Who Are the Japanese? New DNA Study Shocks Scientists

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A genetic study led by scientists from RIKEN’s Center for Integrative Medical Sciences has uncovered evidence that people in Japan descend from three ancestral groups.

The findings, published recently in the journal Science Advances, challenge the longstanding belief that there were two main ancestral groups in Japan: the indigenous Jomon hunter-gatherer-fishers and the rice-farming migrants from east Asia.

Instead, the researchers identified a third group with potential ties to north-east Asia—the so-called Emishi people, thus lending further credence to a ‘tripartite origins’ theory first suggested in 2021.

The Japanese population isn’t as genetically homogenous as everyone thinks, says RIKEN’s Chikashi Terao, who led the study. “Our analysis revealed Japan’s subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country.”

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One topic of particular interest to Terao’s was the study of rare gene variants. “We reasoned that rare variants can sometimes be traced back to specific ancestral populations, and could be informative in revealing fine-scale migration patterns within Japan,” he explains.

Their hunch proved right, helping to reveal the geographic distribution of Japanese ancestry. Jomon ancestry, for instance, is most dominant in the southern, subtropical shores of Okinawa (found in 28.5% of samples) while lowest in the west (just 13.4% of samples). By contrast, people living in western Japan have more genetic affinity with Han Chinese people—which Terao’s team believes is likely associated with the influx of migrants from east Asia between the year 250 and year 794, and is also reflected in the comprehensive historical adoption of Chinese-style legislation, language, and educational systems in this region.

Emishi ancestry, on the other hand, is most common in northeastern Japan, decreasing to the west of the country.

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The researchers also examined JEWEL for genes inherited from Neanderthals and Denisovans, two groups of archaic humans that interbred with Homo sapiens. “We are interested in why ancient genomes are integrated and kept in modern human DNA sequences,” says Terao, who explains that such genes are sometimes associated with certain traits or conditions.

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The analysis by Terao’s team shed light on 44 ancient DNA regions present in Japanese people today, most of which are unique to East Asians. These include a Denisovan-derived one, located within the NKX6-1 gene, known to be associated with type 2 diabetes, which the researchers say could affect a person’s sensitivity to semaglutide, an oral medication used to treat the disease. They also identified 11 Neanderthal-derived segments linked to coronary artery disease, prostate cancer, rheumatoid arthritis, and four other conditions.

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