Phylogeography of Tridentiger bifasciatus (Gobiidae) in the Northwestern Pacific

Abstract

The shimofuri goby (Tridentiger bifasciatus) is native to marine, brackish, and fresh waters along the coasts of the northwest Pacific. Our study examined the population genetic structure, diversity, and demography of T. bifasciatus in the China Seas, including the Yellow Sea, East China Sea, and South China Sea, using the sequences of mitochondrial DNA [mtDNA cytochrome b (cyt b) gene and d-loop region] and nuclear DNA [nuDNA ryanodine receptor 3 (Ryr3) gene]. The mtDNA dataset revealed a significant population differentiation, but the nuDNA dataset displayed the absence of genetic differentiation. The discordance between these two datasets was accounted for by population admixture, selection, and incomplete lineage sorting. Although the mtDNA and nuDNA displayed a discordant population structure, these genetic markers revealed the same population history: (1) the populations retreated into two refugia during glaciations and (2) the populations declined recently. Our study revealed that after glaciations, the re-flooding in Taiwan Strait did not shape the migrations of the southern lineage from the South China Sea to the East China Sea, and displayed that two mtDNA lineages have diverged before they migrated southward during glaciations. These results offer important resources for the further study of conservation genetics.