For decades, the origin story of the Japanese people fit neatly into two chapters: the Jomon, ancient hunter-gatherers who roamed the archipelago for thousands of years, and the Yayoi, continental migrants who brought rice farming and bronze tools roughly 2,000 to 3,000 years ago. That two-part framework, formalized by physical anthropologist Kazuro Hanihara in 1991 and dominant in textbooks ever since, has now been upended by one of the largest genomic studies of the Japanese population ever conducted.
A research team led by scientists at RIKEN and Osaka University sequenced the full genomes of 3,256 people drawn from BioBank Japan, the country’s premier biomedical repository. Their analysis, published in Science Advances, identified a third ancestral population in the Japanese gene pool: a previously overlooked Northeast Asian lineage tied to the Kofun period, roughly the third through sixth centuries CE. The discovery means that modern Japanese ancestry is not a blend of two source populations but three, each arriving in a distinct historical wave.
The study that broke the old model
The findings emerged from the JEWEL (Japanese Whole-genome sequencing Evaluation of Large-scale data) project, which produced high-depth genome sequences for participants sampled from prefectures across Japan. When the team applied statistical methods designed to detect population structure, three ancestry clusters separated cleanly rather than the expected two.
Jomon-linked ancestry appeared at its highest concentrations in Okinawa and Hokkaido, consistent with long-standing observations that the Ryukyuan and Ainu populations retain stronger genetic ties to Japan’s earliest inhabitants. Yayoi-linked ancestry dominated in western and central Honshu, tracking the historical spread of wet-rice agriculture from the Korean Peninsula. But a third signal, distinct from both, was enriched in regions historically associated with early state formation and the massive burial mounds that define the Kofun era.
The pattern was not subtle. Even after the researchers accounted for known Jomon and Yayoi contributions, the third component persisted as a statistically independent cluster, ruling out the possibility that it was simply noise or an artifact of uneven sampling.
Ancient bones had already hinted at this
The JEWEL results did not arrive in a vacuum. A 2021 ancient-DNA study, also published in Science Advances, had already proposed a tripartite ancestry model based on genomes extracted from Jomon, Yayoi, and Kofun-era skeletal remains. That earlier work, led by researchers including Niall Cooke and Shigeki Nakagome, showed that individuals buried in Kofun-period tombs carried a continental genetic signature that could not be collapsed into the Yayoi migration wave alone.
What the JEWEL study adds is confirmation from living people. Ancient DNA can be fragmentary and drawn from small, geographically limited samples. By demonstrating that the same three-component structure shows up across 3,256 modern genomes spanning the length of Japan, the new research establishes that the Kofun-era influx was not a local event but a population-level force that left a lasting imprint on the nation’s gene pool.
A separate 2024 paper in Nature Communications, examining Jomon-related genetic variants in modern Japanese cohorts, corroborates the ancestry gradients the JEWEL team observed. While that study was not designed to test the tripartite model directly, its results are consistent with it, adding an independent line of supporting evidence.
Why it matters for medicine
Japan’s national biobank infrastructure already supports some of the world’s largest genome-wide association studies. But most of that work has treated the Japanese population as genetically uniform, or at most as a simple Jomon-Yayoi blend. The tripartite model suggests that approach may be masking clinically important variation.
Risk alleles tied to metabolic traits, immune function, or drug metabolism could track differently depending on whether a person’s ancestry skews toward the Jomon, Yayoi, or Kofun-linked lineage. Polygenic risk scores, the statistical tools increasingly used to predict an individual’s likelihood of developing conditions like diabetes or heart disease, may lose accuracy when they ignore this deeper structure. Researchers working in precision medicine now have reason to model all three components explicitly, which could reduce false associations and surface risk variants that matter for specific subgroups but get diluted in nationwide analyses.
The JEWEL study also detected traces of Neanderthal and Denisovan DNA in the modern Japanese genome, inherited tens of thousands of years ago through interbreeding events that predate the settlement of the archipelago. While those archaic fragments are small, they offer a separate window into deep migration history and may carry functional consequences that are only beginning to be explored.
What researchers still do not know
The third ancestral component is labeled “Northeast Asian,” but that geographic tag is broad. Whether the source population lived on the Korean Peninsula, in Manchuria, or elsewhere along the continental rim has not been resolved by genomic data alone. Pinpointing a homeland will require more ancient DNA from Kofun-era burial sites, and those remains present preservation challenges that have so far limited the number of high-quality genomes available from the period.
There is also an open question about internal diversity. The label “Northeast Asian” may lump together several continental groups that were already genetically mixed before any of them crossed to Japan. If that turns out to be the case, the tripartite model could eventually give way to an even more granular picture, with multiple overlapping migration waves during the late Yayoi and early Kofun periods.
Individual-level ancestry proportions from the JEWEL dataset have not been publicly released. The published results present patterns aggregated by region, which means outside researchers cannot yet examine how much of each ancestral component any single participant carries. That level of detail will be essential for building clinical tools like ancestry-adjusted risk scores, and its absence is a limitation that the authors themselves acknowledge.
The boundary between “late Yayoi continental influx” and “early Kofun continental influx” also remains debated among specialists. Migration is rarely a clean, single event, and the genetic boundary between the second and third ancestral waves may prove blurrier than the current model implies.
A more accurate starting point, not the final word
For six decades, the dual-structure model offered a tidy explanation for Japanese origins. It was useful, and it was partly right. But the convergence of ancient DNA and large-scale modern genomics now makes clear that it left out a significant chapter: a wave of continental migrants who arrived during the Kofun period and whose genetic legacy is still detectable in people living across Japan as of June 2026.
The tripartite framework is not likely to be the last revision. As sequencing costs fall and more ancient remains are analyzed, researchers expect to trace finer distinctions within each of the three ancestral lines. But for now, the old two-ancestor story has been retired, replaced by a model that better fits the data and opens new paths for both historical research and medical science.
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*This article was researched with the help of AI, with human editors creating the final content.
