About 8,300 years ago, a woman we call IY1 hunted and gathered along what is now Japan's coast. Roughly 2,300 years after that, a man named DO lived during a time when rice farming was becoming common. Though they never met, these two people have now given scientists an extraordinary gift: the most detailed genetic blueprints ever extracted from ancient humans in Japan.
A team at Kanazawa University, led by researcher Koji Ishiya, managed to read through the DNA of both individuals with remarkable clarity. Even though Japan's warm, humid weather and acidic soils usually break down ancient DNA over time, the researchers achieved genome coverage of about 67-fold for IY1 and 46-fold for DO. That level of detail is like going from a blurry photograph to one sharp enough to count individual eyelashes.
The findings, published in the journal Proceedings of the National Academy of Sciences, reveal new details about Japan's prehistoric population history. IY1, from the Jomon period (known for its iconic pottery with cord-marked patterns), genetically matched other Jomon people previously studied, confirming that the Jomon were an early branch in the family tree that led to modern Japanese people. DO, who lived during the Yayoi period (when new technologies like wet-rice farming arrived from mainland Asia), carried genetic ancestry connected to Northeast Asian populations.
One particularly striking discovery involved a gene related to digesting starchy foods. Both individuals carried relatively high copies of the amylase gene, which helps break down starch in saliva. This suggests that the genetic adaptations for eating plant foods may have deeper roots in East Asia than scientists previously thought, potentially developing even before large-scale farming took hold.
The team also found that both lineages shrank during the Last Glacial Maximum, a frigid period roughly 20,000 years ago. The Jomon-related ancestry stabilized after that, while Yayoi-related ancestry gradually grew, possibly as groups migrated from mainland Asia to the Japanese islands.
Ishiya emphasized that high-coverage genomes open doors to understanding not just broad population movements, but the finer details of how people lived and adapted. "The relationship between plant food use and human genetic variation may have a deeper and more regionally diverse history than previously recognized," he said.
The researchers now plan to study more ancient genomes from different parts and time periods of the Japanese archipelago, combining genetic evidence with clues from plant remains, ancient tools, and environmental data to paint a fuller picture of how migration, climate change, and changing food practices shaped the people who came before us.