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Development and Application of Platform for Paleogenomics

Planned Research

Project AreaA New Archaeology Initiative to Elucidate the Formation Process of Chinese Civilization
Project/Area Number 20H05822
Research Category

Grant-in-Aid for Transformative Research Areas (A)

Allocation TypeSingle-year Grants
Review Section Transformative Research Areas, Section (I)
Research InstitutionKanazawa University

Principal Investigator

Gakuhari Ttakashi  金沢大学, 古代文明・文化資源学研究所, 准教授 (70749530)

Co-Investigator(Kenkyū-buntansha) 中込 滋樹  金沢大学, 古代文明・文化資源学研究所, 客員准教授 (40625208)
石谷 孔司  金沢大学, サピエンス進化医学研究センター, 助教 (40826062)
澤藤 りかい  九州大学, 比較社会文化研究院, 講師 (50814612)
和久 大介  東京農業大学, 国際食料情報学部, 助教 (60793578)
Project Period (FY) 2020-11-19 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥91,130,000 (Direct Cost: ¥70,100,000、Indirect Cost: ¥21,030,000)
Fiscal Year 2024: ¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2023: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000)
Fiscal Year 2022: ¥19,890,000 (Direct Cost: ¥15,300,000、Indirect Cost: ¥4,590,000)
Fiscal Year 2021: ¥19,500,000 (Direct Cost: ¥15,000,000、Indirect Cost: ¥4,500,000)
Fiscal Year 2020: ¥14,300,000 (Direct Cost: ¥11,000,000、Indirect Cost: ¥3,300,000)
Keywordsパレオゲノミクス / 考古科学 / 古人骨 / 生物遺体 / 新石器時代 / 東アジア / 中国 / 中国考古学 / 遺跡出土骨 / 日本 / 新石器時代後期 / 古代ゲノム
Outline of Research at the Start

古代中国内外との文化的ハイブリディティ形成過程において、社会の最小単位である個人が他地域文明の個人とどの様に接触し、その交流が各地域文化内でどの様に社会的に受容されていたか、その実態は未だ不明な点が多い。また、西方からの古代中国への文化的インパクトが生じる過程では、もともと中国にはいなかった家畜・野生種・微生物も併せて侵入してきたと考えられる。これら多様な生物群の伝播ルートは、未だその実態を示す直接的な証拠は得られていない。本計画研究では、大規模な古代ゲノムデータ解析を可能とする専用プラットフォームを構築することで、古代中国文明形成期における中国内外のハイブリディティの可視化を試みる。

Outline of Final Research Achievements

This project was conducted with the goal of creating a platform for analyzing the dynamics of human migration in the dawn of ancient Chinese civilization, both in terms of the genetic information of humans themselves and that of non-human organisms. Using this platform, studies were conducted using ancient human remains and other organisms excavated in China and neighboring countries, which successfully visualized the dynamics of human migration in the dawn of Chinese civilization and the population size in each region and time period, providing new information for archaeological research.

Academic Significance and Societal Importance of the Research Achievements

これまでの中国における古代文明の起源研究は、遺跡出土考古遺物の型式学的な評価に基づいた人の移動の推察によって形作られてきた。しかし、考古遺物であるモノの移動は、人自体の移動を示す直接的な証拠にはならないため、人自体のゲノムデータに基づいた人の
移動のダイナミクスを科学的に評価するための仕組みづくりが必要であった。本研究では、中国古代文明における古代ゲノムデータ解析に応用可能な解析プラットフォームの構築を実践し、プラットフォームを用いた応用研究によって多くの成果を得た。さらに、中国古代文明研究では見落とされていた、人の性別に偏りがある移動の証拠を発見し、過去の人口規模の可視化を世界で初めて行った。

Report

(6 results)
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (59 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (19 results) Journal Article (18 results) (of which Int'l Joint Research: 13 results,  Peer Reviewed: 17 results,  Open Access: 17 results) Presentation (20 results) (of which Int'l Joint Research: 5 results,  Invited: 7 results) Funded Workshop (2 results)

  • [Int'l Joint Research] ダブリン大学(アイルランド)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] ソウル大学/キョンヒ大学(韓国)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] 中国社会科学院(中国)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] モンゴル科学アカデミー/モンゴル国立大学(モンゴル)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] トゥールーズ第3大学(フランス)

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research]

