For decades, scientists believed that the Japanese population descended primarily from two ancient groups: Jomon hunter-gatherers who lived in the archipelago for thousands of years, and later migrants from East Asia who brought rice cultivation and new technology to Japan.
But a major genetic analysis from researchers at the RIKEN Center for Integrative Medical Sciences suggests the picture is far more complex.
Using whole-genome sequencing on more than 3,200 people from across Japan, the team found evidence supporting a third ancestral group associated with Northeast Asia and possibly linked to the ancient Emishi people. Conclusion, published in science advancementAdd powerful support to the increasingly debated “Tripartite Origin” theory of Japanese ancestry.
The results also revealed another surprise: Japan’s population is more genetically diverse than many researchers previously thought.
“The Japanese population is not as genetically homogeneous as everyone thinks,” said Chikashi Terao, who led the study at RIKEN. “Our analysis revealed Japan’s sub-population structure at a fine scale, beautifully categorized according to geographic locations in the country.”
A giant DNA map of Japan
To examine Japan’s deep genetic history, researchers analyzed DNA samples collected from seven regions stretching from Hokkaido in the north to Okinawa in the south. The project became one of the largest whole-genome studies ever conducted on a non-European population.
Instead of relying on older DNA microarray methods, the team used whole-genome sequencing, which reads all approximately three billion DNA base pairs in a person’s genome. According to researchers, it provides about 3,000 times more information than traditional techniques.
“Whole-genome sequencing gives us the opportunity to look at more data, which helps us find more interesting things,” Terao explained.
Scientists then combined the genetic information with medical history, disease diagnosis, family history, and clinical test results to create a large database known as the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).
A particularly important focus included rare genetic variants. These unusual DNA changes can sometimes preserve clues about ancient migration patterns and long-lost ancestral populations.
“We reasoned that rare variants could sometimes be discovered in specific ancestral populations, and could be informative in revealing fine-scale migration patterns within Japan,” Terao said.
hidden third ancestor
The analysis highlighted regional differences across Japan.
The Jōmon lineage appeared strongest in Okinawa, where it was found in 28.5% of samples, while western Japan showed much lower levels at 13.4%. The researchers found that people from western Japan had strong genetic ties to Han Chinese populations, likely reflecting major migration waves from continental East Asia between 250 and 794 AD. Those migrations also coincided with the spread of Chinese-style government systems, writing, and education throughout Japan.
The newly identified Emishi-related lineages were concentrated in northeastern Japan and became less common toward the west.
These findings build on earlier ancient DNA studies published in 2021, which first proposed the idea that modern Japanese people come from three major ancestral sources rather than two. Those studies showed that the third migration associated with the Kofun period played a major role in shaping modern Japan.
Recent follow-up studies have continued to strengthen that idea. Researchers analyzing ancient genomes and skeletal remains have found growing evidence that multiple migration waves entered Japan over the centuries, creating a more layered population history than previously thought.
Ancient Neanderthal and Denisovan DNA still influences people today
The study also revealed genetic material inherited from Neanderthals and Denisovans, two ancient human groups that were closely related. homo sapiens thousands of years ago.
Scientists are increasingly interested in why some of these ancient DNA fragments survived in modern humans while others disappeared. In many cases, inherited genes appear to be associated with health, adaptation, or disease risk.
For example, earlier studies have shown that Tibetans inherited a Denisovan-related version of the EPAS1 gene that may have helped humans survive in high-altitude environments. Researchers had previously identified Neanderthal-derived DNA associated with severe COVID-19 complications in some populations.
The Japanese Genome Study identified 44 archaic DNA regions that are still present in modern Japanese populations, many of them unique to East Asians. A Denisovan-derived region within the NKX6-1 gene was associated with type 2 diabetes and may affect how some patients respond to semaglutide treatment.
The researchers also found 11 Neanderthal-derived genetic segments associated with conditions including coronary artery disease, prostate cancer and rheumatoid arthritis.
Towards personalized medicine
In addition to tracing lineage, the researchers believe this work could ultimately improve health care.
The team identified potentially harmful variants in the PTPRD gene that may be associated with high blood pressure, kidney failure and myocardial infarction. They also found common loss-of-function variants in the GJB2 and ABCC2 genes, which are associated with hearing loss and chronic liver disease.
“What we’ve tried to do is find and catalog loss-of-function gene variants that are very specific to Japanese people, and understand why they are more likely to have certain traits and diseases,” Terao said. “We would like to link population differences to differences in genetics.”
This study reflects the broader changes taking place in genetics research. For years, most large genomic databases focused heavily on people of European ancestry, limiting scientists’ understanding of disease risk in other populations.
Terao hopes expanding Jewel with more Asian genomic data will help change that.
“It is very important to expand it to the Asian population so that we can also benefit from its results in the long run,” he said.