Genetic lineage of the Amami islanders inferred from classical genetic markers

The peopling of mainland Japan and Okinawa has been gradually unveiled in the recent years, but previous anthropological studies dealing people in the Amami islands, located between mainland Japan and Okinawa, were less informative because of the lack of genetic data. In this study, we collected DNAs from 104 subjects in two of the Amami islands, Amami-Oshima island and Kikai island, and analyzed the D-loop region of mtDNA, four Y-STRs and four autosomal nonsynonymous SNPs to clarify the genetic structure of the Amami islanders comparing with peoples in Okinawa, mainland Japan and other regions in East Asia. We found that the Amami islanders showed genetically intermediate position between mainland Japan and Okinawa in mtDNA and Y-STR. However, the frequencies of several autosomal SNPs in the Amami islanders indicated significant difference from mainland Japanese, and it may be due to the gene flow from Okinawa but not natural selection. Furthermore, extremely high or low frequencies of several alleles implied the existence of founder effect in Kikai islanders. It should be noted that there is room for the interpretation of the results because of the small sample size and number of alleles in the present study, and geographically broad and detailed samplings and genome-wide analyses are awaited.