    • Related Report
      2024 Annual Research Report
  • [Int'l Joint Research] ダブリン大学(アイルランド)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 中国社会科学院(中国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 中央アジア・アメリカ大学(キルギス)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] モンゴル科学アカデミー(モンゴル)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] ダブリン大学(アイルランド)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] 中国社会科学院(中国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] 中央アジア・アメリカ大学(キルギス)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] 北京大学/中国社会科学院(中国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] ダブリン大学(アイルランド)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] トゥールーズ第3大学(フランス)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] 北京大学/中国社会科学院(中国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] ダブリン大学(アイルランド)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] トゥールーズ第3大学(フランス)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations2024

    • Author(s)
      Yamamoto Kenichi,,,Gakuhari Takashi,,,Nakagome Shigeki, Okada Yukinori
    • Journal Title

      Nature Communications

      Volume: 15 Issue: 1 Pages: 1-15

    • DOI

      10.1038/s41467-024-54052-0

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan2024

    • Author(s)
      Cooke N.P., Murray M., Cassidy L.M., Mattiangeli V., Okazaki K., Kasai K., Gakuhari T., Bradley D.G., Nakagome S.
    • Journal Title

      iScience

      Volume: 27 Issue: 6 Pages: 110050-110050

    • DOI

      10.1016/j.isci.2024.110050

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing.2024

    • Author(s)
      1.Xiaoxi Liu, Satoshi Koyama, Kohei Tomizuka, Sadaaki Takata Yuki Ishikawa, Shuji Ito, Shunichi Kosugi, Kunihiko Suzuki, Keiko Hikino, Masaru Koido, Yoshinao Koike, Momoko Horikoshi, Takashi Gakuhari, Shiro Ikegawa, Kochi Matsuda, Yukihide Momozawa, Kaoru Ito, Yoichiro Kamatani, and Chikashi Terao
    • Journal Title

      Science Advances

      Volume: 10 Issue: 16 Pages: 1-17

    • DOI

      10.1126/sciadv.adi8419

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Male-driven admixture facilitated subsistence shift in northern China2024

    • Author(s)
      Nakagome Shigeki、Cooke Niall P.
    • Journal Title

      Anthropological Science

      Volume: 132 Issue: 2 Pages: 79-84

    • DOI

      10.1537/ase.240520

    • ISSN
      0918-7960, 1348-8570
    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Tracing early pastoralism in Central Europe using sedimentary ancient DNA2024

    • Author(s)
      Zampirolo Giulia、Holman Luke E.、Sawafuji Rikai、Ptakova Michaela、Kovacikova Lenka、Sida Petr、Pokorny Petr、Pedersen Mikkel Winther、Walls Matthew
    • Journal Title

      Current Biology

      Volume: 34 Issue: 20 Pages: 4650-4661

    • DOI

      10.1016/j.cub.2024.08.047

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] East and Southeast Asian hominin dispersal and evolution: A review2024

    • Author(s)
      Sawafuji Rikai、Tsutaya Takumi、Takahata Naoyuki、Pedersen Mikkel Winther、Ishida Hajime
    • Journal Title

      Quaternary Science Reviews

      Volume: 333 Pages: 108669-108669

    • DOI

      10.1016/j.quascirev.2024.108669

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium2024

    • Author(s)
      Lee Juhyeon、Sato Takehiro、Tajima Atsushi、Amgalantugs Tsend、Tsogtbaatar Batmunkh、Nakagome Shigeki、Miyake Toshihiko、Shiraishi Noriyuki、Jeong Choongwon、Gakuhari Takashi
    • Journal Title

      Human Population Genetics and Genomics

      Volume: 4 Pages: 1-11

    • DOI

      10.47248/hpgg2404010004

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The history of ancient Japanese dogs revealed by mitogenomes2024

    • Author(s)
      Xiayire Xiaokaiti, Takao Sato, Kenji Kasai, Kenichi Machida, Kyomi Yamazaki, Naomitsu Yamaji, Hiroki Kikuchi, Jun Gojobori1, Hitomi Hongo, Yohey Terai, Takashi Gakuhari
    • Journal Title

      Anthropological Science

      Volume: 132 Issue: 1 Pages: 1-11

    • DOI

      10.1537/ase.230617

    • ISSN
      0918-7960, 1348-8570
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands2023

    • Author(s)
      Cooke Niall P.、Mattiangeli Valeria、Cassidy Lara M.、Okazaki Kenji、Kasai Kenji、Bradley Daniel G.、Gakuhari Takashi、Nakagome Shigeki
    • Journal Title

