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

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 a...

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Published in:Anthropological Science
Main Authors: Hideaki, Kanzawa-Kiriyama, Timothy Adrian, Jinam, Yosuke, Kawai, Takehiro, Sato, Kazuyoshi, Hosomichi, Atsushi, Tajima, Noboru, Adachi, Hirofumi, Matsumura, Kirill, Kryukov, Naruya, Saitou, Ken-ichi, Shinoda
Format: Article in Journal/Newspaper
Language:English
Published: J-Stage 2019
Subjects:
Online Access:http://ir.unimas.my/id/eprint/42054/
http://ir.unimas.my/id/eprint/42054/1/Late%20Jomon.pdf
https://www.jstage.jst.go.jp/article/ase/advpub/0/advpub_190415/_article/-char/en
https://doi.org/10.1537/ase.190415
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spelling ftunivmsarawak:oai:ir.unimas.my:42054 2023-07-16T03:57:11+02:00 Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan Hideaki, Kanzawa-Kiriyama Timothy Adrian, Jinam Yosuke, Kawai Takehiro, Sato Kazuyoshi, Hosomichi Atsushi, Tajima Noboru, Adachi Hirofumi, Matsumura Kirill, Kryukov Naruya, Saitou Ken-ichi, Shinoda 2019 text http://ir.unimas.my/id/eprint/42054/ http://ir.unimas.my/id/eprint/42054/1/Late%20Jomon.pdf https://www.jstage.jst.go.jp/article/ase/advpub/0/advpub_190415/_article/-char/en https://doi.org/10.1537/ase.190415 en eng J-Stage http://ir.unimas.my/id/eprint/42054/1/Late%20Jomon.pdf Hideaki, Kanzawa-Kiriyama and Timothy Adrian, Jinam and Yosuke, Kawai and Takehiro, Sato and Kazuyoshi, Hosomichi and Atsushi, Tajima and Noboru, Adachi and Hirofumi, Matsumura and Kirill, Kryukov and Naruya, Saitou and Ken-ichi, Shinoda (2019) Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. Anthropological Science, 127 (2). pp. 83-108. ISSN 1348-8570 CC Archaeology QH426 Genetics Article PeerReviewed 2019 ftunivmsarawak https://doi.org/10.1537/ase.190415 2023-06-27T17:48:02Z 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. Article in Journal/Newspaper Arctic Universiti Malaysia Sarawak: UNIMAS Institutional Repository Arctic The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) Anthropological Science 127 2 83 108
institution Open Polar
collection Universiti Malaysia Sarawak: UNIMAS Institutional Repository
op_collection_id ftunivmsarawak
language English
topic CC Archaeology
QH426 Genetics
spellingShingle CC Archaeology
QH426 Genetics
Hideaki, Kanzawa-Kiriyama
Timothy Adrian, Jinam
Yosuke, Kawai
Takehiro, Sato
Kazuyoshi, Hosomichi
Atsushi, Tajima
Noboru, Adachi
Hirofumi, Matsumura
Kirill, Kryukov
Naruya, Saitou
Ken-ichi, Shinoda
Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
topic_facet CC Archaeology
QH426 Genetics
description 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.
format Article in Journal/Newspaper
author Hideaki, Kanzawa-Kiriyama
Timothy Adrian, Jinam
Yosuke, Kawai
Takehiro, Sato
Kazuyoshi, Hosomichi
Atsushi, Tajima
Noboru, Adachi
Hirofumi, Matsumura
Kirill, Kryukov
Naruya, Saitou
Ken-ichi, Shinoda
author_facet Hideaki, Kanzawa-Kiriyama
Timothy Adrian, Jinam
Yosuke, Kawai
Takehiro, Sato
Kazuyoshi, Hosomichi
Atsushi, Tajima
Noboru, Adachi
Hirofumi, Matsumura
Kirill, Kryukov
Naruya, Saitou
Ken-ichi, Shinoda
author_sort Hideaki, Kanzawa-Kiriyama
title Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
title_short Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
title_full Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
title_fullStr Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
title_full_unstemmed Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
title_sort late jomon male and female genome sequences from the funadomari site in hokkaido, japan
publisher J-Stage
publishDate 2019
url http://ir.unimas.my/id/eprint/42054/
http://ir.unimas.my/id/eprint/42054/1/Late%20Jomon.pdf
https://www.jstage.jst.go.jp/article/ase/advpub/0/advpub_190415/_article/-char/en
https://doi.org/10.1537/ase.190415
long_lat ENVELOPE(-112.453,-112.453,57.591,57.591)
geographic Arctic
The ''Y''
geographic_facet Arctic
The ''Y''
genre Arctic
genre_facet Arctic
op_relation http://ir.unimas.my/id/eprint/42054/1/Late%20Jomon.pdf
Hideaki, Kanzawa-Kiriyama and Timothy Adrian, Jinam and Yosuke, Kawai and Takehiro, Sato and Kazuyoshi, Hosomichi and Atsushi, Tajima and Noboru, Adachi and Hirofumi, Matsumura and Kirill, Kryukov and Naruya, Saitou and Ken-ichi, Shinoda (2019) Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. Anthropological Science, 127 (2). pp. 83-108. ISSN 1348-8570
op_doi https://doi.org/10.1537/ase.190415
container_title Anthropological Science
container_volume 127
container_issue 2
container_start_page 83
op_container_end_page 108
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