Paper short abstract:

To clarify human population structure in the Ryukyu Islands, genome-wide SNP typing was performed for the Ryukyu Islanders. The results indicated genetic divergence between the people of the Okinawa Islands and the Miyako Islands. We estimated the divergence time between the subpopulations within the Holocene.

Paper long abstract:

The Ryukyu Islands are located in southwestern part of the Japanese archipelago and consist of the Amami Islands, Okinawa Islands, Miyako Islands, and Yaeyama Islands and the other islands. Archaeological evidence has indicated the prehistoric cultural differentiation between the northern Ryukyu—the Amami Islands and the Okinawa Islands― and the southern Ryukyu—the Miyako Islands and Yaeyama Islands. These geographical and archaeological backgrounds imply a population subdivision between these sub-regions. To clarify detailed population structure in the Ryukyu Islands, we performed genome-wide SNP typing for the people of the Okinawa Islands, the Miyako Islands, and the Yaeyama Islands. Principal component analysis and clustering analysis using SNP data suggested a genetic differentiation between people of the Okinawa and the Miyako Islands, as well as migration from the Okinawa Islands to the Yaeyama Islands. No genetic affinity was observed between aboriginal Taiwanese and any Ryukyu populations. Therefore, the genetic differentiation between people of the Okinawa and the Miyako Islands is likely to have been caused by genetic drift rather than admixture with the aboriginal Taiwanese. Based on the genetic differentiation, we estimated the divergence time between people of the Okinawa and the Miyako Islands within the Holocene. These findings suggest that the Pleistocene people, whose bones have been excavated in the southern Ryukyu, did not have major genetic contribution, if any, to the present-day southern Ryukyu Islanders.