著者

HIDEAKI KANZAWA-KIRIYAMA TIMOTHY A. JINAM YOSUKE KAWAI TAKEHIRO SATO KAZUYOSHI HOSOMICHI ATSUSHI TAJIMA NOBORU ADACHI HIROFUMI MATSUMURA KIRILL KRYUKOV NARUYA SAITOU KEN-ICHI SHINODA

出版者

一般社団法人 日本人類学会

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

vol.127, no.2, pp.83-108, 2019 (Released:2019-08-29)

参考文献数

139

被引用文献数

43 57

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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.

著者

HIDEAKI KANZAWA-KIRIYAMA TIMOTHY A. JINAM YOSUKE KAWAI TAKEHIRO SATO KAZUYOSHI HOSOMICHI ATSUSHI TAJIMA NOBORU ADACHI HIROFUMI MATSUMURA KIRILL KRYUKOV NARUYA SAITOU KEN-ICHI SHINODA

出版者

日本人類学会

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

pp.190415, (Released:2019-05-29)

被引用文献数

3 57

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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.

著者

TIMOTHY A. JINAM YOSUKE KAWAI NARUYA SAITOU

出版者

The Anthropological Society of Nippon

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

vol.129, no.1, pp.3-11, 2021 (Released:2021-04-27)

参考文献数

44

被引用文献数

3 8

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Previous studies suggested two major migration events during the Jomon and Yayoi periods that affected the genetic diversity of modern Japanese (Yaponesians). We explored the possibility of a three-wave migration model by examining three datasets of modern human DNA: (1) whole mitochondrial (mt) DNA genomes of 1642 Yaponesians; (2) mtDNA haplogroup frequencies of 59105 Yaponesians from 47 prefectures; and (3) genome-wide SNP data of two Yaponesians (Ainu, Okinawa) and whole-genome sequence data of Yamato individuals, the Funadomari Jomon F23 individual, and three East Asian populations (Korean, northern Chinese, and southern Chinese). Past population size change was estimated based on dataset 1, and we clearly observed a steep population increase after the Yayoi period. Principal-component analysis and phylogenetic network analysis were applied to dataset 2, and we confirmed the pattern consistent with our model. An admixture program was used on dataset 3, and we found that the two- and three-layer migration models are both compatible with these SNP data. Taken together, these three datasets provide support for our three-wave, ‘inner dual-structure’ model.

著者

Timothy A. Jinam Hideaki Kanzawa-Kiriyama Naruya Saitou

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.90, no.3, pp.147-152, 2015-06-01 (Released:2015-10-27)

参考文献数

49

被引用文献数

9 27

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The Japanese Archipelago stretches approximately 3,000 kilometers from Hokkaido in the north to the Ryukyu Islands in the south, and has seen human activity since at least 30 thousand years ago (KYA). The Jomon period from 16 to 3 KYA is associated with cord-marked pottery and the people at that time, who were hunter-gatherers, occupied a range of locations across the Japanese Archipelago. The Yayoi period from 3 to 1.7 KYA saw the introduction of migrants from the Asian Continent who brought rice agriculture to the archipelago. The dual-structure model, which is based on craniofacial measurements, proposes that admixture between the Jomon and Yayoi people resulted in current-day Japanese. Subsequent genetic studies using uniparental and autosomal markers in current-day and ancient human samples are widely in support of the dual-structure model. These genetic data have also unveiled the uniqueness of the indigenous Ainu and Ryukyuan people while further demonstrating the genetic substructure within the Mainland Japanese.

著者

TIMOTHY A. JINAM YOSUKE KAWAI NARUYA SAITOU

出版者

The Anthropological Society of Nippon

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

pp.201217, (Released:2021-03-31)

被引用文献数

8

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Previous studies suggested two major migration events during the Jomon and Yayoi periods that affected the genetic diversity of modern Japanese (Yaponesians). We explored the possibility of a three-wave migration model by examining three datasets of modern human DNA: (1) whole mitochondrial (mt) DNA genomes of 1642 Yaponesians; (2) mtDNA haplogroup frequencies of 59105 Yaponesians from 47 prefectures; and (3) genome-wide SNP data of two Yaponesians (Ainu, Okinawa) and whole-genome sequence data of Yamato individuals, the Funadomari Jomon F23 individual, and three East Asian populations (Korean, northern Chinese, and southern Chinese). Past population size change was estimated based on dataset 1, and we clearly observed a steep population increase after the Yayoi period. Principal-component analysis and phylogenetic network analysis were applied to dataset 2, and we confirmed the pattern consistent with our model. An admixture program was used on dataset 3, and we found that the two- and three-layer migration models are both compatible with these SNP data. Taken together, these three datasets provide support for our three-wave, ‘inner dual-structure’ model.