      Evolutionary Human Sciences

      Volume: 5 Pages: 1-9

    • DOI

      10.1017/ehs.2023.18

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Complete mitochondrial genome sequencing reveals double-buried Jomon individuals excavated from the Ikawazu shell-mound site were not in a mother-child relationship2022

    • Author(s)
      Daisuke Waku, Takashi Gakuhari, Kae Koganebuchi, Minoru Yoneda, Osamu Kondo, Tadayuki Masuyama, Yasuhiro Yamada, Hiroki Oota
    • Journal Title

      Anthropological Science

      Volume: 129

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comparative Genome Analysis Reveals Accumulation of Single-Nucleotide Repeats in Pathogenic Escherichia Lineages2022

    • Author(s)
      Ishiya Koji、Nakashima Nobutaka
    • Journal Title

      Current Issues in Molecular Biology

      Volume: 44 Issue: 2 Pages: 498-504

    • DOI

      10.3390/cimb44020034

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ancient genomics reveals tripartite origins of Japanese populations2021

    • Author(s)
      Cooke Niall P.、Mattiangeli Valeria、Cassidy Lara M.、Okazaki Kenji、Stokes Caroline A.、Onbe Shin、Hatakeyama Satoshi、Machida Kenichi、Kasai Kenji、Tomioka Naoto、Matsumoto Akihiko、Ito Masafumi、Kojima Yoshitaka、Bradley Daniel G.、Gakuhari Takashi、Nakagome Shigeki
    • Journal Title

      Science Advances

      Volume: 7 Issue: 38 Pages: 1-15

    • DOI

      10.1126/sciadv.abh2419

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 市川市出土縄文・古代犬骨のゲノム解析に向けての事前調査報告2021

    • Author(s)
      覚張隆史・山崎京美
    • Journal Title

      市史研究 いちかわ

      Volume: 12 Pages: 120-131

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor.2021

    • Author(s)
      Marie Saitou, Skyler Resendez, Apoorva J Pradhan, Fuguo Wu, Natasha C Lie, Nancy J Hall, Qihui Zhu, Laura Reinholdt, Yoko Satta, Leo Speidel, Shigeki Nakagome, Neil A Hanchard, Gary Churchill, Charles Lee, G Ekin Atilla-Gokcumen, Xiuqian Mu, Omer Gokcumen
    • Journal Title

      Science Advances

      Volume: 7 Issue: 39 Pages: 1-11

    • DOI

      10.1126/sciadv.abi4476

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Ethics of DNA research on human remains: five globally applicable guidelines2021

    • Author(s)
      Alpaslan-Roodenberg Song、Anthony David、Babiker Hiba、et al. including Matsumura Hirofumi
    • Journal Title

      Nature

      Volume: 599 Issue: 7883 Pages: 41-46

    • DOI

      10.1038/s41586-021-04008-x

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT2021

    • Author(s)
      Shiba Takahiko、Komatsu Keiji、Sudo Takeaki、Sawafuji Rikai、Saso Aiko、Ueda Shintaroh、Watanabe Takayasu、Nemoto Takashi、Kano Chihiro、Nagai Takahiko、Ohsugi Yujin、Katagiri Sayaka、Takeuchi Yasuo、Kobayashi Hiroaki、Iwata Takanori
    • Journal Title

      Frontiers in Cellular and Infection Microbiology

      Volume: 11 Pages: 723821-723821

    • DOI

      10.3389/fcimb.2021.723821

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Faecal proteomics as a novel method to study mammalian behaviour and physiology2021

    • Author(s)
      Takumi Tsutaya Meaghan Mackie Rikai Sawafuji Takako Miyabe窶侵ishiwaki Jesper V. Olsen Enrico Cappellini
    • Journal Title

      Molecular Ecology Resources

      Volume: 0 Issue: 6 Pages: 1-12

    • DOI

      10.1111/1755-0998.13380

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Multivariate statistical monitoring system for microbial population dynamics2021

    • Author(s)
      Ishiya Koji、Aburatani Sachiyo
    • Journal Title

      Physical Biology

      Volume: 19 Issue: 1 Pages: 016003-016003

    • DOI

      10.1088/1478-3975/ac3ad6

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] パレオゲノミクスのシンカ -古DNAが可能とするもの-2024

