Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago

A fine-scale genetic analysis of the Miyako Islands, part of the UNESCO-listed Ryukyu Archipelago, reveals distinct subpopulations with divergent demographic histories. Using genome-wide single-nucleotide polymorphisms (SNPs) from 1,240 individuals, researchers identified three subpopulations—Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema—with the latter showing unique gene flow patterns linked to historical immigration during the Gusuku period (900–500 BP). Haplotype-based analyses and coalescent demographic inference suggest that the Irabu/Ikema population split from the ancestral Ryukyu group around 41 generations ago, followed by further divergences. These findings provide critical insights into the genetic structure of modern Miyako populations, with implications for disease association studies.

Matsunami, M., Koganebuchi, K., Imamura, M., Ishida, H., Kimura, R., & Maeda, S. (2021). Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago. Molecular Biology and Evolution, 38(5), 2045–2056. https://doi.org/10.1093/molbev/msab005