Genetic variation and population structure of marbled sole Pleuronectes yokohamae and cresthead flounder P. schrenki in Japan inferred from mitochondrial DNA analysis

• Mitochondrial DNA analysis was performed in Pleuronectes yokohamae and P. schrenki.
• Haplotype sharing in the two species suggested an interspecific hybridization.
• Population structuring of P. yokohamae was influenced by isolation by distance.
• Genetic differentiation was not clear among the populations of P. schrenki.
• Migration character may explain different population structure of the two species.

Nucleotide sequence analysis in the first half of the mitochondrial control region was used to estimate genetic variation and population structure of marbled sole Pleuronectes yokohamae and cresthead flounder Pleuronectes schrenki, obtained from 10 localities in Japan. Overall estimate of pairwise population FST and NJ tree suggested genetic distinction between P. yokohamae and P. schrenki. SAMOVA also demonstrated two distinct genetic groups of the samples, MS (marbled sole, Honshu and southernmost Hokkaido) and CF(cresthead flounder, Hokkaido), which was pertinent to the natural range of P. yokohamae and P. schrenki, respectively. However, the haplotypes common to P. yokohamae and P. schrenki were found in all four samples of the CF group and two of six samples of the MS group. Haplotype and nucleotide diversities were high within MS and CF groups, and the mismatch distribution analysis showed a bimodal profile in both groups, suggesting secondary contact between allopatrically evolved MS and CF groups. Thus, the observed haplotype sharing between two species might have been the consequence of interspecific hybridization after their divergence. In addition, FST estimates and Mantel test suggested that the population structure of P. yokohamae might have been influenced by low or restricted gene flow with isolation by distance, whereas no such population structuring was implied for P. schrenki. The observed difference in population structuring between two species was surmised by the difference of migration character.