The genetic structure of the Asian tri-spine horseshoe crab, Tachypleus tridentatus, was investigated in three populations of Taiwan Strait using mitochondrial (mt) AT-rich region DNA sequences. We examined 23 individuals from Kinmen, an island located on the western side of Taiwan Strait, and 12 each from Tiexianwei and Dongwei near Magong Island in the Penghu Archipelago, in the middle of Taiwan Strait. DNA sequence analysis of 369 base pairs (bp) of the mt AT-rich region revealed 10 haplotypes among the 47 individuals, with a mean haplotypic diversity (h) of 0.626± 0.075 and nucleotide diversity (π) of 0.0039± 0.00055. Pairwise F-statistics (FST) revealed significantly high gene flow between Kinmen and Dongwei (FST=–0.0351, p>0.05, Nem=∞), but marked population subdivision and restricted gene flow between Kinmen and Tiexianwei (FST=0.1382, p<0.05, Nem=3.1176). Between populations at Magong Island, gene flow was moderate (FST=0.0634, p>0.05, Nem=7.3913). Mismatch distribution analysis indicated that the relatively low haplotype and nucleotide diversity observed in the Tiexianwei T. tridentatus population can be attributed to a recent bottleneck, probably due to isolation of Tiexianwei in semi-closed Magong Bay that prevents gene flow from neighboring populations.
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