Ancient genomics reveals tripartite origins of Japanese populations

Prehistoric Japan underwent rapid transformations in the last 3,000 years, first from foraging to wet-rice farming, and then to state-formation. A long-standing hypothesis posits that mainland Japanese populations derive dual-ancestry from indigenous Jomon hunter-gatherer-fishers and later Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. Here, we report 12 ancient Japanese genomes from pre- and post-farming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1,000 over several millennia, with a deep divergence from continental populations dated to 20,000-15,000 years ago, a period which saw the insularisation of Japan through rising sea-levels. Wet-rice cultivation was introduced in the Yayoi period by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.