Ancient genomes reveal early-stage admixture and genetic diversity in the Northwestern Kyushu Yayoi.

The demographic history of the Japanese archipelago was shaped by major episodes of migration and admixture, most notably the transition approximately 3,000 years ago from the Jomon period, a long-established hunter-gatherer tradition, to the Yayoi period, when migrants from the Eurasian continent introduced agriculture and new technologies. However, the timing, extent, and regional variability of the admixture between continental migrants and indigenous Jomon populations remain poorly understood. Northwestern Kyushu has drawn particular attention because skeletal analyses have indicated that Yayoi individuals from this region retain Jomon-like morphological features. However, their genetic background remains unclear. Here, we report whole genome sequences from four Northwestern Kyushu Yayoi individuals excavated from Nagasaki Prefecture, Japan. The two individuals retained nearly full Jomon ancestry, demonstrating that unadmixed Jomon descendants persisted alongside the admixed populations until the transitional phase between the Early and Middle Yayoi periods. The other two individuals showed clear evidence of an admixture, and genetic analyses indicated that gene flow between migrants and the indigenous Jomon population had already begun in this region approximately 2.5–2.6 kya. These findings suggest that the admixture in northwestern Kyushu occurred gradually rather than through a single large-scale migration event at the onset of the Yayoi period, offering new insights into the complex demographic dynamics that shaped the genetic landscape of ancient Japan.The online version contains supplementary material available at 10.1038/s41598-026-34996-7.