Van Dover, C. L. et al. Environmental management of deep-sea chemosynthetic ecosystems: justification of and considerations for a spatially based approach. ISA Technical Study: No.9. (International Seabed Authority, 2011).
Ikehata, K., Suzuki, R., Shimada, K., Ishibashi, J., & Urabe, T. Mineralogical and Geochemical Characteristics of Hydrothermal Minerals Collected from Hydrothermal Vent Fields in the Southern Mariana Spreading Center. In Subseafloor biosphere linked to hydrothermal systems: TAIGA Concept. 275–288 (Springer Tokyo, 2015).
Rona, P. A. & Scott, S. D. A special issue on sea-floor hydrothermal mineralization; new perspectives; preface. Econ. Geol. 88, 1935–1976 (1993).
Glasby, G. P., Iizasa, K., Yuasa, M. & Usui, A. Submarine hydrothermal mineralization on the Izu-Bonin arc, south of Japan: an overview. Mar. Georesources Geotech. 18, 141–176 (2000).
Van Dover, C. L. Inactive sulfide ecosystems in the deep sea: a review. Front. Mar. Sci. 6, 461. https://doi.org/10.3389/fmars.2019.00461 (2019).
Google Scholar
Boschen, R. E., Rowde, A. A., Clark, M. R. & Gardner, J. P. Mining of deep-sea seafloor massive sulfides: a review of the deposits, their benthic communities, impacts from mining, regulatory frameworks and management strategies. Ocean Coast. Manag. 84, 54–67 (2013).
Washburn, T. W. et al. Ecological risk assessment for deep-sea mining. Ocean Coast. Manag. 176, 24–39 (2019).
Matsui, T., Sugishima, H., Okamoto, N., Igarashi, Y. Evaluation of turbidity and resedimentation through seafloor disturbance experiments for assessment of environmental impacts associated with exploitation of seafloor massive sulfides mining. Proceedings of the Twenty-eighth. International Ocean and Polar Engineering Conference. 144–151 (2018).
International Seabed Authority. Recommendations for the guidance of contractors for the assessment of the possible environmental impacts arising from exploration for marine minerals in the Area. https://www.isa.org.jm/documents/isba19ltc8 (2013).
Suzuki, K., Yoshida, K., Watanabe, H. & Yamamoto, H. Mapping the resilience of chemosynthetic communities in hydrothermal vent fields. Sci. Rep. 8, 9364. https://doi.org/10.1038/s41598-018-27596-7 (2018).
Google Scholar
Yahagi, T., Watanabe, H., Ishibashi, J. I. & Kojima, S. Genetic population structure of four hydrothermal vent shrimp species (Alvinocarididae) in the Okinawa Trough, Northwest Pacific. Mar. Ecol. Prog. Ser. 529, 159–169 (2015).
Google Scholar
Mullineaux, L. S. Deep-sea hydrothermal vent communities. In Marine community ecology and conservation (eds Bertness, M. D. et al.) 383–400 (Sinauer, 2013).
Van Dover, C. L., German, C. R., Speer, K. G., Parson, L. M. & Vrijenhoek, R. C. Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295, 1253–1257 (2002).
Google Scholar
Yahagi, T., Kayama-Watanabe, H., Kojima, S. & Kano, Y. Do larvae from deep-sea hydrothermal vents disperse in surface waters?. Ecology 98, 1524–1534 (2017).
Hebert, P. D. & Gregory, T. R. The promise of DNA barcoding for taxonomy. Syst. Biol. 54, 852–859 (2005).
Iguchi, A. et al. Comparative analysis on the genetic population structures of the deep-sea whelks Buccinum tsubai and Neptunea constricta in the Sea of Japan. Mar. Biol. 151, 31–39 (2007).
Goode, G. B. & Bean, T. H. A catalogue of the fishes of Essex County, Massachusetts, including the fauna of Massachusetts Bay and the contiguous deep waters. Bull. Essex Inst. 11, 1–38 (1879).
Johnson, J. Y. Descriptions of some new genera and species of fishes obtained at Madeira. Proc. Zool. Soc. Lond. 1862, 167–180 (1862).
Bate, C. S. Report on the Crustacea Macrura collected by the Challenger during the years 1873–76. Report on the scientific results of the Voyage of H.M.S. Challenger during the years 1873–76. Zoology 24, 1–942 (1888).
Folmer, O., Black, M., Hoeh, W. R., Lutz, R. & Vrijenhoek, R. C. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol Biotech. 3, 294–299 (1994).
Google Scholar
Pilgrim, E. M., Blum, M. J., Reusser, D. A., Lee, H. & Darling, J. A. Geographic range and structure of cryptic genetic diversity among Pacific North American populations of the non-native amphipod Grandidierella japonica. Biol. Invasions 15, 2415–2428 (2013).
Suyama, Y. & Matsuki, Y. MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Sci. Rep. 5, 16963. https://doi.org/10.1038/srep16963 (2015).
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/ (2020).
Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962. https://doi.org/10.1371/journal.pone.0163962 (2016).
Google Scholar
Paradis, E. pegas: an R package for population genetics with an integrated–modular approach. Bioinformatics 26, 419–420 (2010).
Google Scholar
Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).
Google Scholar
Darriba, D. et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37, 291–294 (2020).
