Studies of mitochondrial DNA phylogeography of several Japanese coastal marine species have shown the existence of Pacific Ocean and Sea of Japan groups, which diverged because of the isolation of the Sea of Japan in the Pleistocene glacial periods. Here we performed a combined analysis of mitochondrial DNA (mtDNA) cytochrome b and 8 microsatellite loci among Chaenogobius annularis populations to reveal the levels of congruence between the 2 markers, the admixture of the 2 groups, and the post-glacial history of the Sea of Japan group. Population-level and individual-level genetic analyses based on these markers showed no or minimal admixtures between the Pacific Ocean and Sea of Japan groups, despite the temporal opening of the Sea of Japan in multiple interglacial periods. The genetic diversity within the Sea of Japan group was much lower than that within the Pacific Ocean group. However, the Shimonoseki population, sampled in southern parts of the Sea of Japan, revealed higher mitochondrial nucleotide diversity and microsatellite allelic richness, suggesting post-glacial expansion from the southern area, accompanied by genetic drift, i.e. The founder effect. Congruent patterns of mtDNA and microsatellite DNA markers suggest long-term vicariance and severe genetic drift in the Sea of Japan group since the divergence in the early Pleistocene.
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