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Modern Japanese people largely descend from three ancestral groups, a new study suggests. The research also reveals genetic ties with our closest extinct relatives — the Neanderthals and Denisovans — and how these genes may affect present-day disease risk.

In one of the largest non-European analyses of its kind, scientists sequenced the DNA of more than 3,200 Japanese people across seven regions of the country, extending from the snowy mountains of Hokkaido in the north to the subtropical southern shores of Okinawa.

The researchers collated these genetic data, along with relevant clinical information, into a large new database called the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).

The team discovered that modern Japanese people mostly descended from three ancestral groups: Neolithic Jomon hunter-gatherers; a group believed to have been the ancient predecessors of the Han Chinese; and an unidentified group with ties to Northeast Asia. This finding further challenges a contested, three-decades-long hypothesis that Japanese people originated from the Jomon people and, later, rice-farming Yayoi migrants from continental Asia.

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We attempted to gain hints about the potential ancestral origins of K1 to K3. Previous studies have suggested that Japanese carry Jomon and EA ancestry (represented by Han Chinese). Recently, the presence of Northeast Asian (NEA) ancestry has been proposed on the basis of analyses of ancient genomes. In this context, we analyzed our data together with modern and ancient genetic data of Jomon, EA, and NEA. Using f4 ratio statistic, we estimated that Okinawa had the highest Jomon ancestry (28.5%), followed by Northeast (18.9%), and the lowest in West (13.4%). These results align with prior studies demonstrating a high genetic affinity between Jomon and Okinawa people.

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