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We examined the phylogeography of the common Japanese intertidal goby Chaenogobius annularis using the mitochondrial cytochrome b gene, the NADH dehydrogenase subunit 2 gene, and the surrounding transfer RNA from 195 specimens collected in 27 localities around the Japanese Archipelago and the Korean Peninsula, and reconstructed the historical processes of its current distribution. In total, 169 unique haplotypes were obtained, and phylogenetic trees showed 2 genetically distinct lineages: the Pacific Ocean and the Sea of Japan lineages, whose divergence was estimated to have occurred in the early Pleistocene, related to the paleo environmental history of the Sea of Japan. After the divergence, the Sea of Japan lineage rapidly attained its current distribution, whereas the present-day distribution of the Pacific Ocean lineage was formed as a result of vicariance and dispersal.

Phylogeography of the intertidal goby Chaenogobius annularis associated with paleoenvironmental changes around the Japanese Archipelago