The gizzard shad (Konosirus punctatus) is a common pelagic fish in the East China Sea. To evaluate the influence of Kuroshio Current in shaping the genetic structure of marine species, 10 populations of K. punctatus from Chinese and Japanese coastal waters were collected for analysis based on the mitochondrial DNA marker. All the Japanese populations exhibited higher nucleotide diversity than did Chinese populations. Two distinct clades were identified by the neighbour-joining tree based on haplotypes of Cyt b and the control region. Both AMOVA and pairwise Fst strongly supported the significant genetic divergence between Chinese and Japanese clades, which suggested strictly limited gene exchange. The mismatch distribution of Chinese clade and Japanese Clade B appeared to be unimodal, and Tajima’s D and Fu’s Fs statistics were significantly negative, and, therefore, the hypothesis of selective neutrality was rejected. The results indicated that the Kuroshio Current may not be the strong barrier for the dispersal of K. punctatus in the East China Sea. The climate of Pleistocene periods had played an important role in phylogeographical patterns of K. punctatus and the dispersal strategy of coastal species may be the major current physical barrier for the gene flow among populations from Chinese and Japanese coastal waters.
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