A pair of exceptionally well-preserved ancient genomes is reshaping the story of how the people of Japan emerged, revealing genetic continuity with modern Japanese populations, multiple streams of ancestry arriving from the Asian mainland, and surprisingly complex adaptations linked to starch-rich foods long before intensive agriculture transformed East Asia.
The genomes belonged to two individuals who lived thousands of years apart. One, identified as IY1, was a woman from the Initial Jomon period who lived approximately 8,300 years ago. The other, known as DO, was a man from the Middle Yayoi period who lived about 2,300 years ago. Researchers led by Koji Ishiya of Kanazawa University reconstructed their genomes at an unusually high level of detail, producing approximately 67-fold autosomal coverage for IY1 and 46-fold coverage for DO. In genomic research, coverage refers to the average number of times each position in DNA is sequenced; higher coverage makes it easier to distinguish genuine ancient variants from damage and technical errors.
Recovering such detailed genetic information from ancient remains in Japan is particularly challenging. Warm, humid conditions accelerate DNA degradation, while acidic soils can further destroy the mineral structure that protects genetic material. Ancient DNA is also vulnerable to chemical alterations that create false mutations. The depth achieved in these two genomes therefore allowed the researchers to examine not only broad population relationships but also demographic history and complex genetic regions that are often inaccessible in low-coverage ancient samples.
IY1’s genetic profile clustered with previously analyzed Jomon individuals, supporting the existence of an early-diverging Jomon-related lineage. The Jomon peoples lived across the Japanese archipelago for thousands of years before and during the development of agriculture in neighboring regions. Their descendants contributed ancestry to present-day Japanese populations, but the new data emphasize that this contribution was part of a long and complicated population history rather than a simple replacement of one group by another.
The genome of DO told a different story. Compared with Jomon individuals, he was genetically closer to present-day mainland Japanese and carried ancestry components associated with Northeast Asia. When the researchers modeled Yayoi genetic variation, they found evidence consistent with contributions from several ancient continental populations, including groups connected to the Amur River region, Inner Mongolia, and Shandong. These populations should not automatically be interpreted as the direct ancestors of the Yayoi. Instead, they function as genetic proxies for related populations that may have participated in a broad network of migration and interaction across East Asia.
The findings support a model in which the Yayoi population history was shaped by more than one movement of people from the continent. During the Yayoi period, new communities, technologies, and subsistence practices spread through parts of the Japanese archipelago, including rice cultivation in many regions. Genetic evidence now suggests that the people associated with these changes were themselves connected to diverse continental populations. This complexity helps explain why modern Japanese ancestry cannot be reduced to a single continental source layered onto an isolated Jomon population.
The study also reconstructed population trajectories reaching back to the Last Glacial Maximum, the coldest phase of the most recent ice age, which peaked roughly 20,000 years ago. Demographic analyses indicated that the ancestral populations of both IY1 and DO experienced declines around this period. The Yayoi-related lineage later showed gradual growth, possibly beginning on the Eurasian continent before migration into the Japanese archipelago. The Jomon-related lineage, by contrast, remained comparatively stable. These patterns suggest that climate-driven population contraction and later expansion influenced the genetic foundations of prehistoric East Asia.
One of the most unexpected results involved the amylase gene region. Salivary amylase begins the digestion of starch in the mouth, and variation in the number of copies of the amylase gene can influence the amount of enzyme produced. Both ancient individuals carried relatively high amylase copy numbers. Because copy-number variation can be difficult to measure accurately in degraded DNA, the high coverage of these genomes was essential. The result indicates that substantial starch-related genetic diversity existed in prehistoric East Eurasia before the spread of large-scale agriculture, challenging the assumption that such variation arose only after farming became dominant.
The discovery does not prove that either individual depended on a particular crop or that high amylase copy number was a direct response to rice cultivation. Human diets are shaped by local ecology, food processing, cultural practice, and seasonal availability, while genetic traits can follow multiple evolutionary pathways. Instead, the genomes show that the relationship between plant-food use and human biology was already regionally diverse. The researchers plan to examine additional high-coverage genomes from different areas and periods of the Japanese archipelago, combining DNA evidence with plant and animal remains, stable-isotope studies, and reconstructions of ancient environments. Together, these approaches could reveal how migration, climate change, and changing food systems interacted to create the genetic diversity seen in Japan today.
Subject of Research: Ancient human genomics, Jomon and Yayoi population history, Japanese ancestry, demographic change, and prehistoric starch-related genetic variation.
Article Title: High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan
News Publication Date: 23 July 2026
Web References: https://doi.org/10.1073/pnas.2606162123
References: Ishiya et al., Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.2606162123
Image Credits: Adapted from Ishiya et al. (2026), Proceedings of the National Academy of Sciences.
Keywords: Ancient DNA, genomics, Jomon, Yayoi, Japanese ancestry, population history, Northeast Asia, human evolution, amylase, starch digestion, prehistoric diet, archaeology.
