For decades, scientists believed the Japanese population largely descended from two ancient groups: the Jomon hunter-gatherers who lived in the archipelago for thousands of years, and later migrants from East Asia who brought rice farming and new technologies to Japan.
But a major genetic analysis from researchers at RIKEN’s Center for Integrative Medical Sciences suggests the picture is far more complicated.
Using whole-genome sequencing on more than 3,200 people from across Japan, the team found evidence supporting a third ancestral group tied to northeastern Asia and possibly linked to the ancient Emishi people. The findings, published in Science Advances, add powerful support to the increasingly discussed “tripartite origins” theory of Japanese ancestry.
The results also revealed something else surprising: Japan’s population is genetically more diverse than many researchers once assumed.
“The Japanese population isn’t as genetically homogenous as everyone thinks,” said Chikashi Terao, who led the study at RIKEN. “Our analysis revealed Japan’s subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country.”
A Massive DNA Map of Japan
To investigate 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 nearly all three billion DNA base pairs in a person’s genome. According to the researchers, this provides roughly 3,000 times more information than traditional techniques.
“Whole-genome sequencing gives us the chance to look at more data, which helps us find more interesting things,” Terao explained.
The scientists then combined the genetic information with medical histories, disease diagnoses, family histories, and clinical test results to build a large database known as the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).
One especially important focus involved rare genetic variants. These uncommon DNA changes can sometimes preserve clues about ancient migration patterns and long-lost ancestral populations.
“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,” Terao said.
The Hidden Third Ancestor
The analysis uncovered striking regional differences across Japan.
Jomon ancestry appeared strongest in Okinawa, where it was found in 28.5% of samples, while western Japan showed much lower levels at 13.4%. Researchers found that people in western Japan had stronger genetic connections to Han Chinese populations, likely reflecting major migration waves from continental East Asia between 250 and 794 CE. Those migrations also coincided with the spread of Chinese-style government systems, writing, and education throughout Japan.
The newly identified Emishi-related ancestry was concentrated in northeastern Japan and became less common farther west.
The findings build on earlier ancient DNA studies published in 2021 that first proposed the idea that modern Japanese people descend from three major ancestral sources instead of two. Those studies suggested that a third migration connected to the Kofun period played a major role in shaping modern Japan.
Recent follow-up studies have continued strengthening that idea. Researchers analyzing ancient genomes and skeletal remains have found increasing evidence that multiple migration waves entered Japan over centuries, creating a much more layered population history than previously believed.
Ancient Neanderthal and Denisovan DNA Still Affects People Today
The study also explored genetic material inherited from Neanderthals and Denisovans, two ancient human groups that interbred with Homo sapiens tens of thousands of years ago.
Scientists have become increasingly interested in why some of these ancient DNA fragments survived in modern humans while others disappeared. In many cases, the inherited genes appear linked to health, adaptation, or disease risk.
For example, earlier studies showed that Tibetans inherited a Denisovan-related version of the EPAS1 gene that may have helped humans survive in high-altitude environments. Researchers also previously identified Neanderthal-derived DNA associated with severe Covid-19 complications in some populations.
The Japanese genome study identified 44 archaic DNA regions still present in modern Japanese populations, many of them unique to East Asians. One Denisovan-derived region inside the NKX6-1 gene was associated with type 2 diabetes and may influence how some patients respond to semaglutide treatments.
Researchers also found 11 Neanderthal-derived genetic segments connected to conditions including coronary artery disease, prostate cancer, and rheumatoid arthritis.
Toward Personalized Medicine
Beyond tracing ancestry, the researchers believe the work could eventually improve healthcare.
The team identified potentially harmful variants in the PTPRD gene that may be linked to hypertension, 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 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.”
The study reflects a broader shift happening in genetics research. For years, most large genomic databases heavily focused 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’s quite important to expand this to the Asian population so that in the long run, the results can benefit us too,” he said.