Google Scholar
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RaxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
Google Scholar
Ronquist, F. R. & Huelsenbeck, J. P. MRBAYES 3: Bayesian inference of phylogeny. Bioinformatics 19, 1572–1574 (2003).
Google Scholar
Puillandre, N., Brouillet, S. & Achaz, G. ASAP: assemble species by automatic partitioning. Mol. Ecol. Resour. 21, 609–620 (2021).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, http://journal.embnet.org/index.php/embnetjournal/article/view/200/479 (2011).
Rochette, N. C., Rivera-Colón, A. G. & Catchen, J. M. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol. Ecol. 28, 4737–4754 (2019).
Google Scholar
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Google Scholar
Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).
Google Scholar
Goudet, J. Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2013).
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5–6. https://CRAN.R-project.org/package=vegan (2019).
Dana, J. D. Synopsis of the genera of Gammaracea. Am. J. Sci. Arts 8, 135–140 (1849).
Hansen, H. J. Malacostraca marina Groenlandiæ occidentalis Oversigt over det vestlige Grønlands Fauna af malakostrake Havkrebsdyr. Vidensk. Meddel. Natuirist. Foren Kjobenhavn, Aaret 9, 5–226 (1888).
Van Dover, C. L. The ecology of deep-sea hydrothermal vents (Princeton University Press, 2000).
Tunnicliffe, V. The biology of hydrothermal vents: ecology and evolution. Oceanogr. Mar. Biol. Annu. Rev. 29, 319–407 (1991).
Priede, I. G., Bagley, P. M., Smith, A., Creasey, S. & Merrett, N. R. Scavenging deep demersal fishes of the Porcupine Seabight, north-east Atlantic: observations by baited camera, trap and trawl. J. Mar. Biol. Assoc. U. K. 74, 481–498 (1994).
Causse, R., Biscoito, M. & Briand, P. First record of the deep-sea eel Ilyophis saldanhai (Synaphobranchidae, Anguilliformes) from the Pacific Ocean. Cybium 29, 413–416 (2005).
King, N. J., Bagley, P. M. & Priede, I. G. Depth zonation and latitudinal distribution of deep-sea scavenging demersal fishes of the Mid-Atlantic Ridge, 42 to 53°N. Mar. Ecol. Prog. Ser. 319, 263–274 (2006).
Google Scholar
Leitner, A. B., Durden, J. M., Smith, C. R., Klingberg, E. D. & Drazen, J. C. Synaphobranchid eel swarms on abyssal seamounts: largest aggregation of fishes ever observed at abyssal depths. Deep Sea Res. Oceanogr. Res. Part I Pap. 167, 103423. https://doi.org/10.1016/j.dsr.2020.103423 (2021).
Google Scholar
Fishelson, L. Comparative internal morphology of deep-sea eels, with particular emphasis on gonads and gut structure. J. Fish. Biol. 44, 75–101 (1994).
Bailey, D. M. et al. High swimming and metabolic activity in the deep-sea eel Synaphobranchus kaupii revealed by integrated in situ and in vitro measurements. Physiol. Biochem. Zool. 78, 335–346 (2005).
Trenkel, V. M. & Lorance, P. Estimating Synaphobranchus kaupii densities: contribution of fish behaviour to differences between bait experiments and visual strip transects. Deep Sea Res. Oceanogr. Res. Part I Pap. 58, 63–71 (2011).
Google Scholar
Raupach, M. J. et al. Genetic homogeneity and circum-Antarctic distribution of two benthic shrimp species of the Southern Ocean, Chorismus antarcticus and Nematocarcinus lanceopes. Mar. Biol. 157, 1783–1797 (2010).
Google Scholar
Dambach, J., Raupach, M. J., Leese, F., Schwarzer, J. & Engler, J. O. Ocean currents determine functional connectivity in an Antarctic deep-sea shrimp. Mar. Ecol. 37, 1336–1344 (2016).
Google Scholar
Dambach, J., Raupach, M. J., Mayer, C., Schwarzer, J. & Leese, F. Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). BMC Res. Notes 6, 75. https://doi.org/10.1186/1756-0500-6-75 (2013).
Google Scholar
Ritchie, H., Jamieson, A. J. & Piertney, S. B. Phylogenetic relationships among hadal amphipods of the Superfamily Lysianassoidea: Implications for taxonomy and biogeography. Deep Sea Res. Part I 105, 119–131 (2015).
Google Scholar
Bowen, B. W. et al. Phylogeography unplugged: comparative surveys in the genomic era. Bull. Mar. Sci. 90, 13–46 (2014).
Ritchie, H., Jamieson, A. J. & Piertney, S. B. Population genetic structure of two congeneric deep-sea amphipod species from geographically isolated hadal trenches in the Pacific Ocean. Deep Sea Res. Part I. 119, 50–57 (2017).
Iguchi, A. et al. Deep-sea amphipods around cobalt-rich ferromanganese crusts: taxonomic diversity and selection of candidate species for connectivity analysis. PLoS ONE 15, e0228483. https://doi.org/10.1371/journal.pone.0228483 (2020).
Google Scholar
Baco, A. R. et al. A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design. Mol. Ecol. 25, 3276–3298 (2016).
Taylor, M. L. & Roterman, C. N. Invertebrate population genetics across Earth’s largest habitat: the deep-sea floor. Mol. Ecol. 26, 4872–4896 (2017).
Google Scholar
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