Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations

A genetic divergence between the Ryukyu Jomon population and the Hondo (Japanese mainland) Jomon was identified, dating back approximately 6,900 years before present (YBP). This study, which sequenced 273 modern and 25 ancient whole genomes from the Ryukyu Archipelago, revealed that the Ryukyu Jomon experienced severe population bottlenecks with an effective size of around 2,000 individuals. Admixture between the Ryukyu Jomon and historic Hondo migrants occurred roughly 1,000 YBP, coinciding with the introduction of iron tools and agriculture in the Central Ryukyus. The findings highlight distinct demographic histories between modern Hondo and Ryukyu populations, contributing to our understanding of cultural transitions in the region.

Matsunami, M., Kawai, Y., Speidel, L., Koganebuchi, K., Takigami, M., Kakuda, T., Adachi, N., Kameda, Y., Katagiri, C., Shinzato, T., Shinzato, A., Takenaka, M., Doi, N., Bird, N., Hellenthal, G., Yoneda, M., Omori, T., Ozaki, H., et al. (2026). Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations. https://doi.org/10.64898/2026.04.03.712818