Local Jōmon Ancestry in Japanese Genomes

Long before rice paddies, samurai or the first Japanese state, the archipelago was home to hunter-gatherer-fishers now called the Jōmon. Their way of life endured for more than ten millennia, and they made some of the world’s earliest pottery. The Jōmon did not simply disappear when farming arrived: a portion of their ancestry survives in Japanese people today (Cooke et al., 2021; Yamamoto et al., 2024).

About 3,000 years ago, migrants with Northeast Asian ancestry brought wet-rice agriculture during the Yayoi transition. Centuries later, as political power consolidated during the Kofun period, another substantial influx introduced ancestry related to other East Asian populations. The groups mixed. Modern Japanese origins are therefore not a story of a timeless, isolated population—or of one population wholly replacing another.

For decades, the leading model was simpler: indigenous Jōmon plus continental farmers. Ancient DNA complicated it. Genomes spanning the Jōmon, Yayoi and Kofun periods support a tripartite origin for present-day Japanese: Jōmon ancestry, a Northeast Asian component associated with the spread of farming, and a later East Asian component associated with state formation (Cooke et al., 2021). A study involving more than 250,000 modern participants later showed that this Jōmon legacy still helps structure genomic variation across the archipelago (Yamamoto et al., 2024).

This turns a present-day Japanese genome into a historical mosaic. One stretch of chromosome can be more Jōmon-like; the next can be more mainland-like, because recombination has repeatedly cut and reshuffled ancestral chromosomes. Every Japanese chromosome is, in that sense, an archaeological site.

And that creates the real mystery. Did these ancestries merely mix, or did natural selection edit the mosaic after admixture—preserving Jōmon-derived segments in some regions while thinning them in others? The question has become especially timely after Watanabe and colleagues analysed 42 Jomon genomes and reported signals consistent with cold adaptation in pathways involving thermogenesis, lipid metabolism and cold sensation (Watanabe et al., 2026). Here I ask whether Jōmon ancestry is unusually enriched or depleted around variants used in three polygenic scores: educational attainment, height and skin colour.