The Jomon people were prehistoric residents of the Japanese archipelago who occupied the region from ca. 16,500 to 2,300 years before present (BP). While recent accumulation of ancient genomes and genome-wide data of the Jomons has substantially enhanced our understanding of their genetic profiles and contribution to present-day populations, their genetic history in the Jomon-period archipelago, spanning over 14,000 years in time and 2,000 km in distance, remains scarcely investigated. Here we report multiple findings illuminating the Jomon genetic history based on the analysis of the genetic relationship between published ancient genome-wide data of 23 Jomon and Jomon-like individuals. First, the Initial Jomon individual from Shikoku, dated to ca. 9,000 BP, forms a common outgroup to the remaining later Jomon individuals, suggesting a population turnover in western Japan. Second, genetically Jomon-like individuals outside the Jomon archaeological context, found in the Miyako Island in Ryukyu and the Yokjido island in the southern coast of Korea, show the closest genetic affinity with the Late Jomon individual from Shikoku, narrowing down their sources in space and time. This study highlights a dynamic history of the Jomon people in and out of the Japanese archipelago and calls for a large-scale investigation of the ancient Jomon genomes.

Jomon, population structure, admixture, Japanese prehistory, maritime migration