LAUSR

Abstract Advances in population genetics have brought about the use of management units (MUs) for the assessment and management of marine resources. Some marine species with an apparently continuous distribution actually have local genetically distinct populations across their range, so careful consideration is required in the delineation of MUs. To delineate MUs for Pacific cod (Gadus macrocephalus) in the coastal area of the Sea of Japan, we studied the geographic distribution and genetic variation of the species. Two geographically separate groups were identified based on the analysis of trawl survey data. A spatially explicit clustering analysis of 309 sequences of the mitochondrial NADH dehydrogenase 2 gene identified two groups of samples: one in the central to northern Sea of Japan (NJ) and another in the westernmost shelf area around the Tsushima Strait (WJ). The population structure was further confirmed by analysis of molecular variance and a significant pairwise Φst value between the two groups. The NJ population had experienced a post-glacial population expansion, whereas the WJ population size remained stable, probably reflecting different oceanographic conditions in the two regions. The two populations diverged from each other during the last glacial period, likely due to habitat discontinuity. Finally, based on the species’ genetic population structure and the geographic distributions, we parsimoniously propose that a single boundary be set along the coast of western Honshu Island to divide MUs in the Sea of Japan.