Scientists have long told a simple story about Japanese origins: ancient Jomon hunter-gatherers mixed with East Asian migrants who brought rice farming and new technologies. A sweeping new genetic analysis upends that narrative, revealing the population descended from not two but three major ancestral groups, with far greater internal diversity than anyone expected.
Researchers at RIKEN's Center for Integrative Medical Sciences sequenced the complete genomes of over 3,200 people across seven regions, from Hokkaido to Okinawa, generating roughly 3,000 times more genetic data than earlier techniques allowed. The findings, published in Science Advances, provide the first strong evidence for a third ancestral source linked to northeastern Asia and possibly the ancient Emishi people.
"The Japanese population isn't as genetically homogenous as everyone thinks," said Chikashi Terao, who led the project. "Our analysis revealed Japan's subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country."
The team's breakthrough came from focusing on rare genetic variants, DNA changes so uncommon they can pinpoint specific ancestral populations and trace migration patterns across centuries. Combined with medical histories and disease records, the researchers built a massive database called JEWEL to map genetic diversity with unprecedented precision.
A map written in DNA
The regional differences proved striking. Okinawa showed the strongest Jomon ancestry at 28.5% of samples, while western Japan held only 13.4%, indicating different settlement histories. Western Japan instead showed stronger genetic ties to Han Chinese populations, reflecting major migrations between 250 and 794 CE that brought not just people but Chinese government systems, writing, and education.
The newly discovered Emishi-related ancestry concentrated in northeastern Japan and faded westward, filling in a gap that scientists had suspected for years but lacked the genetic evidence to prove. Earlier studies from 2021 had proposed the three-ancestry model, but whole-genome sequencing now supplied the hard data.
Beyond ancestry, the study uncovered something unexpected lurking in modern Japanese DNA: ancient fragments from Neanderthals and Denisovans, extinct human groups that interbred with our ancestors tens of thousands of years ago. Researchers identified 44 archaic DNA regions still present in Japanese populations, many unique to East Asians.
A Denisovan-derived segment in the NKX6-1 gene linked to type 2 diabetes may influence how some patients respond to semaglutide treatments. Eleven Neanderthal-derived segments connected to coronary artery disease, prostate cancer, and rheumatoid arthritis suggest our ancient cousins left behind not just heritage but health risks.
The team also identified harmful variants in genes tied to hypertension, kidney failure, and hearing loss, and loss-of-function variants linked to chronic liver disease. These variants appear specific to Japanese populations, explaining why different groups face different disease risks.
Terao's broader ambition extends beyond ancestry. For decades, major genetic databases skewed heavily European, leaving vast blind spots in understanding disease across other populations. Expanding JEWEL with more Asian data could reshape how medicine approaches risk prediction and treatment for billions of people currently underrepresented in genomic research.
"It's quite important to expand this to the Asian population so that in the long run, the results can benefit us too," Terao said.
Author Jessica Williams: "This study demolishes the old textbook story of Japanese ancestry and hints at a future where medicine finally stops treating non-European populations as genetic afterthoughts."
Comments