Genetic Structure of Japanese Populations of Tachypleus tridentatus by mtDNA AT-Rich Region Sequence Analysis

Abstract

Tachypleus tridentatus is distributed from coastal Southeast Asia to western Japan. The northernmost population of this species, the Japanese population, is rapidly decreasing due to loss of tidal flats and spawning beaches, and the deterioration of coastal waters. To examine the genetic structure and the genetic diversity of the Japanese population, over 290 samples from nine localities were analyzed using hemolymph, egg, and muscle. The AT-rich region (control region, 369 base pairs) of mitochondrial DNA (mtDNA) was analyzed. Sequences of nuclear integrations of mtDNA (numt) were found in this species, with high sequence similarity to mtDNA. Therefore, to identify “true” mtDNA sequences, long PCR was conducted to amplify the majority of the circular mtDNA molecule. Specific primers were then designed for amplification of the mtDNA AT-rich region. Seven haplotypes were identified based on the sequence of the AT-rich regions from the Japanese populations. All haplotypes were related and closely connected by a single substitution. Haplotype AT1 was dominant and was observed in all regions examined. Two genetic groups were detected based on distribution of haplotypes and significant F _ST or Φ _ST. Sampling localities in the eastern group were almost monomorphic for AT1, with a few rare haplotypes, resulting in a low haplotype diversity, while the western group was comprised of haplotypes AT1, AT2, and AT3, and consequently higher haplotype diversity than in the eastern groups. These results suggested that the northernmost population of this species might have been formed recently and that the dispersal rate has been relatively low, leading to the formation of genetically distinct populations.