High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers

Kato, M.; Mizuno, F.; Taniguchi, Y.; Kondo, O.; Matsushita, M.; Matsushita, T.; Saso, A.; Yoneda, M.; Kurosaki, K.; Wang, L.; Ishiya, K.; Aoto, S.; Watanabe, Y.; Naka, I.; Kim, J.; Ueda, S.; Ohashi, J.

doi:10.64898/2025.12.14.694187

bioRxiv · 10.64898/2025.12.14.694187

High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers

Kato, M.·Mizuno, F.·Taniguchi, Y.·Kondo, O.·Matsushita, M.·Matsushita, T.·Saso, A.·Yoneda, M.·Kurosaki, K.·Wang, L.·Ishiya, K.·Aoto, S.·Watanabe, Y.·Naka, I.·Kim, J.·Ueda, S.·Ohashi, J.

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Abstract

We analyzed eight high-coverage Jomon genomes spanning 9,000-2,800 years ago across the Japanese archipelago. Population genomic analyses revealed substantial genetic homogeneity across time and space reflecting post-glacial isolation, yet temporal stratification emerged: Initial Jomon (Iyai) individuals formed the earliest branch with weaker affinities to present-day Japanese. Using genomes from Todoroki and Chidorikubo sites, we estimated Jomon ancestry in mainland Japanese at [~]20%, substantially higher than previous estimates ([~]13%). Polygenic score analyses, based on the direct analysis of Jomon genomes, provided the genetic evidence for their phenotypic predispositions, including elevated BMI and metabolic trait scores, reduced immune-related scores, and larger cardiac dimensions, patterns consistent with hunter-gatherer adaptations. These ancestral genetic influences, including elevated risks for obesity and dyslipidemia, persist in present-day Japanese. Our findings demonstrate that Jomon populations maintained genetic continuity despite ecological diversity, while their greater-than-expected contribution to present-day Japanese reshapes population history models and reveals how ancient adaptations continue influencing contemporary disease susceptibility.

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Kato, M., Mizuno, F., Taniguchi, Y., Kondo, O., Matsushita, M., Matsushita, T., Saso, A., Yoneda, M., Kurosaki, K., Wang, L., Ishiya, K., Aoto, S., Watanabe, Y., Naka, I., Kim, J., Ueda, S., Ohashi, J.. 2025-12-16. High-Coverage Jomon Genomes Provide Insights into Population Structure and Genetic Traits of Ancient Japanese Hunter-Gatherers. https://doi.org/10.64898/2025.12.14.694187

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