Genetic variation and divergence in populations of ayu Plecoglossus altivelis, including endangered subspecies, inferred from PCR-RFLP analysis of the mitochondrial DNA D-loop region

Abstract

The ayu Plecoglossus altivelis altivelis, including two ecological forms (amphidoromous and landlocked), is a common and commercially important freshwater fish in Japan, whereas the endangered subspecies P. a. ryukyuensis (Ryukyu-ayu) inhabits a limited area of the Ryukyu Islands in southern Japan. The efficiency of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis containing the entire D-loop region was examined to evaluate genetic variability and divergence in ayu populations, including the endemic two populations of the Ryukyu-ayu on the same island, and was compared with genetic data obtained from nuclear markers presented previously. The haplotype diversities (h) of the two populations of Ryukyu-ayu (0.251 and 0) were far smaller than those of the two common forms (0.766-0.928), suggesting that strong founder and/or bottleneck effects occurred in the subspecies populations. A common haplotype was not observed between the two populations of Ryukyu-ayu, suggesting little or no gene flow between them. The net nucleotide sequence divergence value (dA) between the two populations of Ryukyu-ayu (0.276%) was almost same as that between the two forms of the former subspecies (0.265%). These results almost coincided with the results derived from nuclear markers and suggest that PCR-RFLP analysis of the mitochondrial DNA D-loop region is useful for evaluating genetic variability and divergence among ayu populations.