crustacea; Decapoda; Matutidae), Mitochondrial DNA, vol.27, issue.2, pp.1313-1314, 2016.

M. H. Tan, H. M. Gan, Y. P. Lee, and C. M. Austin, The complete mitogenome of the swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae), Mitochondrial DNA, vol.27, issue.2, pp.1275-1276, 2016.

R. L. Tatusov, E. V. Koonin, and D. J. Lipman, A genomic perspective on protein families, Science, vol.278, issue.5338, pp.631-637, 1997.

S. Teixeira, K. Olu, C. Decker, R. L. Cunha, S. Fuchs et al., High connectivity across the fragmented chemosynthetic ecosystems of the deep Atlantic Equatorial Belt: efficient dispersal mechanisms or questionable endemism?, Molecular Ecology, vol.22, issue.18, pp.4663-4680, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01250915

,

J. Thubaut, N. Puillandre, B. Faure, C. Cruaud, and S. Samadi, The contrasted evolutionary fates of deep-sea chemosynthetic mussels (Bivalvia, Bathymodiolinae), Ecology and Evolution, vol.3, issue.14, pp.4748-4766, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01250918

J. Toullec, E. Corre, P. Mandon, M. Gonzalez-aravena, C. Ollivaux et al., Characterization of the neuropeptidome of a Southern Ocean decapod, the Antarctic shrimp Chorismus antarcticus : Focusing on a new decapod ITP-like peptide belonging to the CHH peptide family, General and Comparative Endocrinology, issue.252, pp.60-78, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01578105

J. Toullec, J. Vinh, J. Le-caer, B. Shillito, and D. Soyez, Structure and phylogeny of the crustacean hyperglycemic hormone and its precursor from a hydrothermal vent crustacean: the crab Bythograea thermydron, Peptides, vol.23, issue.1, pp.31-42, 2002.
URL : https://hal.archives-ouvertes.fr/hal-01637048

L. M. Tsang, C. D. Schubart, S. T. Ahyong, J. C. Lai, E. Y. Au et al., Evolutionary History of True Crabs (Crustacea: Decapoda: Brachyura) and the Origin of Freshwater Crabs, Molecular Biology and Evolution, vol.31, issue.5, pp.1173-1187, 2014.

V. Tunnicliffe, The Nature and Origin of the Modern Hydrothermal Vent Fauna, PALAIOS, vol.7, issue.4, p.338, 1992.

V. Tunnicliffe, A. G. Mcarthur, and D. Mchugh, A biogeographical perspective of the deep-sea hydrothermal vent fauna, Advances in marine biology, pp.353-442, 1998.

P. A. Tyler and C. M. Young, Reproduction and dispersal at vents and cold seeps, Journal of the Marine Biological Association of the United Kingdom, vol.79, issue.2, pp.193-208, 1999.

P. A. Tyler, C. R. German, E. Ramirez-llodra, and C. L. Van-dover, Understanding the biogeography of chemosynthetic ecosystems, Oceanologica Acta, vol.25, issue.5, pp.227-241, 2002.

P. V. Uschakov, Essays on the polychaetous annelids in memory of Dr Olga Hartman, pp.29-38, 1977.

C. L. Van-dover, J. Trask, J. Gross, and A. Knowlton, Reproductive biology of free-living and commensal polynoid polychaetes at the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge), Marine Ecology Progress Series, issue.181, pp.201-214, 1999.

C. Van-dover, The ecology of deep-sea hydrothermal vents, 2000.

C. Van-dover, Trophic relationships among invertebrates at the Kairei hydrothermal vent field (Central Indian Ridge), Marine Biology, vol.141, issue.4, pp.761-772, 2002.

A. L. Vereshchaka, A new family for a deep-sea caridean shrimp from North Atlantic hydrothermal vents, Journal of the Marine Biological Association of the United Kingdom, vol.77, issue.2, pp.425-438, 1997.

A. L. Vereshchaka, D. N. Kulagin, and A. A. Lunina, Phylogeny and New Classification of Hydrothermal Vent and Seep Shrimps of the Family Alvinocarididae (Decapoda), PLOS ONE, vol.10, issue.7, 2015.

J. R. Voight, A deep-sea octopus (Graneledone cf. boreopacifica) as a shell-crushing hydrothermal vent predator, Journal of Zoology, vol.252, issue.3, pp.335-341, 2000.

K. Von-rintelen, T. J. Page, Y. Cai, K. Roe, B. Stelbrink et al., Drawn to the dark side: A molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses, Molecular Phylogenetics and Evolution, vol.63, issue.1, pp.82-96, 2012.

V. Sternberg, R. Cumberlidge, and N. , On the heterotreme-thoracotreme distinction in the Eubrachyura de Saint Laurent, 1980 (Decapoda, Brachyura), Crustaceana, vol.74, issue.4, pp.321-338, 2001.

V. Sternberg, R. Cumberlidge, N. Rodriguez, and G. , On the marine sister groups of the freshwater crabs (Crustacea: Decapoda: Brachyura), Journal of Zoological Systematics and Evolutionary Research, vol.37, issue.1, pp.19-38, 1999.

