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Evolution of Yaponesians based on genome sequence analyses of modern humans

Planned Research

Project AreaDeciphering Origin and Establishment of Japonesians mainly based on genome sequence data
Project/Area Number 18H05506
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionNational Institute of Genetics

Principal Investigator

SAITOU Naruya  国立遺伝学研究所, ゲノム・進化研究系, 特任教授 (30192587)

Co-Investigator(Kenkyū-buntansha) 井ノ上 逸朗  国立遺伝学研究所, ゲノム・進化研究系, 教授 (00192500)
吉浦 孝一郎  長崎大学, 原爆後障害医療研究所, 教授 (00304931)
Jinam TimothyA  国立遺伝学研究所, ゲノム・進化研究系, 助教 (20648258)
松波 雅俊  琉球大学, 医学(系)研究科(研究院), 助教 (60632635)
Project Period (FY) 2018-06-29 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥98,280,000 (Direct Cost: ¥75,600,000、Indirect Cost: ¥22,680,000)
Fiscal Year 2022: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2021: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2020: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2019: ¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2018: ¥21,320,000 (Direct Cost: ¥16,400,000、Indirect Cost: ¥4,920,000)
Keywordsヤポネシア人 / 現代人ゲノム / ゲノム進化 / オキナワ人 / ヤマト人 / ヤポネシア / 現代ゲノム / 人類進化 / 日本列島人 / ゲノム多様性 / うちなる二重構造 / ヤホネシア人
Outline of Final Research Achievements

We collected DNA samples from following areas: Miyako Island in Okinawa, Makurazaki, Goto Islands, Izumo, Tottori, Tokushima, and Hachijo Island. Samples were collected only from people whose four grandparents are all from that same area. Matsunami collected samples from Okinawa, Saitou and Yoshiura collected samples from Kyushu, and Saitou collected samples from other area. We determined genome-wide SNP data for these samples, and Jinam analyzed data, then published papers. As for Hachijo Island, we could not collect ample number of samples when we visited there in March 2023. We thus plan to visit Hachijo Island again in June 2023, and collect additional saliva samples. Inoue detected ancient viruses from Jomon period coprolites, and published a paper after determination and analysis of their nucleotide sequences.

Academic Significance and Societal Importance of the Research Achievements

ヤポネシア(日本列島)のあちこちに在住する日本人からDNAサンプルを収集し、理化学研究所の発表したデータとあわせてゲノム多様性を解析したことにより、「うちなる二重構造」モデルを検証できたことは、学術的に高い意義がある。
社会的意義としては、一般の方々にも関心を持っていただける、日本人の起源に関する研究テーマだったので、多くの一般向け講演会をおこなったり、一般向けの雑誌からの執筆依頼に応じて、研究成果の流布につとめた。

Report

(6 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (53 results)

All 2022 2021 2020 2019 2018 Other

All Journal Article (13 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 13 results,  Open Access: 10 results) Presentation (28 results) (of which Int'l Joint Research: 6 results,  Invited: 14 results) Book (11 results) Remarks (1 results)

  • [Journal Article] Extraction of CRISPR-targeted sequences from the metagenome2022

    • Author(s)
      Sugimoto Ryota、Nishimura Luca、Nguyen Phuong Thanh、Inoue Ituro
    • Journal Title

      STAR Protocols

      Volume: 3 Issue: 3 Pages: 101525-101525

    • DOI

      10.1016/j.xpro.2022.101525

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Detection of Ancient Viruses and Long-Term Viral Evolution2022

    • Author(s)
      Nishimura Luca、Fujito Naoko、Sugimoto Ryota、Inoue Ituro
    • Journal Title

      Viruses

      Volume: 14 Issue: 6 Pages: 1336-1336

    • DOI

      10.3390/v14061336

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Allelic and haplotypic HLA diversity in indigenous Malaysian populations explored using Next Generation Sequencing2022

    • Author(s)
      Jinam Timothy A.、Hosomichi Kazuyoshi、Nakaoka Hirofumi、Phipps Maude E.、Saitou Naruya、Inoue Ituro
    • Journal Title

      Human Immunology

      Volume: 83 Issue: 1 Pages: 17-26

    • DOI

      10.1016/j.humimm.2021.09.005

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Preface to the special issue on the Yaponesia Genome Project2021

