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

A groundbreaking analysis of eight high-coverage Jomon genomes, spanning 9,000 to 2,800 years ago, reveals that ancient Japanese hunter-gatherers exhibited substantial genetic homogeneity with temporal stratification. Initial Jomon (Iyai) individuals formed the earliest branch, showing weaker affinities to present-day Japanese. The study estimates Jomon ancestry in mainland Japanese at approximately 20%, significantly higher than previous estimates of around 13%. Polygenic score analyses provided genetic evidence for phenotypic predispositions in Jomon populations, including elevated BMI and metabolic trait scores, reduced immune-related scores, and larger cardiac dimensions—adaptations consistent with hunter-gatherer lifestyles. These ancestral influences persist today, contributing to contemporary disease susceptibility, such as obesity and dyslipidemia. The findings challenge existing population history models and underscore the enduring impact of ancient adaptations on modern Japanese genetics.

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., Isshiki, M., Naka, I., Kim, J., Ueda, S., & Ohashi, J. (2025). 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