Geographic variation and diversity in the mitochondrial DNA of the medaka, Oryzias latipes, as determined by restriction endonuclease analysis

Analysis of mitochondrial DNA (mtDNA) restriction fragment length polymorphism in Japanese wild populations of the medaka, Oryzias latipes revealed a large number of mtDNA haplotypes that form three distinct clusters (clusters A, B and C). The average nucleotide diversities among these three clusters are 8.9% (A versus B), 8.4% (A versus C), and 7.3% (B versus C). Cluster A consists of seven haplotypes and was subdivided into two subclusters. The nucleotide diversity in cluster A is low, ranging from 0.3% to 1.4% (mean 0.8%). Cluster B has 55 haplotypes and was subdivided into 11 subclusters. The nucleotide diversity in cluster B is high, ranging from 0.1 to 4.8% (mean 1.5%). Cluster C consists of only one haplotype, found in two sites of the Kanto district. The geographic distributions of mtDNA haplotypes in clusters A and B appear fully concordant with the previously described ranges of the Northern Population and the Southern Population defined by allozymes. Moreover, the distributions of mtDNA haplotypes in the subclusters show strong geographical associations. The distribution patterns of mtDNA haplotypes suggest some migration events of the medaka.