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

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  • KANZAWA-KIRIYAMA HIDEAKI
    Department of Anthropology, National Museum of Nature and Science, Tsukuba
  • JINAM TIMOTHY A.
    Division of Population Genetics, National Institute of Genetics, Mishima
  • KAWAI YOSUKE
    Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo
  • SATO TAKEHIRO
    Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
  • HOSOMICHI KAZUYOSHI
    Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
  • TAJIMA ATSUSHI
    Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
  • ADACHI NOBORU
    Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
  • MATSUMURA HIROFUMI
    Second Division of Physical Therapy, School of Health Sciences, Sapporo Medical University, Sapporo
  • KRYUKOV KIRILL
    Department of Molecular Life Science, School of Medicine, Tokai University, Isehara
  • SAITOU NARUYA
    Division of Population Genetics, National Institute of Genetics, Mishima
  • SHINODA KEN-ICHI
    Department of Anthropology, National Museum of Nature and Science, Tsukuba

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

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<p>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.</p>

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