In order to examine the stock management unit of the slime flounder Microstomus achne, this study estimated the population structure of this species on the basis of sequence variations of 480 base pairs of the mitochondrial control region and morphological variations in three meristic counts of dorsal, anal, and pectoral fin-rays. High genetic diversity of this species in the mitochondrial control region was observed, but no genetic differentiation was detected between individuals from the Sea of Japan and the Pacific Ocean. On the other hand, the number of dorsal and anal fin-rays differed significantly between individuals from those two regions, with Pacific individuals having a higher number of fin-rays. The pelagic larval period of this species is very long (about 85 days), and although dispersal in the early life stage has resulted in gene flow between the Sea of Japan and the Pacific Ocean, the migration range after settlement is relatively limited, suggesting that migration between the Sea of Japan and the Pacific Ocean is restricted. Thus, these results suggest that it is necessary to distinguish between the Sea of Japan and the Pacific Ocean as a stock management unit for this species.
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