AI interpretationAI-generated
High-coverage Jomon genomes reveal 20% ancestry in modern Japanese and ancient adaptations.
This study analyzed eight high-coverage genomes from Jomon hunter-gatherers who lived in Japan between 9,000 and 2,800 years ago. The genomes show strong genetic uniformity across time and space, but the earliest Initial Jomon individual from Iyai is genetically distinct and less related to modern Japanese. Using genomes from the Todoroki and Chidorikubo sites, the researchers estimate that modern mainland Japanese carry about 20% Jomon ancestry, higher than the previous estimate of 13%. The Jomon had genetic predispositions for higher BMI, metabolic traits, larger heart size, and lower immune scores, which still influence disease risks in Japanese people today.
- Jomon populations were genetically homogeneous across the archipelago, reflecting post-glacial isolation.
- Initial Jomon individuals from Iyai form the earliest branch and have weaker affinities to present-day Japanese.
- Modern mainland Japanese have ~20% Jomon ancestry, higher than the earlier estimate of ~13%.
Sample interpretation
The site_samples table lists 3 ancient individuals, all from the Initial Jomon culture and from site DRR893171. Their Y-chromosome haplogroups are D-Z1513, D-CTS4292, and D-CTS220, all belonging to haplogroup D. Mitochondrial haplogroups include N9b (2 samples) and N9b3 (1 sample). These genetic markers are typical of ancient Jomon and support their distinct ancestry compared to later Japanese populations.
For genealogy enthusiasts
For ancestry enthusiasts, this study shows that Jomon ancestry is more prevalent in modern Japanese than previously thought, and that ancient hunter-gatherer adaptations still affect health today. It also highlights the genetic continuity of Jomon despite ecological diversity, reshaping models of Japanese population history.
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.