Conservation Genetics

, Volume 14, Issue 6, pp 1279–1284

Population genetics of a tropical sea cucumber species (Stichopus monotuberculatus) in China

  • Lihong Yuan
  • Chaoqun Hu
  • Lvping Zhang
  • Jianjun Xia
Short Communication

Abstract

Stichopus monotuberculatus is a valuable tropical sea cucumber that is distributed throughout the Indo-Pacific Ocean, including Guangxi, Hainan Land and Xisha Islands of China. Increasing demand and over-fishing, however, have seriously depleted the wild populations of this species in China. In this study, we applied both mitochondrial and nuclear DNA markers to characterize the population genetic subdivisions and phylogeographic histories of S. monotuberculatus sampled from Southern China. Based on both classes of molecular markers, our results demonstrated significant genetic structure among S. monotuberculatus populations, and revealed that the three populations (Q, S and B) experienced demographic expansion during the late Pleistocene (50,000–190,000 years BP). This study provides the basic information on natural population structure of S. monotuberculatus that may help to preserve and manage tropical sea cucumbers in China.

Keywords

Stichopus monotuberculatus Genetic diversity Population structure 

Supplementary material

10592_2013_506_MOESM1_ESM.doc (40 kb)
Supplementary material 1 (DOC 39 kb)
10592_2013_506_MOESM2_ESM.doc (124 kb)
Supplementary material 2 (DOC 124 kb)
10592_2013_506_MOESM3_ESM.doc (34 kb)
Supplementary material 3 (DOC 34 kb)
10592_2013_506_MOESM4_ESM.doc (40 kb)
Supplementary material 4 (DOC 39 kb)
10592_2013_506_MOESM5_ESM.doc (48 kb)
Supplementary material 5 (DOC 47 kb)
10592_2013_506_MOESM6_ESM.doc (39 kb)
Supplementary material 6 (DOC 39 kb)

References

  1. Bell JD, Purcell SW, Nash WJ (2008) Restoring small-scale fisheries for tropical sea cucumbers. Ocean Coast Manag 51:589–593CrossRefGoogle Scholar
  2. Chang Y, Ding J, Song J, Yang W (2004) Biological research and aquaculture on sea cucumbers and sea urchins. Ocean Press, Beijing, pp 155–161Google Scholar
  3. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659PubMedCrossRefGoogle Scholar
  4. Conand C (2004) Present status of world sea cucumber resources and utilisation: an international overview (advances in sea cucumber aquaculture and management). FAO 463:13–23Google Scholar
  5. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedGoogle Scholar
  6. Excoffier L, Laval G, Schneider S (2006) Arlequin (v3.01): an integrated software for population genetics data analysis. Evolutionary Bioinformatics Online (http://cmpg.unibe.ch/software/arlequin3/)
  7. Falconer DS (1981) Introduction to quantitative genetics. Longman, UKGoogle Scholar
  8. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925PubMedGoogle Scholar
  9. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486Google Scholar
  10. Guo SW, Thompson EA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372PubMedCrossRefGoogle Scholar
  11. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  12. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806PubMedCrossRefGoogle Scholar
  13. Lavery S, Moritz C, Fielder DR (1996) Genetic patterns suggest exponential population growth in a declining species. Mol Biol Evol 13:1106–1113CrossRefGoogle Scholar
  14. Liao Y (1997) Fauna Sinica: Phylum Echinodermata Class Holothuroidea. Science Press, BeijingGoogle Scholar
  15. Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Mol Ecol 19:3038–3051PubMedCrossRefGoogle Scholar
  16. Marko PB, Hart MW (2011) The complex analytical landscape of gene flow inference. Trends Ecol Evol 26:448–456PubMedCrossRefGoogle Scholar
  17. Oetting WS, Lee HK, Flanders DJ et al (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458PubMedCrossRefGoogle Scholar
  18. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  19. Raymond M, Rousset F (1995) GENEPOP: population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  20. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225CrossRefGoogle Scholar
  21. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569PubMedGoogle Scholar
  22. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138CrossRefGoogle Scholar
  23. Rowe FWE, Richmond MD (2004) A preliminary account of the shallow-water echinoderms of Rodrigues, Mauritius, Western Indian Ocean. J Nat Hist 38:3273–3314CrossRefGoogle Scholar
  24. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497PubMedCrossRefGoogle Scholar
  25. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555–562PubMedGoogle Scholar
  26. Sun X-J, Li Q, Kong L-F (2010) Comparative mitochondrial genomics within sea cucumber (Apostichopus japonicus): provide new insights into relationships among color variants. Aquaculture 309:280–285CrossRefGoogle Scholar
  27. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMedGoogle Scholar
  28. Team HP (1976) A study on the artificial breeding and cultivation of Stichopus japonicus (Selenka). Studia Marian Sinica 11:173–181Google Scholar
  29. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  30. Toral-Granda V (2008) Galapagos Islands: a hotspot of sea cucumber fisheries in Latin America and the Caribbean (A global review of fisheries and trade). FAO 516:231–253Google Scholar
  31. Uthicke S (2001) Nutrient regeneration by abundant coral reef holothurians. J Exp Mar Biol Ecol 265:153–170CrossRefGoogle Scholar
  32. Uthicke S, Benzie JA (2003) Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Mol Ecol 12:2635–2648PubMedCrossRefGoogle Scholar
  33. Xia J, Hu C, Fan S, Luo P, Zhang L (2010) PERMANENT GENETIC RESOURCES NOTE: isolation and characterization of fifteen novel microsatellite markers in the sea cucumber (Stichopus monotuberculatus Quoy & Gaimard, 1833). Mol Ecol Resour 10:1104Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Lihong Yuan
    • 1
    • 2
    • 3
  • Chaoqun Hu
    • 1
    • 2
  • Lvping Zhang
    • 1
    • 2
  • Jianjun Xia
    • 1
    • 2
  1. 1.Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
  2. 2.Key Laboratory of Applied Marine Biology of Guangdong Province (LAMB), South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
  3. 3.Guangdong Entomological Institute & South China Institute of Endangered AnimalsGuangzhouChina

Personalised recommendations