ArticleProceedings of the National Academy of Sciences of the United States of America2026
High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Prehistoric population movements played a central role in shaping the genetic diversity across Eurasia. As the eastern terminus of the Eurasian continent, the Japanese archipelago provides a pivotal context for reconstructing the genetic interplay between prehistoric indigenous lineages and continental migrations. However, high-resolution genomic evidence from mainland Japan is limited due to poor DNA preservation. In the present study, we report two low-contamination, high-coverage ancient genomes from mainland Japan, namely an Initial Jomon individual (>67-fold) and a Middle Yayoi individual (>46-fold). The genomes enabled diploid genotyping and individual-level demographic inferences at unparalleled resolutions. Demographic reconstructions revealed that while both lineages underwent population contractions during the Last Glacial Maximum (LGM), their subsequent trajectories diverged; the Jomon lineage was characterized by long-term postglacial stability with no discernible expansion, whereas the Yayoi-related ancestral population exhibited gradual and sustained growth. Our analysis further identified a distinct genetic continuity between the Middle Yayoi and present-day mainland Japanese, refining the evolutionary trajectory of modern genetic profiles. Furthermore, the genomic profile of the Yayoi individual reflected a complex ancestral background shaped by continental interactions before their arrival on the archipelago. Notably, the higher salivary amylase (
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