Population genetics of sandfish (Holothuria scabra) in the Andaman Sea, Thailand inferred from 12S rDNA and microsatellite polymorphism

Abstract

Population genetics of sandfish Holothuria scabra originated from four different locations (Phangnga, Satun, Trang and Krabi) in the Andaman Sea (west of peninsular Thailand) was examined by polymorphism of 12S rDNA sequences and microsatellites. In total, 30 haplotypes of 12S rDNA were observed (N=23, 14, 25 and 27 for respective samples). Limited sequence divergence (π=0.820%) but high haplotype diversity (0.873) were found. θST (0.0853) indicated that the female gene pool between Phangnga and Krabi samples was genetically differentiated (P < 0.05). In addition, significant genetic heterogeneity in haplotype distribution frequencies was observed between Phangnga and other samples and between Satun and Trang (P < 0.05). Microsatellite analysis revealed a moderate level of genetic diversity of these samples (N=31, 16, 30 and 42 for respective samples). The average number of alleles per locus and observed heterozygosity within geographic samples ranged from 6.667–10.667 and 0.604–0.699. Significant genetic differentiation was found for overall samples (FST=0.081, P < 0.05) and between Phangnga and each of the other samples (P < 0.01). An analysis of molecular variance (AMOVA) indicated that the gene pool of H. scabra in the Andaman Sea was genetically differentiated into 2 genetic stocks: Phangnga (A) and the remaining samples; Krabi, Satun and Trang (B) (P < 0.05). Phylogenetic and structure analyses revealed a distinct separation between these stocks. Our results provide valuable genetic information for management of natural stocks of H. scabra in Thailand.