The traditional model, which I’ve alluded to before on this weblog before, is that Japan is a synthesis of Jomon and Yayoi, with the latter dominant, and bringing rice-agriculture to the islands. A new paper in Science indicates it may be more complicated than that.
Prehistoric Japan underwent rapid transformations in the past 3000 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 succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced 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.
The Kofun period begins around 300 AD. The implication here is that there was a mass migration from the Asian continent less than 2,000 years ago, likely from Korea. The first agriculturalists, the Yayoi, seem to be a mix of native Jomon and individuals with strong affinities to populations in Manchuria.
Here’s a stylized representation that captures the turnover:
The Jomon are interesting because these results indicate low effective population, and, deep connections with ANE (Ancient North Eurasians). They also seem a clade deep within Northeast Asians, dating to the Pleistocene.
In any case, the authors admit that their sampling of the Yayoi is weak, so there needs to be follow-up here. If it does turn out that the Japanese are mostly Kofun-period, then I think that recalibrates our sense of its history a great deal. The Japan of the 7th century which enters into history was a very young nation.