Conservation Genetics

, Volume 17, Issue 4, pp 811–821 | Cite as

Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island

  • Taha Soliman
  • Iria Fernandez-Silva
  • James Davis Reimer
Research Article


Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ ST = 0.49, P < 0.0001; 16S: Φ ST = 0.34, P < 0.0001; H3: Φ ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.


Genetic diversity Coastal development Genetic structure mtDNA Okinawa Sea cucumber 



The authors thank Dr. François Michonneau for providing technical advice during the DNA extraction and T. Ohara, O. Takama, K. Hamamoto, Dr. J. Montenegro, M. Mizuyama, and R. Diaz for help with sample collection. T.S. was supported by Ministry of Higher Education of the Egyptian Government during this study in Japan. J.D.R. was funded by a Japan Society for the Promotion of Science (JSPS) ‘Zuno-Junkan’ grant entitled ‘Studies on origin and maintenance of marine biodiversity and systematic conservation planning’. I.F.-S. was funded by a JSPS postdoctoral fellowship for overseas researchers. We thank two anonymous reviewers for their constructive comments, which improved the manuscript.

Supplementary material

10592_2016_823_MOESM1_ESM.ppt (196 kb)
Appendix S1. F ST pairwise values for Holothuria edulis across Okinawa Main Island inferred from mtDNA and nDNA. Sample sites are indicated in Table 1 and Fig. 1. Supplementary material 1 (PPT 196 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Taha Soliman
    • 1
    • 2
    • 3
  • Iria Fernandez-Silva
    • 1
    • 4
    • 5
  • James Davis Reimer
    • 1
    • 6
  1. 1.Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and ScienceUniversity of the RyukyusOkinawaJapan
  2. 2.Aquaculture DepartmentNational Institute of Oceanography and FisheriesAlexandriaEgypt
  3. 3.Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
  4. 4.Section of IchthyologyCalifornia Academy of SciencesSan FranciscoUSA
  5. 5.Department of Biochemistry, Genetics and ImmunologyUniversity of VigoVigoSpain
  6. 6.Tropical Biosphere Research CenterUniversity of the RyukyusOkinawaJapan

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