    • Author(s)
      石谷孔司
    • Organizer
      サピエンス進化医学研究センター第1回公開シンポジウム
    • Related Report
      2024 Annual Research Report
  • [Presentation] 高度に効率化された古DNA解析パイプラインの開発2024

    • Author(s)
      石谷孔司
    • Organizer
      第47回日本分子生物学会年会
    • Related Report
      2024 Annual Research Report
  • [Presentation] 考古試料からの 網羅的なパレオメタゲノム評価技術の開発2024

    • Author(s)
      石谷孔司
    • Organizer
      日本微生物生態学会第37回広島大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] Human biological sex determination using X/Y-linked k-mer signatures2024

    • Author(s)
      Koji Ishiya
    • Organizer
      1st Asia & Pacific Bioinformatics Joint Conference
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] パレオゲノミクス解析プラットフォーム: 効率化とオンサイト解析の実現に向けて2024

    • Author(s)
      石谷孔司・覺張隆史
    • Organizer
      第78回日本人類学会大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] サキタリ洞遺跡における古代土壌DNA解析2024

    • Author(s)
      澤藤りかい・澤浦亮平・山崎真治・藤田祐樹・Mikkel W. Pedersen
    • Organizer
      第78回日本人類学会大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] 古代分子が解き明かす過去の病気2024

    • Author(s)
      澤藤りかい
    • Organizer
      第78回日本人類学会大会一般公開シンポジウム
    • Related Report
      2024 Annual Research Report
  • [Presentation] 遺跡出土動物遺存体のゲノム解析から見たヒトの動き2024

    • Author(s)
      覚張隆史
    • Organizer
      第78回日本人類学会大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] パレオゲノミクスから探る現代日本人集団の歴史2024

    • Author(s)
      中込滋樹・山本賢一・覚張隆史・岡田随象
    • Organizer
      第78回日本人類学会大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] 中国北部における文化の転換とヒトの移動2024

    • Author(s)
      中込滋樹
    • Organizer
      第78回日本人類学会大会
    • Related Report
      2024 Annual Research Report
  • [Presentation] ライフサイエンスと考古学をつなぐ先端技術-パレオゲノミクスのその先へ-2024

    • Author(s)
      覚張隆史
    • Organizer
      日本地球化学会
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Application of Latent Semantic Analysis to Metagenomic Data2024

    • Author(s)
      Koji Ishiya
    • Organizer
      the 23rd European Conference on Computational Biology
    • Related Report
      2024 Annual Research Report
    • Invited
  • [Presentation] Insights into demography, selection, and pathogen loads2024

    • Author(s)
      Shigeki Nakagome
    • Organizer
      International Symposium for Paleogenomics -Great Journey Linking Medicine & Archaeology-
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 海外の遺跡出土骨からゲノムを読む オンサイトパレオゲノミクスの創出と課題2023

    • Author(s)
      覚張隆史
    • Organizer
      MBSJ 2023 (日本分子生物学会)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Genomic insights into human past and health from a study of insular East Asia2023

    • Author(s)
      Shigeki Nakagome
    • Organizer
      Trinity Translational Medical Institute Conference 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] パレゲノミクス2.0~異分野連携に向けたパレオゲノミクスデータの活用~2023

    • Author(s)
      石谷孔司
    • Organizer
      金沢大学サピエンス進化医学研究センター キックオフシンポジウム
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 遺跡出土人骨からゲノムを読む 進化医学と考古学の融合研究に向けて2023

    • Author(s)
      覚張隆史
    • Organizer
      第42回金沢腎セミナー
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 遺跡出土骨の全ゲノム解析における方法論的検討2021

    • Author(s)
      覚張隆史
    • Organizer
      日本動物考古学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 現代人歯石からの食物DNA解析2021

    • Author(s)
      澤藤りかい・上原麗・加藤均・植田信太郎・木村亮介・石田肇
    • Organizer
      日本人類学会大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 古代の病原体DNA解析; その動向と評価について2021

    • Author(s)
      澤藤りかい
    • Organizer
      人文学のための古代DNAセミナー
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Funded Workshop] International Symposium for Paleogenomics -Great Journey Linking Medicine & Archaeology-2024

    • Related Report
      2023 Annual Research Report
  • [Funded Workshop] Paleogenomics; the eastern and western edges of Eurasia.2022

    • Related Report
      2021 Annual Research Report

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Published: 2020-11-24   Modified: 2026-01-16  

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