Abstract
Sequence analysis on the mitochondrial DNA control region was conducted for seven samples of amphidromous ayu Plecoglossus altivelis, six from the Japanese Archipelago and one from the Korean Peninsula, to understand their genetic variation and geographic population structure. The larger extent of net nucleotide substitution between Korean and Japanese samples, shown by intrasample clustering of the Korean samples in neighbor-joining phylogram, indicated that the Korean sample represented a genetically distinct population. Within the Japanese Archipelago, intrasample nucleotide diversities were high and masked intersample nucleotide divergences, with no obvious correspondence between genetic (net nucleotide substitution) and geographical distances. This may imply that at the mitochondrial DNA level there was no genetic differentiation among samples and they belonged to a single large population. However, minute but significant heterogeneities in the degree of intrasample nucleotide diversity and the frequency of nucleotide substitution at specific sites among Japanese Archipelago samples suggests the population is substructured as a metapopulation.