    • Author(s)
      Saitou N.
    • Journal Title

      Anthropological Science

      Volume: 129 Issue: 1 Pages: 1-2

    • DOI

      10.1537/ase.210114

    • NAID

      130008030486

    • ISSN
      0918-7960, 1348-8570
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Modern human DNA analyses with special reference to the inner dual-structure model of Yaponesian2021

    • Author(s)
      Jinam T. A., Kawai Y., and Saitou N.
    • Journal Title

      Anthropological Science

      Volume: 129 Issue: 1 Pages: 3-11

    • DOI

      10.1537/ase.201217

    • NAID

      130008030443

    • ISSN
      0918-7960, 1348-8570
    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people2021

    • Author(s)
      Jinam Timothy、Kawai Yosuke、Kamatani Yoichiro、Sonoda Shunro、Makisumi Kanro、Sameshima Hideya、Tokunaga Katsushi、Saitou Naruya
    • Journal Title

      Journal of Human Genetics

      Volume: - Issue: 7 Pages: 681-687

    • DOI

      10.1038/s10038-020-00898-3

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Robust ridge regression for estimating the effects of correlated gene expressions on phenotypic traits2020

    • Author(s)
      Hirofumi Michimae, Masatoashi Matsunami, Takeshi Emura
    • Journal Title

      Environmental and Ecological Statistics

      Volume: 27 Issue: 1 Pages: 41-72

    • DOI

      10.1007/s10651-019-00434-3

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan2019

    • Author(s)
      Kanzawa-Kiriyama Hideaki、Jinam Timothy A.、Kawai Yosuke、Sato Takehiro、Hosomichi Kazuyoshi、Tajima Atsushi、Adachi Noboru、Matsumura Hirofumi、Kryukov Kirill、Saitou Naruya、Shinoda Ken-Ichi
    • Journal Title

      Anthropological Science

      Volume: 127 Issue: 2 Pages: 83-108

    • DOI

      10.1537/ase.190415

    • NAID

      130007696474

    • ISSN
      0918-7960, 1348-8570
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Evaluation of Face2Gene using facial images of patients with congenital dysmorphic syndromes recruited in Japan2019

    • Author(s)
      Mishima Hiroyuki、Suzuki Hisato、Doi Michiko、Miyazaki Mutsuko、Watanabe Satoshi、Matsumoto Tadashi、Morifuji Kanako、Moriuchi Hiroyuki、Yoshiura Koh-ichiro、Kondoh Tatsuro、Kosaki Kenjiro
    • Journal Title

      Journal of Human Genetics

      Volume: 64 Issue: 8 Pages: 789-794

    • DOI

      10.1038/s10038-019-0619-z

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan2019

    • Author(s)
      Hideaki Kanzawa-Kiriyama, Timothy A. Jinam, Yosuke Kawai, Takehiro Sato, Kazuyoshi Hosomichi, Atsushi Tajima, Noboru Adachi, Hirofumi Matsumura, Kirill Kryukov, Naruya Saitou, and Ken-ichi Shinoda
    • Journal Title

      Anthropological Science

      Volume: 127

    • NAID

      130007696474

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population.2019

    • Author(s)
      Hirata J, Hosomichi K, Sakaue S, Kanai M, Nakaoka H, Ishigaki K, Suzuki K, Akiyama M, Kishikawa T, Ogawa K, Masuda T, Yamamoto K, Hirata M, Matsuda K, Momozawa Y, Inoue I, Kubo M, Kamatani Y, Okada Y.
    • Journal Title

      Nat Genet

      Volume: 51 Issue: 3 Pages: 470-480

    • DOI

      10.1038/s41588-018-0336-0

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multiple conserved elements structuring inverted repeats in the mammalian coat color-related gene Asip2019

    • Author(s)
      Sakuma Y., Matsunami M., Takada T., and Suzuki H.
    • Journal Title

      Zoological Science

      Volume: 36 Issue: 1 Pages: 23-30

    • DOI

      10.2108/zs180081

    • NAID

      40021802414

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Detection of de novo single nucleotide variants in offspring of atomic-bomb survivors close to the hypocenter by whole-genome sequencing.2018

    • Author(s)
      Horai M, Mishima H, Hayashida C, Kinoshita A, Nakane Y, Matsuo T, Tsuruda K, Yanagihara K, Sato S, Imanishi D, Imaizumi Y, Hata T, Miyazaki Y, Yoshiura KI.
    • Journal Title

      J Hum Genet.

