The current genetic disturbance in wild populations of Japanese medaka (Oryzias latipes species complex) has resulted from artificial introductions of non-native populations and the commercial orange-red body color medaka variety (‘himedaka’). Because the mitochondorial cytochrome b (cytb) “mitotype B1a” sensu Takehana et al. (2003) is native to the eastern area around the Seto-Inland Sea (ESIS), as well as occurring in himedaka, it had been believed that the mitotype B1a detected in the Kanto region (eastern Japan) had resulted from artificial introduction from ESIS or through himedaka. This study, based on sequencing and RFLP analyses of the mitochondrial hyperpolymorphic gene (ND2) in 99 O. latipes and 9 himedaka individuals, revealed three additional haplotype groups (I, II and III) in the mitotype B1a. The major haplotype group (Group I) apparently represents an artificial introduction, originally from ESIS or himedaka. However, Group II seemed to be native to the Kanto region, to which it was limited, since it was genetically divergent from the other groups. In addition, group III was found to belong not to mitotype B1a but to another mitotype, the ambiguous RFLP banding patterns found in the cytb analysis of the two mitotypes seemingly having led to the former misconception. To avoid such misunderstanding, more accurate analyses, such as sequencing or RFLP analysis of the ND2 gene as undertaken here, are required. Such should provide important new information for the conservation of genetic divergence in the Kanto region.
