A third ancestral group may be hiding inside the DNA of modern populations in Japan. A genetic study found the ancestry of people in Japan today may not fit into the long-standing two-origin model as once thought.
After analyzing the genomes of more than 3,200 people across Japan, evidence of a third ancestral component linked to northeastern Asia alongside the Indigenous Jomon hunter-gatherers and later East Asian migrants was found.
Published in Science Advances, the study used whole-genome sequencing to examine DNA from seven regions stretching from Hokkaido to Okinawa. The results support the “tripartite origins” theory proposed in 2021 and point to genetic differences across different parts of Japan.
Different Regions of Japan Showed Distinct Ancestry Patterns
The team analyzed the full genomes of 3,256 people from seven regions across Japan. Looking at entire genomes instead of smaller DNA samples gave them a much better picture of population differences and ancient migration patterns still preserved in modern DNA.
Okinawa carried the strongest traces of Jomon ancestry, accounting for roughly 28.5 percent of ancestry. Western Japan, meanwhile, showed closer genetic connections to mainland East Asia, likely reflecting later migration into the region.
The third ancestry signal appeared most strongly in northeastern Japan. The researchers linked it to populations from northeastern Asia and possibly the historical Emishi people, who once lived in northern Japan and whose origins are still debated.
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Modern Japanese Genomes Still Carry Neanderthal and Denisovan DNA
The genomes also carried traces of Neanderthals and Denisovans, two extinct human relatives that interbred with Homo sapiens.
The team identified 44 archaic DNA regions still present in modern Japanese populations, many unique to East Asia.
One Denisovan-linked DNA segment was associated with type 2 diabetes and may influence how some people respond to semaglutide, the drug widely used to treat diabetes and obesity. Other Neanderthal-linked regions were connected to coronary artery disease, rheumatoid arthritis, prostate cancer, and Graves’ disease.
