For years, scientists believed the origins of the Japanese population could be traced back mainly to two ancient groups. But a major new DNA study is now challenging that long-held belief and revealing a far more layered story.
Researchers from RIKEN’s Center for Integrative Medical Sciences analyzed thousands of genomes from across Japan and uncovered evidence pointing to a previously overlooked ancestral group connected to northeastern Asia. The findings are now adding fresh momentum to the growing “tripartite origins” theory of Japanese ancestry, as per a report by Science Daily.
The study, published in Science Advances, also revealed that Japan’s population is genetically more diverse than researchers once assumed.
Historians and scientists largely agreed that modern Japanese people descended from two major populations: the ancient Jomon hunter-gatherers and later migrants from East Asia who introduced rice farming and new technologies to the islands. But researchers now believe the story is much more complex.
Could Japan’s ancestry story be incomplete?
The new research examined the genomes of more than 3,200 people living across seven regions of Japan, stretching from Hokkaido in the north to Okinawa in the south. Scientists used whole-genome sequencing instead of older DNA analysis methods, allowing them to study nearly all three billion DNA base pairs in each genome.
According to the research team, this method provides roughly 3,000 times more information than traditional DNA microarray techniques.
"Whole-genome sequencing gives us the chance to look at more data, which helps us find more interesting things," said Chikashi Terao, who led the study at RIKEN.
The scientists combined the DNA findings with family histories, disease records, clinical tests, and medical data to build a large genomic database called the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library, also known as JEWEL.
The results revealed that Japan’s genetic landscape is far more regionally diverse than previously believed.
"The Japanese population isn't as genetically homogenous as everyone thinks," Terao explained. "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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Who was the mysterious third ancestral group?
One of the study’s most significant findings involved evidence supporting a third ancestral source linked to northeastern Asia and possibly connected to the ancient Emishi people.
Researchers found this ancestry was strongest in northeastern Japan and became less common farther west.
Meanwhile, Okinawa showed the highest levels of Jomon ancestry at 28.5%, while western Japan displayed much lower percentages at 13.4%. Scientists also discovered that western Japanese populations shared stronger genetic ties with Han Chinese populations, as per a report by Science Daily.
Researchers believe this reflects major migration waves from continental East Asia between 250 and 794 CE, a period that also saw the spread of Chinese-style government systems, writing, and education throughout Japan.
The findings support earlier ancient DNA studies from 2021 that first proposed the “tripartite origins” theory. Those studies suggested modern Japanese ancestry was shaped by three major ancestral groups instead of two.
Recent research examining ancient skeletons and genomes has continued strengthening that theory, suggesting Japan experienced several migration waves over centuries.
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Why does ancient DNA still matter today?
The study also examined inherited DNA from Neanderthals and Denisovans, two extinct human relatives that interbred with early Homo sapiens thousands of years ago.
Researchers identified 44 ancient DNA regions still present in modern Japanese populations, many unique to East Asians.
One Denisovan-related genetic region inside the NKX6-1 gene was linked to type 2 diabetes and may affect how some patients respond to semaglutide treatments.
Scientists also identified 11 Neanderthal-derived genetic segments associated with conditions such as coronary artery disease, rheumatoid arthritis, and prostate cancer, as per a report by Science Daily.
The team uncovered additional gene variants tied to hypertension, kidney failure, hearing loss, chronic liver disease, and myocardial infarction.
"What we've tried to do is to find and catalog loss-of-function gene variants that are very specific to Japanese people, and to understand why they are more likely to have some specific traits and diseases," Terao said. "We'd like to connect population differences with differences in genetics."
Beyond ancestry, researchers believe the findings could eventually play a major role in personalized medicine and improve healthcare research for Asian populations.
For years, most large genomic studies focused heavily on people of European ancestry, leaving important gaps in scientists’ understanding of disease risk in other groups.
Terao hopes projects like JEWEL can help close that gap.
"It's quite important to expand this to the Asian population so that in the long run, the results can benefit us too," he said.
FAQS
What did the new DNA study discover?
Researchers found evidence of a third ancestral group connected to northeastern Asia.
Why is the discovery important?
It changes long-standing theories about the origins of modern Japanese people.
