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 60

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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 60

---

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 AIKO SASO GEN SUWA NARUYA SAITOU

出版者

The Anthropological Society of Nippon

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

vol.121, no.2, pp.89-103, 2013 (Released:2013-08-27)

参考文献数

55

被引用文献数

18 23

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We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.

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 9

---

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

HIDEAKI KANZAWA-KIRIYAMA AIKO SASO GEN SUWA NARUYA SAITOU

出版者

The Anthropological Society of Nippon

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

pp.121113, (Released:2013-03-07)

被引用文献数

8 23 7

---

We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.

著者

Morteza M. Saber Marziyeh Karimiavargani Takanori Uzawa Nilmini Hettiarachchi Michiaki Hamada Yoshihiro Ito Naruya Saitou

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

pp.20-00012, (Released:2021-03-24)

参考文献数

56

被引用文献数

4

---

Down syndrome in humans is caused by trisomy of chromosome 21. DSCR4 (Down syndrome critical region 4) is a de novo-originated protein-coding gene present only in human chromosome 21 and its homologous chromosomes in apes. Despite being located in a medically critical genomic region and an abundance of evidence indicating its functionality, the roles of DSCR4 in human cells are unknown. We used a bioinformatic approach to infer the biological importance and cellular roles of this gene. Our analysis indicates that DSCR4 is likely involved in the regulation of interconnected biological pathways related to cell migration, coagulation and the immune system. We also showed that these predicted biological functions are consistent with tissue-specific expression of DSCR4 in migratory immune system leukocyte cells and neural crest cells (NCCs) that shape facial morphology in the human embryo. The immune system and NCCs are known to be affected in Down syndrome individuals, who suffer from DSCR4 misregulation, which further supports our findings. Providing evidence for the critical roles of DSCR4 in human cells, our findings establish the basis for further experimental investigations that will be necessary to confirm the roles of DSCR4 in the etiology of Down syndrome.

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

9

---

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

Naruya SAITOU Shayire SHOKAT

出版者

日本沙漠学会

雑誌

沙漠研究 (ISSN:09176985)

巻号頁・発行日

vol.26, no.4, pp.223-226, 2017 (Released:2017-05-04)

参考文献数

24

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Family Camelidae includes Guanaco and Vicuna in South America and two-humped camels (Camelus bactrians and C. ferus) and one-humped camels (C. dromedarius) are distributed from Eurasia to Northern Africa. We reviewed studies on mitochondrial and nuclear DNA of camels. We collected 37 complete mitochondrial DNA sequences of Camelid including those of now extinct Camelops which distributed in North America from DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Neighbor-joining trees were constructed for these sequences, and evolution of family Camelidae and genus Camelus are discussed with special reference to demographic changes of C. bactrians and C. dromedarius.

著者

Takashi Kitano Norimasa Matsuoka Naruya Saitou

出版者

The Genetics Society of Japan

雑誌

Genes & Genetic Systems (ISSN:13417568)

巻号頁・発行日

vol.72, no.1, pp.25-34, 1997 (Released:2002-11-26)

参考文献数

30

被引用文献数

13 16

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The phylogenetic relationship among the salmonid fishes of the genus Oncorhynchus has been analyzed using various kinds of markers for a long time. However, there are three major disagreements among those studies; (1) the authenticity of the Pacific salmon group as a monophyletic cluster, (2) the phylogenetic relationship among three Pacific salmons (pink salmon, sockeye salmon, and chum salmon), and (3) the phylogenetic position of masu salmon. We used allozyme electrophoresis to clarify the phylogenetic relationship between the Pacific salmon group and the Pacific trout group. Furthermore, we reanalysed published mitochondrial DNA D-loop sequences (Shedlock et al., 1992). Allozymic data and mtDNA data indicated the following consistent results; (1) all Pacific salmons formed a monophyletic cluster, (2) chum salmon and pink salmon were clustered within those Pacific salmons, (3) masu salmon formed a cluster with other Pacific salmons and diverged first in this group.

著者

NARUYA SAITOU RYOSUKE KIMURA HITOSHI FUKASE AKIRA YOGI SADAYUKI MURAYAMA HAJIME ISHIDA

出版者

日本人類学会

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

vol.119, no.3, pp.231-237, 2011 (Released:2011-12-21)

参考文献数

62

被引用文献数

2 5 3

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Two mainland Japanese males were examined with a computer tomography (CT) X-ray scanner to reconstruct three-dimensional CT simulation images of their cranial anatomy and to check for the presence/absence of 23 nonmetric cranial traits. Surface anatomy for scoring 19 nonmetric cranial variations was clearly observed among the 23 variations. Evaluation of the four other traits might have been disturbed due to dental treatment history, small variations in the images, or X-ray radiation condition. However, these disturbances could be overcome by a combination of simple thin-sliced CT images and magnetic resonance imaging. We have thus developed a new anatomical field for elucidating human morphology.