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

NOBORU ADACHI HIDEAKI KANZAWA-KIRIYAMA TAKASHI NARA TSUNEO KAKUDA IWAO NISHIDA KEN-ICHI SHINODA

出版者

The Anthropological Society of Nippon

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

pp.2012132, (Released:2021-03-31)

被引用文献数

6

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Starting 16000 years ago, the Neolithic lifestyle known as the Jomon culture spread across the Japanese archipelago. Although extensively studied by archaeology and physical anthropology, little is known about the genetic characteristics of the Jomon people. Here, we report the entire mitogenome and partial nuclear genome of skeletal remains from the initial Jomon period that were excavated from the Higashimyo shell midden site at Saga City, Kyushu Island, Japan. This is the first genome analysis of the initial Jomon people of Kyushu Island. These results provide important data for understanding the temporal transition and regional differences of the Jomon people. The mitochondrial DNA and Y-chromosome haplogroups were similar to those found in the previously reported later Jomon people. Moreover, comparison of three nuclear genomes from the initial to final Jomon periods indicated genetic continuity throughout the Jomon period within the Japanese archipelago with no significant evidence of admixture. This indicates that the genetic differentiation found among the Jomon people was promoted by the progression of regionalization throughout the Jomon period. Further accumulation of high-quality Jomon genome data spanning a wide range of regions and ages will clarify both intimate regional and temporal differences of the Jomon people and details of their admixture history with rice farmers, as suggested by Jomon mitochondrial genome data. The results obtained from this study provide important information for further analysis.

著者

NOBORU ADACHI HIDEAKI KANZAWA-KIRIYAMA TAKASHI NARA TSUNEO KAKUDA IWAO NISHIDA KEN-ICHI SHINODA

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.13-22, 2021 (Released:2021-04-27)

参考文献数

42

被引用文献数

1 6

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Starting 16000 years ago, the Neolithic lifestyle known as the Jomon culture spread across the Japanese archipelago. Although extensively studied by archaeology and physical anthropology, little is known about the genetic characteristics of the Jomon people. Here, we report the entire mitogenome and partial nuclear genome of skeletal remains from the initial Jomon period that were excavated from the Higashimyo shell midden site at Saga City, Kyushu Island, Japan. This is the first genome analysis of the initial Jomon people of Kyushu Island. These results provide important data for understanding the temporal transition and regional differences of the Jomon people. The mitochondrial DNA and Y-chromosome haplogroups were similar to those found in the previously reported later Jomon people. Moreover, comparison of three nuclear genomes from the initial to final Jomon periods indicated genetic continuity throughout the Jomon period within the Japanese archipelago with no significant evidence of admixture. This indicates that the genetic differentiation found among the Jomon people was promoted by the progression of regionalization throughout the Jomon period. Further accumulation of high-quality Jomon genome data spanning a wide range of regions and ages will clarify both intimate regional and temporal differences of the Jomon people and details of their admixture history with rice farmers, as suggested by Jomon mitochondrial genome data. The results obtained from this study provide important information for further analysis.

著者

KEIICHI OMOTO HISAO BABA EISAKU KANAZAWA MINORU YONEDA KEN-ICHI SHINODA HIDEAKI KANZAWA-KIRIYAMA TSUNEO KAKUDA NOBORU ADACHI KAZUHIRO SAKAUE FERNANDO A. ALMEDA JR. LESLIE E. BAUZON

出版者

The Anthropological Society of Nippon

雑誌

Anthropological Science (ISSN:09187960)

巻号頁・発行日

pp.200706, (Released:2020-10-07)

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We examined fragmentary human skeletal remains from Escalon Cave near Surigao City, northeastern Mindanao, the Philippines, with respect to the morphology of bones and teeth, radiocarbon dating, and mitochondrial DNA (mtDNA) haplogroup. These remains contained parts of the left temporal bone, the right humerus, the right femur, the upper right first and second premolars, and the first molar. They are presumed to belong to an early-middle adult male, whom we named the Escalon Man. Using the femur sample, we estimated the 14C date of the individual at 2692 ± 39 years BP (uncalibrated). His stature, estimated from the maximum femur length, was about 170 cm—this makes him much taller than the Aeta and the Mamanwa, who are indigenous negrito hunter-gatherers of the Philippines. The femur is sturdy and shows well-developed muscle markings. Numerous narrow grooves on the humerus were found in close proximity to each other, but we could not prove whether these are artificial cut marks made by humans with sharp-edged tools or scratches from some non-human entity. The mesiodistal crown diameters of the molar and premolars are large and resemble those of native Oceanians. Analysis of mtDNA haplogroup was carried out using a DNA sample extracted from a molar. A next-generation sequencer was used to determine the nucleotide sequences of the mtDNA genome. The results indicated that the Escalon Man belongs to the haplogroup E1a1a, which is known to be the marker of Austronesian-speaking agriculturist populations that originated in Taiwan and spread southwards through the Philippines to the Western Pacific, since about 4000 BP. Thus, the Escalon Man was likely a member of the late Neolithic or early Metal Age agriculturist peoples who settled in northeastern Mindanao and who may be the ancestors of the territory’s present-day occupants, such as the Manobo.

著者

Takahiro KUNISADA Ken-ichi SHINODA

出版者

The Anthropological Society of Nippon

雑誌

Journal of the Anthropological Society of Nippon (ISSN:00035505)

巻号頁・発行日

vol.98, no.4, pp.471-482, 1990 (Released:2008-02-26)

参考文献数

17

被引用文献数

1 1

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縄文時代人骨3体から DNA を抽出し, PCR 法を用いてミトコンドリア DNAを増幅して解析を行い,その方法論的な問題点を考察した。今回用いた方法では,試料の保存状態•部位にかかわらず,ほぼ安定して DNA の分離と増幅が可能であり,その有効性が確かめられた。分離された DNA は,そのほとんどがヒト由来のものではなかったが, PCR 法によりヒトミトコンドリア由来の DNA の増幅を確認することができた。ミトコンドリア DNAのV 領域および D ループ領域に対する制限酵素を用いた解析では多型は検出できなかった。しかし増幅した V 領域の塩基配列を決定したところ,1個体では1箇所の変異が見出された。

著者

Ken-ichi Shinoda

出版者

国立科学博物館

雑誌

Bulletin of the National Museum of Nature and Science. Series D, Anthropology (ISSN:24340979)

巻号頁・発行日

vol.40, 2014-11-22