Marine Biodiversity

, Volume 48, Issue 1, pp 677–684 | Cite as

Isolation and characterization of novel polymorphic microsatellite loci for the deep-sea hydrothermal vent limpet, Lepetodrilus nux, and the vent-associated squat lobster, Shinkaia crosnieri

  • Yuichi NakajimaEmail author
  • Chuya Shinzato
  • Mariia Khalturina
  • Masako Nakamura
  • Hiromi Kayama Watanabe
  • Satoshi Nakagawa
  • Noriyuki Satoh
  • Satoshi Mitarai
Short Communication


Recent genetic research has begun to reveal population structures of deep-sea, hydrothermal vent species, but detailed assessments of genetic diversity and connectivity in hydrothermal vent populations, based on multiple genetic loci, are still scarce, especially in the Northwest Pacific. Accordingly, we isolated 38 novel polymorphic microsatellite loci from the limpet, Lepetodrilus nux, and 14 from the squat lobster, Shinkaia crosnieri, two dominant hydrothermal vent species, using next-generation sequencing. These loci revealed polymorphism levels of 5–20 alleles per locus in L. nux and 5–25 in S. crosnieri. Observed and expected heterozygosities ranged from 0.240 to 0.960 and 0.283 to 0.938 in L. nux and from 0.450 to 0.950 and 0.620 to 0.941 in S. crosnieri, respectively. Twelve loci in L. nux and four loci in S. crosnieri showed significant deviation from Hardy–Weinberg equilibrium (p < 0.05). Microsatellite loci evaluated in this study will enable detailed measurements of genetic diversity and connectivity among populations, and better understanding of evolutionary divergence processes of L. nux and S. crosnieri in deep-sea communities in the Northwest Pacific.


Chemosynthetic ecosystem Northwest Pacific Nuclear genetic marker Okinawa Trough Population genetics Simple sequence repeat 



We are grateful to Dr. Hiroyuki Yamamoto, chief scientist of the KR12-02 and NT13-22 cruises, and to officers and crews of the ‘Natsushima,’ and the operation team of ROV ‘Hyper-Dolphin’ for collecting the specimens. This work was financially supported by The Canon Foundation and Okinawa Institute of Science and Technology Graduate University. We thank Dr. Steven D. Aird (Okinawa Institute of Science and Technology Graduate University) for editing the manuscript.