C. E. Wagner, I. Keller, S. Wittwer, O. M. Selz, S. Mwaiko et al., , 2013.

, Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation, Molecular Ecology, vol.22, issue.3, pp.787-798

Y. Wang and Z. Sha, A new species of the genus Manuscaris Komai & Tsuchida, 2015 (Decapoda, Caridea, Alvinocarididae) from the Manus Basin hydrothermal vents, Crustaceana, vol.89, issue.13, pp.1541-1550, 2016.

Y. Wang and Z. Sha, A new species of the genus Alvinocaris Williams and Chace, 1982 (Crustacea: Decapoda: Caridea: Alvinocarididae) from the Manus Basin hydrothermal vents, Southwest Pacific, Zootaxa, vol.4226, issue.1, p.126, 2017.

N. Ward and G. Moreno-hagelsieb, Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?, PLoS ONE, vol.9, issue.7, 2014.

R. M. Waterhouse, M. Seppey, F. A. Simão, M. Manni, P. Ioannidis et al., , 2017.

, BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics, Molecular Biology and Evolution, vol.35, issue.3, pp.543-548

G. J. Watson, F. M. Langford, S. M. Gaudron, and M. G. Bentley, Factors influencing spawning and pairing in the scale worm Harmothoe imbricata (Annelida: Polychaeta), The Biological Bulletin, vol.199, issue.1, pp.50-58, 2000.

M. Webb, Additional notes on sclerolinum brattstromi (pogonophora) and the establishment of a new family, sclerolinidae, Sarsia, vol.16, issue.1, pp.47-58, 1964.

M. Webb, Lamellibrachia barhami, gen. nov., sp. nov.,(Pogonophora), from the Northeast Pacific, Bulletin of Marine Science, vol.19, issue.1, pp.18-47, 1969.

R. E. Weber, Respiratory pigments, Physiology of annelids, pp.393-446, 1978.

A. B. Williams, A new crab family from the vicinity of submarine thermal vents on the Galapagos Rift (Crustacea: Decapoda: Brachyura), Proceedings of the Biological society of Washington, vol.93, pp.443-472, 1980.

A. B. Williams, New marine decapod crustaceans from waters influenced by hydrothermal discharge, brine and hydrocarbon seepage, 1988.

A. B. Williams and F. C. Dobbs, A new genus and species of caridean shrimp (Crustacea: Decapoda: Bresiliidae) from hydrothermal vents on Loihi Seamount, Proceedings of the Biological society of Washington, pp.228-228, 1995.

A. B. Williams and P. A. Rona, Two New Caridean Shrimps (Bresiliidae) from a Hydrothermal Field on the Mid-Atlantic Ridge, Journal of Crustacean Biology, vol.6, issue.3, p.446, 1986.

K. A. Wilson and R. H. Gore, Studies on decapod Crustacea from the Indian River region of Florida. XVI. The second known specimen and first continental record for Discias serratirostris Lebour, 1949 (Caridea, Bresiliidae), Crustaceana, vol.37, issue.2, pp.311-315, 1979.

T. Wolff, Composition and endemism of the deep-sea hydrothermal vent fauna, Cahiers de Biologie marine, vol.46, issue.2, pp.97-104, 2005.

H. M. Wood, V. L. González, M. Lloyd, J. Coddington, and N. Scharff, Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea), Molecular Phylogenetics and Evolution, 2018.

Z. Xu, T. Li, E. Li, K. Chen, Z. Ding et al., Comparative transcriptome analysis reveals molecular strategies of oriental river prawn Macrobrachium nipponense in response to acute and chronic nitrite stress, Fish & Shellfish Immunology, issue.48, pp.254-265, 2016.

J. S. Yang, H. Nagasawa, Y. Fujiwara, S. Tsuchida, and W. J. Yang, The complete mitogenome of the hydrothermal vent crab Gandalfus yunohana (Crustacea: Decapoda: Brachyura): a link between the Bythograeoidea and Xanthoidea, Zoologica Scripta, vol.39, issue.6, pp.621-630, 2010.

J. Yang, B. Lu, D. Chen, Y. Yu, F. Yang et al., When Did Decapods Invade Hydrothermal Vents? Clues from the Western Pacific and Indian Oceans, Molecular Biology and Evolution, vol.30, issue.2, pp.305-309, 2013.

X. Yuhui, Z. Lijun, H. Yue, W. Xiaoqi, Z. Chen et al., Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys, 705, pp.41-60, 2017.

F. Zal, D. Desbruyeres, and C. Jouin-toulmond, Sexual dimorphism in Paralvinella grasslei, a polychaete annelid from deep-sea hydrothermal vents. Comptes rendus de l'Académie des sciences. Série 3, Sciences de la vie, vol.317, pp.42-48, 1994.

E. M. Zdobnov, F. Tegenfeldt, D. Kuznetsov, R. M. Waterhouse, F. A. Simão et al., , 2017.

, OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs, Nucleic Acids Research, vol.45, issue.1, pp.744-749

J. Zhang, Q. Sun, Z. Luan, C. Lian, and L. Sun, Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent, Scientific Reports, vol.7, issue.1, 2017.

Y. Zhang, J. Sun, G. W. Rouse, H. Wiklund, F. Pleijel et al., Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida), Molecular Phylogenetics and Evolution, issue.125, pp.220-231, 2018.

Q. Zhao, Y. Wang, Y. Kong, D. Luo, X. Li et al., Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study, BMC bioinformatics, p.2, 2011.