Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan

Funadomari Jomon people were hunter-gatherers living on Rebun Island, in Hokkaido, Japan approximately 3,500 to 3,800 years ago. In this study, we determined the high-depth and low-depth nuclear genome sequences from a Funadomari Jomon female (F23) and male (F5). We genotyped HLA class I and other anthropological traits. We also identified a pathogenic mutation in the CPT1A gene, causing the Pro479Leu nonsynonymous change, in both F23 and F5. The phylogenetic relationships among F23, modern/ancient Eurasians, and Native Americans showed a deep divergence of F23 in East Eurasia, probably before the split of the ancestor of Native Americans from East Eurasians, but after the split of 40,000 year old Tianyuan. This indicated that the Northern Jomon people were genetically isolated from continental East Eurasians for a long period. However, coastal East Asians are genetically slightly closer to Jomon than other East Eurasians. Moreover, the Y chromosome of F5 belonged to haplogroup D1b2b, which is rare in modern Japanese. These findings provided insights into the history and reconstructions of the ancient human population structures in East Eurasia.