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

Bibliographic Data

ID6135437
AuthorsHideaki Kanzawa-Kiriyama (National Museum of Nature and Science), Hideaki Kanzawa‐kiriyama (0000-0002-7442-5736, National Museum of Nature and Science), Timothy A Jinam (0000-0003-4757-096X, National Institute of Genetics), Yosuke Kawai (0000-0003-1332-156X, The University of Tokyo), Takehiro Sato (0000-0001-9866-0346, Kanazawa University), Kazuyoshi Hosomichi (0000-0003-2712-1825, Kanazawa University), Atsushi Tajima (0000-0001-6808-5491, Kanazawa University), Noboru Adachi (0000-0002-5314-8047, University of Yamanashi), H Matsumura (0000-0001-5453-7987, Sapporo Medical University), Kirill Kryukov (0000-0002-0286-0288, Tokai University), Naruya Saitou (National Institute of Genetics), Ken-Ichi Shinoda (National Museum of Nature and Science), Ken‐ichi Shinoda (National Museum of Nature and Science)
Year2019
Volume127
Issue2
Pages83-108
Publication date2019-01-01
Peer ReviewedYes
Open AccessYes
TypeARTICLE
VenueAnthropological Science (JOURNAL)
Journal identifiersISSN: 0918-7960 • E-ISSN: 1348-8570
PublisherAnthropological Society of Nippon (PUBLISHER • JP)
DOI10.1537/ase.190415
OpenAlexW2946906865
LanguageEN
Citations received20
References cited125

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 \nnuclear 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 \nthe 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 \nwere 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 \ncan be considered as the Jomon Reference Genome for future studies

Biology · Evolutionary biology · Geography · Population · Cancer-related molecular mechanisms research · Demography · Forensic and Genetic Research · RNA modifications and cancer