Genetic variation among Japanese populations of chum salmon inferred from the nucleotide sequences of the mitochondrial DNA control region

Abstract

We examined the nucleotide sequences of 500 bp variable portion from the 5′ end of mitochondrial (mt) DNA control region in about 500 individuals from 12 populations that were captured in 11 rivers, six in Hokkaido and five in Honshu, Japan. Comparison of the sequences showed 10 variable sites, defining a total of 12 haplotypes in the examined individuals. All the 12 haplotypes occurred in seven Hokkaido populations, whereas only six haplotypes were found in the five Honshu populations. Among these haplotypes, two were common in all the Hokkaido and Honshu populations. The AMOVA analysis inferred a genetic differentiation among three geographic regions, i.e. Hokkaido, Pacific Ocean coast in Honshu, and Japan Sea coast in Honshu. Haplotype diversity was higher in the populations of Hokkaido than those of Honshu, indicating a greater genetic variation in the Hokkaido than the Honshu populations. The estimates of pairwise population FST suggested that the regional differentiation was mostly ascribed to the divergence between populations in Hokkaido and the Pacific coast in Honshu.