What if the story of Japan’s origins isn’t just a tale of two peoples, but a complex mosaic involving a mysterious third group? A groundbreaking DNA study led by geneticist Chikashi Terao at RIKEN’s Center for Integrative Medical Sciences has flipped long-standing beliefs on their head, revealing a richer and more intricate ancestral history for the Japanese population. This research analyzed whole genomes from more than 3,200 individuals across Japan and reshaped our understanding of the archipelago’s diverse genetic tapestry.
A third ancestral line reshapes Japan’s history
For decades, scholars understood Japan’s genetic makeup as primarily a blend of two groups: the Jomon hunter-gatherers native to the islands and the Yayoi migrants who brought agriculture and metalworking from nearby Asia. But Terao and his team have unveiled a third ancestral lineage: the Emishi, an ancient northeast Asian population historically known for resisting the central Japanese state. This new evidence positions the Emishi as a significant contributor particularly in northeastern Japan, introducing a fresh complexity into Japan’s genetic landscape.
This tri-lineage model addresses puzzling regional genetic differences, showing that Emishi ancestry decreases gradually moving westward. By sequencing whole genomes with impressive resolution, researchers detected rare gene variants linked to the Emishi, underscoring the interplay between these three ancestral lines over thousands of years.
Regional genetic diversity across the archipelago
The study’s participants spanned the full length of Japan, from Hokkaido to Okinawa, highlighting sharp geographic patterns in ancestry. Okinawa had the highest Jomon genetic presence at 28.5%, contrasting sharply with western regions where Jomon ancestry dips to just 13.4%. Conversely, western Japan shows more affinity to Han Chinese populations, reflecting historical Yayoi migrations and centuries of cultural connectivity, including the adoption of governance and educational systems influenced by China.
These findings challenge the perception of Japan as a genetically homogenous nation. Instead, they reveal a population shaped by multiple migration waves and cultural exchanges, explaining much of today’s genetic diversity.
Implications for disease research and personalized medicine
Beyond rewriting history, this research advances medical genetics in Japan. Terao explained that understanding how different ancestral backgrounds distribute certain genetic variants is key to tackling diseases. The team created JEWEL (Japanese Encyclopedia of Whole-genome/Exome Library), a comprehensive reference integrating genomic data with clinical histories and family medical records. JEWEL helps map rare variants linked to disease risks across ancestry groups, making it a powerful tool for developing personalized medicine strategies.
For example, specific gene variants prevalent in one ancestral group could indicate higher susceptibility to particular illnesses, guiding tailored healthcare interventions. This approach aligns with the broader trend in genomics towards precision medicine, which experts believe can revolutionize treatment by considering genetic backgrounds.
Archaic DNA’s lasting impact on modern health
The study also explored how archaic human DNA—from Neanderthals and Denisovans—still influences Japanese health. Researchers identified 44 ancient DNA segments shaping gene expression and disease vulnerability across the population. A notable discovery was a Denisovan-derived variant in the NKX6-1 gene, implicated in type 2 diabetes and potentially affecting responses to semaglutide, a common medication for managing the disease.
Additionally, 11 Neanderthal DNA fragments were associated with significant conditions like coronary artery disease, rheumatoid arthritis, and prostate cancer. These results echo findings in other populations, such as Tibetan high-altitude adaptation linked to Denisovan DNA, and Neanderthal gene clusters affecting COVID-19 severity.
This research from RIKEN deepens our understanding of how multi-layered ancestry and archaic DNA shape contemporary populations and their health risks, signaling just how intertwined history, genetics, and medicine truly are.
What do you think about unraveling Japan’s complex ancestral past? Share your thoughts, questions, or personal insights — your perspective helps keep this fascinating conversation going!