      Volume: 63 Issue: 3 Pages: 357-363

    • DOI

      10.1038/s10038-017-0392-9

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] External Edge Elimination (3E) method for phylogeney construction2022

    • Author(s)
      斎藤成也
    • Organizer
      日本進化学会第24回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ヤポネシア人の起源をもとめて2022

    • Author(s)
      斎藤成也
    • Organizer
      日本遺伝学会第94回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ヤポネシア人への道 はるかなり2022

    • Author(s)
      斎藤成也
    • Organizer
      日本遺人類学会・日本霊長類学会合同大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ゲノムから探る日本列島人の起源と成立2022

    • Author(s)
      斎藤成也
    • Organizer
      日本股関節学会学術集会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ゲノム情報から復元された琉球列島人の集団史2022

    • Author(s)
      松波雅俊
    • Organizer
      東京外国語大学アジア・アフリカ言語文化研究所・海外学術フォーラム
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ヤポネシアのしっぽの集団ゲノミクス:これまでとこれから2022

    • Author(s)
      松波雅俊
    • Organizer
      第76回日本人 類学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ヤポネシア人の「うちなる二重構造」モデルを支持するデータ2020

    • Author(s)
      斎藤成也
    • Organizer
      日本人類遺伝学会
    • Related Report
      2020 Annual Research Report
  • [Presentation] ユーラシアにおける東西交流DNAとゲノムからさぐる2019

    • Author(s)
      斎藤成也
    • Organizer
      日本文化人類学会大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Yaponesia Genome Project - combination of genome sequence analyses of modern humans, animals, and plants as well as archeological and linguistic data analyses2019

    • Author(s)
      斎藤成也
    • Organizer
      国際分子進化学会(SMBE2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Whole genome sequence analysis of the Aeta, a First Sundaland people from the Philippines2019

    • Author(s)
      Timothy A. Jinam
    • Organizer
      国際分子進化学会(SMBE2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Okinawa Bioinformation Bank Project: understanding human genetic diversity in the Ryukyu Archipelago2019

    • Author(s)
      松波雅俊
    • Organizer
      国際分子進化学会(SMBE2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ゲノムからみたヤポネシア人2019

    • Author(s)
      斎藤成也
    • Organizer
      臨床遺伝2019 in Sapporo
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 新人の拡散にしたがった新しい大陸名の提唱2019

    • Author(s)
      斎藤成也
    • Organizer
      日本進化学会第21回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 琉球列島人の集団ゲノム解析2019

    • Author(s)
      松波雅俊
    • Organizer
      日本進化学会第21回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Modern genomes of people who live in South East Asia and their relationships with Yaponesians2019

    • Author(s)
      Timothy A. Jinam
    • Organizer
      日本遺伝学会第91回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Problem when softwares for molecular evolution are applied to linguistic data2019

    • Author(s)
      斎藤成也
    • Organizer
      日本言語地理学会第1回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Genome-wide association studies for metabolic traits in the Ryukyu populations2019

    • Author(s)
      松波雅俊
    • Organizer
      American Society of Human Genetics(ASHG2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ヤポネシアゲノムプロジェクトの紹介2019

    • Author(s)
      斎藤成也
    • Organizer
      日本人類遺伝学会第64回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] ヤポネシアゲノムプロジェクトにおけるHLA遺伝子群を用いた集団遺伝学2019

    • Author(s)
      井ノ上逸朗
    • Organizer
      日本人類遺伝学会第64回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 沖縄バイオインフォメーションバンクの情報から琉球列島人の遺伝的多様性を探る2019

    • Author(s)
      松波雅俊
    • Organizer
      日本人類遺伝学会第64回大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Genome Sequence for diagnosis and successive research of genetics disorders2019

    • Author(s)
      吉浦孝一郎
    • Organizer
      第59回日本先天異常学会学術集会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Origins of Yaponesians from genetic and linguistic viewpoints2019

    • Author(s)
      Saitou Naruya & Endo Mitsuaki
    • Organizer
      Transeurasian millets and beans, languages and genes
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 東ユーラシアにおけるヤポネシア人の起源とその成立2018

