Conservation implications of low genetic diversity of the unique Okinawa Islands subpopulation of Oryzias latipes based on nuclear DNA markers

This study included 508 individuals of Oryzias latipes from 15 sites in mainland Japan and 10 sites in the Ryukyu Archipelago and Taiwan used in Imai et al. (2017), and new samples from four sites in the Ryukyu Archipelago, four sites in China and South Korea, and one from hi-medaka. We developed four new PCR-RFLP nuclear DNA markers (Orla16- 185-MboI, Orla1-29-BstUI, Orla1-51-AluI, and P0Ex-HinfI) based on three universal microsatellite primer sets and an exon-primed intron-crossing (EPIC) primer set for fish. STRUCTURE analysis indicated that Amami-oshima, Iheya, Izena, Ginama, Ogimi, and Bios no Oka formed a cluster, while specimens from Fukuchi, the former Kadena Ammunition Storage area, Zamani, and other Okinawa Islands formed a different cluster. The genetic diversity of subpopulations from Fukuchi, the former Kadena Ammunition Storage area, and Zamani was higher than those from other Okinawa Islands. The individual exclusion test (>90% condition) was applied to the Okinawa Islands subpopulation using GeneClass2. It will be important to apply these genetic markers for periodical genetic monitoring of this subpopulation