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

Abstract

The Funadomari Jomon people were hunter-gatherers living on Rebun Island, Hokkaido, Japan c. 3500-3800 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), respectively. We genotyped the nuclear DNA of F23 and determined the human leukocyte antigen (HLA) class-I genotypes and the phenotypic traits. Moreover, a pathogenic mutation in the CPT1A gene was identified in both F23 and F5. The mutation provides metabolic advantages for consumption of a high-fat diet, and its allele frequency is more than 70% in Arctic populations, but is absent elsewhere. This variant may be related to the lifestyle of the Funadomari Jomon people, who fished and hunted land and marine animals. We observed high homozygosity by descent (HBD) in F23, but HBD tracts longer than 10 cM were very limited, suggesting that the population size of Northern Jomon populations were small. Our analysis suggested that population size of the Jomon people started to decrease c. 50000 years ago. The phylogenetic relationship 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 40000-year-old Tianyuan, indicating that the Northern Jomon people were genetically isolated from continental East Eurasians for a long period. Intriguingly, we found that modern Japanese as well as Ulchi, Korean, aboriginal Taiwanese, and Philippine populations were genetically closer to F23 than to Han Chinese. Moreover, the Y chromosome of F5 belonged to haplogroup D1b2b, which is rare in modern Japanese populations. These findings provided insights into the history and reconstructions of the ancient human population structures in East Eurasia, and the F23 genome data can be considered as the Jomon Reference Genome for future studies.

Prefecture-level population structure of the Japanese based on SNP genotypes of 11,069 individuals

“…2-5) in agreement with previous studies [8,9,19]. In the previous studies, it has been indicated that the Jomon people are genetically closer to the Ryukyuans than to the mainland Japanese [3,4]. In other words, the mainland Japanese are genetically closer to the Yayoi immigrants from continental East Asia than the Ryukyuans are.…”

The Genomic Formation of Human Populations in East Asia

“…Ancient Taiwan groups and Austronesian-speakers share significantly more alleles with Tai-Kadai speakers in southern mainland China and in Hainan Island 42 than they do with other East Asians (Table S8), consistent with the hypothesis that ancient populations related to present-day Tai-Kadai speakers are the source for the spread of agriculture to Taiwan island around 5000 years ago 43 . The Jomon share alleles at an elevated rate with ancient Taiwan individuals and Ami/Atayal as measured by statistics of the form f 4 (Jomon, Mbuti; Ancient Taiwan/Austronesian-speaker, other Asians) compared with other East Asian groups, with the exception of groups in the Amur Basin Cluster (Table S8) 44 .…”

Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes

“…Haplogroup N9b is represented mainly by lineages of four major subhaplogroups: N9b1, N9b2, N9b3, and N9b4 [34][35][36]. We identified a novel N9b1 mitogenome (MH807371) in one individual from Primorye (Agzu), hence expanding the established geographical scope of the N9b1 haplogroup and disclosing a link between a component of the Udegey ancestry and the Hokkaido Jomon from Japan [36][37][38]. The second prevalent haplogroup is M7a2a3a, which was detected in 8/46 (17.4%) of the Udegey samples (Table 1, Additional file 7: Figure S6).…”