    • Author(s)
      斎藤成也
    • Organizer
      韓国の釜山大学博物館特別講演会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 現代出雲人と出雲神話をつなげるゲノムDNA研究2018

    • Author(s)
      斎藤成也
    • Organizer
      日本DNA多型学会第27回学術集会 公開シンポジウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ミトコンドリアDNA研究の興亡2018

    • Author(s)
      斎藤成也
    • Organizer
      第72 回日本人類学会大会 公開シンポジウム2「DNAからみたヒトの進化」
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ヤポネシア現代ゲノム班の活動計画~琉球地域を中心として~2018

    • Author(s)
      松波雅俊
    • Organizer
      第72 回日本人類学会一般シンポジウム12「新学術領域「ヤポネシアゲノム」始動!」
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 日本人のなか耳垢型多型2018

    • Author(s)
      吉浦孝一郎
    • Organizer
      第72 回日本人類学会大会 公開シンポジウム2「DNAからみたヒトの進化」
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Genomic History of Negritos in Sundaland2018

    • Author(s)
      Timothy A. Jinam
    • Organizer
      第72 回日本人類学会一般シンポジウム7「グローバル気候変動と現代型サピエンス全移動史」
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Book] 図解 人類の進化2021

    • Author(s)
      斎藤成也ら
    • Total Pages
      269
    • Publisher
      講談社
    • ISBN
      9784065261361
    • Related Report
      2021 Annual Research Report
  • [Book] 人類はできそこないである2021

    • Author(s)
      斎藤成也
    • Total Pages
      226
    • Publisher
      SBクリエイティブ社
    • ISBN
      9784815603113
    • Related Report
      2021 Annual Research Report
  • [Book] ヒトゲノム事典2021

    • Author(s)
      斎藤成也・井ノ上逸朗・松波雅俊ら
    • Total Pages
      431
    • Publisher
      一色出版
    • ISBN
      9784910389127
    • Related Report
      2021 Annual Research Report
  • [Book] Evolution of the Human Genome II2021

    • Author(s)
      Timothy Jinam, Saitou Naruyaほか
    • Total Pages
      260
    • Publisher
      Springer
    • ISBN
      9784431569022
    • Related Report
      2021 Annual Research Report
  • [Book] フィールドと文献からみる日琉諸語の系統と歴史2021

    • Author(s)
      林 由華、衣畑 智秀、木部 暢子
    • Total Pages
      316
    • Publisher
      開拓社
    • ISBN
      9784758923545
    • Related Report
      2020 Annual Research Report
  • [Book] 商工ジャーナル2020年1月号2020

    • Author(s)
      斎藤成也
    • Total Pages
      4
    • Publisher
      商工ジャーナル
    • Related Report
      2020 Annual Research Report
  • [Book] ラリルレロボットの未来2020

    • Author(s)
      斎藤 成也、太田 聡史
    • Total Pages
      272
    • Publisher
      勁草書房
    • ISBN
      9784326050185
    • Related Report
      2020 Annual Research Report
  • [Book] 生体の科学2020

    • Author(s)
      斎藤成也
    • Total Pages
      5
    • Publisher
      医学書院
    • Related Report
      2020 Annual Research Report
  • [Book] 最新DNA研究が解き明かす。日本人の誕生2020

    • Author(s)
      斎藤成也、木村亮介、鈴木留美子、河合洋介、松波雅俊
    • Total Pages
      240
    • Publisher
      秀和システム
    • ISBN
      9784798060224
    • Related Report
      2020 Annual Research Report
  • [Book] 日本語の起源をめぐる日本言語学史の光と影2020

    • Author(s)
      斎藤成也
    • Total Pages
      360
    • Publisher
      三省堂
    • ISBN
      9784385365084
    • Related Report
      2019 Annual Research Report
  • [Book] 遺伝医学への招待改訂第6版2020

    • Author(s)
      吉浦孝一郎
    • Total Pages
      196
    • Publisher
      南江堂
    • ISBN
      9784524249312
    • Related Report
      2019 Annual Research Report
  • [Remarks] ヤポネシアゲノム A01班の研究報告

    • URL

      http://www.yaponesian.jp/research_han0100001.html

    • Related Report
      2019 Annual Research Report

URL: 

Published: 2018-07-20   Modified: 2024-01-30  

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