  1. Adams DK, Arellano SM, Govenar B (2012) Larval dispersal: vent life in the water column. Oceanography 25:256–268CrossRefGoogle Scholar
  2. Aronesty E (2011) ea-utils: "Command-line tools for processing biological sequencing data".
  3. Baba K, Williams AB (1998) New Galatheoidea (Crustacea, Decapoda, Anomura) from hydrothermal systems in the West Pacific Ocean: Bismarck Archipelago and Okinawa Trough. Zoosystema 20:143–156Google Scholar
  4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
  5. Breusing C, Biastoch A, Drews A, Metaxas A, Jollivet D, Vrijenhoek RC, Bayer T, Melzner F, Sayavedra L, Petersen JM, Dubilier N, Schilhabel MB, Rosenstiel P, Reusch TBH (2016) Biophysical and population genetic models predict the presence of “phantom” stepping stones connecting mid-Atlantic ridge vent ecosystems. Curr Biol 26:2257–2267Google Scholar
  6. Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD (2012) Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7:e30953Google Scholar
  7. Chan T-Y, Lee D-A, Lee C-S (2000) The first deep-sea hydrothermal animal reported from Taiwan: Shinkaia crosnieri Baba and Williams, 1998 (Crustacea: Decapoda: Galatheidae). Bull Mar Sci 67:799–804Google Scholar
  8. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510CrossRefPubMedGoogle Scholar
  9. Desbruyères D, Segonzac M, Bright M (2006) Handbook of deep-sea hydrothermal vent fauna. Denisia 18, Linz, AustriaGoogle Scholar
  10. Johnson SB, Young CR, Jones WJ, Warén A, Vrijenhoek RC (2006) Migration, isolation, and speciation of hydrothermal vent limpets (Gastropoda; Lepetodrilidae) across the Blanco Transform Fault. Biol Bull 210:140–157Google Scholar
  11. Johnson SB, Warén A, Vrijenhoek RC (2008) DNA barcoding of Lepetodrilus limpets reveals cryptic species. J Shellfish Res 27:43–51Google Scholar
  12. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659CrossRefPubMedGoogle Scholar
  13. Lutz RA, Jablonski D, Turner RD (1984) Larval development and dispersal at deep-sea hydrothermal vents. Science 226:1451–1454CrossRefPubMedGoogle Scholar
  14. Matabos M, Thiébaut E, Le Guen D, Sadosky F, Jollivet D, Bonhomme F (2008) Geographic clines and stepping-stone patterns detected along the East Pacific Rise in the vetigastropod Lepetodrilus elevatus reflect species crypticism. Mar Biol 153:545–563Google Scholar
  15. Mitarai S, Watanabe H, Nakajima Y, Shchepetkin AF, McWilliams JC (2016) Quantifying dispersal from hydrothermal vent fields in the western Pacific Ocean. Proc Nat Acad Sci USA 113:2976–2981CrossRefPubMedPubMedCentralGoogle Scholar
  16. Miyake H, Kitada M, Itoh T, Nemoto S, Okuyama Y, Watanabe H, Tsuchida S, Inoue K, Kado R, Ikeda S, Nakamura K, Omata T (2010) Larvae of deep-sea chemosynthetic ecosystem animals in captivity. Cah Biol Mar 51:441–451Google Scholar
  17. Nakajima R, Yamamoto H, Kawagucci S, Takaya Y, Nozaki T, Chen C, Fujikura K, Miwa T, Takai K (2015) Post-drilling changes in seabed landscape and megabenthos in a deep-sea hydrothermal system, the Iheya North field, Okinawa Trough. PLoS ONE 10:e0123095CrossRefPubMedPubMedCentralGoogle Scholar
  18. Nakamura M, Watanabe H, Sasaki T, Ishibashi J, Fujikura K, Mitarai S (2014) Life history traits of Lepetodrilus nux in the Okinawa Trough, based upon gametogenesis, shell size, and genetic variability. Mar Ecol Prog Ser 505:119–130CrossRefGoogle Scholar
  19. Okutani T, Fujikura K, Sasaki T (1993) New taxa and new distribution records of deepsea gastropods collected from or near the chemosynthetic communities in the Japanese waters. Bull Natl Sci Mus Tokyo A 19:123–143Google Scholar
  20. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  21. Plouviez S, Shank TM, Faure B, Daguin-Thiebaut C, Viard F, Lallier FH, Jollivet D (2009) Comparative phylogeography among hydrothermal vent species along the East Pacific Rise reveals vicariant processes and population expansion in the south. Mol Ecol 18:3903–3917Google Scholar
  22. Raymond M, Rousset F (1995) Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249CrossRefGoogle Scholar
  23. Roterman CN, Copley JT, Linse KT, Tyler PA, Rogers AD (2013) Development of polymorphic microsatellite loci for three species of vent-endemic megafauna from deep-sea hydrothermal vents in the Scotia Sea, Southern Ocean. Conserv Genet Resour 5:835–839CrossRefGoogle Scholar
  24. Roterman CN, Copley JT, Linse KT, Tyler PA, Rogers AD (2016) Connectivity in the cold: the comparative population genetics of vent-endemic fauna in the Scotia Sea, Southern Ocean. Mol Ecol 25:1073–1088CrossRefPubMedGoogle Scholar
  25. Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106Google Scholar
  26. Sasaki T, Okutani T, Fujikura K (2003) New taxa and new records of patelliform gastropods associated with chemoautosynthesis-based communities in Japanese waters. Veliger 46:189–210Google Scholar
  27. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234CrossRefPubMedGoogle Scholar
  28. Thaler AD, Zelnio K, Saleu W, Schultz TF, Carlsson J, Cunningham C, Vrijenhoek RC, Van Dover CL (2011) The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific. BMC Evol Biol 11:372CrossRefPubMedPubMedCentralGoogle Scholar
  29. Thaler AD, Plouviez S, Saleu W, Alei F, Jacobson A, Boyle EA, Schultz TF, Carlsson J, Van Dover CL (2014) Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis Lauensis) from southwestern Pacific back-arc basins. PLoS ONE 9:e101345Google Scholar
  30. Van Dover CL, German CR, Speer KG, Parson LM, Vrijenhoek RC (2002) Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295:1253–1257CrossRefPubMedGoogle Scholar
  31. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538CrossRefGoogle Scholar
  32. Vrijenhoek RC (1997) Gene flow and genetic diversity in naturally fragmented metapopulations of deep-sea hydrothermal vent animals. J Hered 88:285–293CrossRefPubMedGoogle Scholar
  33. Vrijenhoek RC, Feldman RA, Lutz RA, Craddock C, Hashimoto J (1997) Genetic characterization of Lepetodrilus limpets from hydrothermal vents in the Mariana Trough. JAMSTEC Journal of Deep Sea Research, Special Volume “Deep sea research in subduction zones, spreading centers and backarc basins”, pp 111–116Google Scholar
  34. Vrijenhoek RC (2010) Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations. Mol Ecol 19:4391–4411CrossRefPubMedGoogle Scholar
  35. Xu T, Sun J, Lv J, Watanabe HK, Li T, Zou W, Rouse GW, Wang S, Qian P-Y, Bao Z, Qiu J-W (2017) Genome-wide discovery of single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) in deep-sea mussels: Potential use in population genomics and cross-species application. Deep Sea Res II 137:318–326Google Scholar
  36. Yang C-H, Tsuchida S, Fujikura K, Fujiwara Y, Kawato M, Chan T-Y (2016) Connectivity of the squat lobsters Shinkaia crosnieri (Crustacea: Decapoda: Galatheidae) between cold seep and hydrothermal vent habitats. Bull Mar Sci 92:17–31CrossRefGoogle Scholar

Copyright information

© Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  1. 1.Marine Biophysics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
  2. 2.Atmosphere and Ocean Research InstituteThe University of TokyoKashiwaJapan
  3. 3.Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
  4. 4.School of Marine Science and TechnologyTokai UniversityShimizuJapan
  5. 5.Japan Agency for Marine-Earth Science and TechnologyYokosukaJapan
  6. 6.Division of Applied Biosciences, Graduate School of AgricultureKyoto UniversityKyotoJapan

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