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.
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10592-013-0506-7/MediaObjects/10592_2013_506_Fig1_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10592-013-0506-7/MediaObjects/10592_2013_506_Fig2_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10592-013-0506-7/MediaObjects/10592_2013_506_Fig3_HTML.gif)
References
Bell JD, Purcell SW, Nash WJ (2008) Restoring small-scale fisheries for tropical sea cucumbers. Ocean Coast Manag 51:589–593
Chang Y, Ding J, Song J, Yang W (2004) Biological research and aquaculture on sea cucumbers and sea urchins. Ocean Press, Beijing, pp 155–161
Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1659
Conand C (2004) Present status of world sea cucumber resources and utilisation: an international overview (advances in sea cucumber aquaculture and management). FAO 463:13–23
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 131:479–491
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/)
Falconer DS (1981) Introduction to quantitative genetics. Longman, UK
Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925
Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486
Guo SW, Thompson EA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
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 23:1801–1806
Lavery S, Moritz C, Fielder DR (1996) Genetic patterns suggest exponential population growth in a declining species. Mol Biol Evol 13:1106–1113
Liao Y (1997) Fauna Sinica: Phylum Echinodermata Class Holothuroidea. Science Press, Beijing
Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Mol Ecol 19:3038–3051
Marko PB, Hart MW (2011) The complex analytical landscape of gene flow inference. Trends Ecol Evol 26:448–456
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 30:450–458
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Raymond M, Rousset F (1995) GENEPOP: population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225
Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
Rowe FWE, Richmond MD (2004) A preliminary account of the shallow-water echinoderms of Rodrigues, Mauritius, Western Indian Ocean. J Nat Hist 38:3273–3314
Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497
Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555–562
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 309:280–285
Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595
Team HP (1976) A study on the artificial breeding and cultivation of Stichopus japonicus (Selenka). Studia Marian Sinica 11:173–181
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 25:4876–4882
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 516:231–253
Uthicke S (2001) Nutrient regeneration by abundant coral reef holothurians. J Exp Mar Biol Ecol 265:153–170
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 12:2635–2648
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 10:1104
Acknowledgments
This work was funded by the National Key Technology R&D Program (2012BAD18B03-02) and Fishery Scientific and Technical Program of Guangdong Province (A201101D02, A201100D01) assigned to CQ Hu. LH Yuan is supported by the Guangzhou Pearl River Scientific and Technological New Star Project (2012J2200003) and the China Postdoctoral Science Foundation (20100480788). We gratefully thank the Deep Ocean Observation and Research Station on XiSha Islands (South China Sea Institute of Oceanology, CAS) for the support on samples collection and acknowledge the support of K.C. Wong Education Foundation, Hong Kong. We appreciate the anonymous reviewers’ and Dr. Ting Chen’s favorable comments on this version.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Yuan, L., Hu, C., Zhang, L. et al. Population genetics of a tropical sea cucumber species (Stichopus monotuberculatus) in China. Conserv Genet 14, 1279–1284 (2013). https://doi.org/10.1007/s10592-013-0506-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10592-013-0506-7