High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian

Abstract

The migration of prehistoric humans led to intriguing interactions and changes in cultural and genetic heritage. In Eurasia, prehistoric migration and population replacement have affected present-day humans. The available high-quality genetic evidence for prehistoric migration in eastern Eurasia, particularly in the Far East, is still limited. We succeeded in obtaining low-contaminant, high-coverage genomes from middle-Yayoi (>46-fold coverage) and Initial Jomon (>67-fold coverage) individuals from mainland Japan. This study demonstrated that the Yayoi individual exhibited a genetic profile distinct from that of the indigenous Jomon population of the Japanese archipelago, suggesting that Yayoi ancestry was connected to the peopling of the Eurasian continent. Our high-coverage genome provides interesting insights into the evolution of copy number polymorphisms related to the dietary styles of ancient Japanese people. The copy number estimates of the amylase gene for the Yayoi individual were comparable to those of present-day East Asians who have diets high in starch. This suggests that the population in the middle Yayoi period may have already adapted to high-starch diets, which may have been related to paddy rice agriculture introduced from the continent. Furthermore, the individual from the initial Jomon period showed high amylase copy numbers comparable to those from modern East Eurasia, including modern Japanese. This suggests that some Jomon people may have consumed a high-starch diet then. The high-coverage whole-genome sequence also revealed differences in the demographic backgrounds of the two ancestral populations during the Yayoi and Jomon periods. Our results shed light on the prehistorical events and origins of related migrations from Eurasia at that time and their genetic background, cultural transformations, and links to modern Japanese people.