Who are the Japanese? Massive DNA project uncovers a forgotten ancestral population

For decades, the accepted explanation for the origins of the Japanese people was relatively straightforward. Modern Japanese populations were understood to descend from two major ancestral groups: the Jomon, ancient hunter-gatherers who inhabited the Japanese archipelago for thousands of years, and the Yayoi, migrants from continental East Asia who arrived bringing rice farming, new technologies, and significant genetic change. This dual-origins model shaped how scientists, historians, and the Japanese public understood their own ancestry. It was tidy, well-supported by earlier research, and, as a major new study has now confirmed, substantially incomplete. Researchers at RIKEN's Centre for Integrative Medical Sciences have published findings that add a previously overlooked third ancestral group to the picture, one linked to the ancient Emishi people of northeastern Japan, and in doing so have pushed the tripartite origins theory of Japanese ancestry from hypothesis to the most well-supported model available. The implications extend well beyond history, into medicine, disease risk, and the future of personalised healthcare in Asia.To investigate Japan's deep genetic history, the RIKEN team analysed 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 sequencing studies ever conducted on a non-European population.Rather than relying on older DNA microarray methods, the team used whole-genome sequencing, a technique that reads nearly all three billion DNA base pairs in a person's genome. According to the researchers, this provides roughly 3,000 times more genetic information than traditional techniques. The resulting database, called the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), combined genetic data with medical histories, disease diagnoses, family histories, and clinical test results."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.One particular focus was rare genetic variants, uncommon DNA changes that can 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 explained. The analysis uncovered striking regional differences across Japan that the dual-origins model could not fully account for. Jomon ancestry appeared strongest in Okinawa, where it was found at 28.5% of samples, whilst western Japan showed much lower levels at 13.4%. 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 that also coincided with the spread of Chinese-style government, writing, and education into Japan.Most significantly, the team found evidence of a distinct third ancestral source concentrated in northeastern Japan that became progressively less common farther west. This ancestry appears linked to the ancient Emishi people a group who historically inhabited northeastern Honshu and resisted incorporation into the Japanese imperial state for centuries."The Japanese population isn't as genetically homogenous as everyone thinks," Terao said. "Our analysis revealed Japan's subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country."These findings build directly on earlier ancient DNA research. A 2021 study published in Science Advances by Nakagome et al. at Trinity College Dublin first proposed the tripartite origins model, sequencing twelve ancient Japanese genomes and finding evidence of a third Kofun-period migration that contributed approximately 71% of modern Japanese ancestry. The RIKEN study now adds large-scale modern genomic evidence supporting and extending that framework. Beyond ancestry, the study examined genetic material inherited from Neanderthals and Denisovans, two archaic human groups that interbred with Homo sapiens tens of thousands of years ago. Scientists have become increasingly interested in why some of this ancient DNA persisted in modern populations, whilst most disappeared and whether it carries health consequences.The Japanese genome analysis identified 44 archaic DNA regions still present in modern Japanese populations, many 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, a finding with direct clinical relevance given the global rise of diabetes and the widespread use of GLP-1 medications.The team also found 11 Neanderthal-derived genetic segments connected to coronary artery disease, prostate cancer, and rheumatoid arthritis. These findings are consistent with earlier research. A 2020 study published in Nature by Zeberg and Pääbo identified a Neanderthal-derived genetic variant associated with severe COVID-19 complications in some populations, and extended that line of inquiry specifically to East Asian populations that had been underrepresented in previous archaic DNA research. The study's medical implications go beyond archaic DNA. The team identified potentially harmful variants in the PTPRD gene linked to hypertension, kidney failure, and myocardial infarction, as well as common loss-of-function variants in the GJB2 and ABCC2 genes associated with hearing loss and chronic liver disease.For years, most large genomic databases focused heavily on people of European ancestry, limiting scientists' ability to assess disease risk across other populations. The RIKEN study is an explicit effort to address that imbalance."What we've tried to do is to find and catalogue 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. It's quite important to expand this to the Asian population so that in the long run, the results can benefit us too."