Paleogenomics on Jomon and Yayoi human remains by using next generation sequencer

• Project/Area Number: 23657167
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Physical anthropology
• Research Institution: Kitasato University
• Principal Investigator: OOTA Hiroki 北里大学, 医学部, 准教授 (40401228)
• Co-Investigator(Kenkyū-buntansha): HANIHARA Tsunehiko 北里大学, 医学部, 教授 (00180919) ; ISHIDA Hajime 琉球大学, 医学部, 教授 (70145225) ; KIMURA Ryosuke 琉球大学, 亜熱帯島嶼科学超域研究推進機構, 准教授 (00453712) ; MANO Shuhei 統計数理研究所, 数理・推論研究系, 准教授 (20372948)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2011: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
• Keywords: パーソナルゲノム / 縄文人 / 弥生人 / 次世代シークエンサー / 日本人の起源 / 沖縄 / 先島諸島 / アイヌ

Research Abstract

We successfully extracted DNAs from ancient human and animal bones that could be analyzed by next generation sequencers. The DNAs were degraded to less than 70bp and modified chemically. The extractions contained a huge amount of bacterial DNAs. Haplotype analyses strongly suggested the very close relationship between Ainu and Ryukyuan.

Research Products

• [Journal Article] Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation (2012)
  • Author(s): S.Nakagome,S.Mano,L.Kozlowski,J.M.BuJnicki,H.Shibata,Y.Fukumaki,J.R.Kidd,K.K.Kidd,S.Kawamura,H.Oota
  • Journal Title: Molecular Biology and Evolution Volume: 29 Pages: 1569-1585
  • Peer Reviewed
• [Journal Article] Effects of the Asian-specific nonsynoymous EDAR variation on multiple dental traits : possible hichhiking phenotypes (2012)
  • Author(s): Park J-H, Yamaguchi T, Hanihara T
  • Journal Title: Journal of Human Genetics Volume: 57 Issue: 8 Pages: 508-514
  • DOI: 10.1038/jhg.2012.60
  • Peer Reviewed
• [Journal Article] The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan Populations. (2012)
  • Author(s): Jinam T, Nishida N, Hirai M, Kawamura S, Oota H, Umetsu K, Kimura R, Ohashi J, Tajima A, Yamamoto T, Tanabe H, Mano S, Suto Y, Kaname T, Naritomi K, Yanagi K, Niikawa N, Omoto K. Saitou N
  • Journal Title: Journal of Human Genetics Volume: 57巻 Issue: 12 Pages: 787-79
  • DOI: 10.1038/jhg.2012.114
  • NAID: 10031145887
  • Peer Reviewed
• [Journal Article] Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders (2012)
  • Author(s): K. Koganebuchi, T. Katsumura, S. Nakagome, H. Ishida, S. Kawamura, H. Oota
  • Journal Title: Anthropological Science Volume: 120 Issue: 3 Pages: 199-208
  • DOI: 10.1537/ase.120322
  • NAID: 10031145903
  • ISSN: 0918-7960, 1348-8570
  • Peer Reviewed
• [Journal Article] Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation (2012)
  • Author(s): S. Nakagome, S. Mano, L. Kozlowski, J. M. Bujnicki, H. Shibata, Y. Fukumaki, J. R. Kidd, K. K. Kidd, S. Kawamura, H. Oota
  • Journal Title: Molecular Biology and Evolution Volume: (In press) Issue: 6 Pages: 1569-85
  • DOI: 10.1093/molbev/mss006
  • Peer Reviewed
• [Journal Article] A population genetic study on the relationship between medaka fish and the spread of wet-rice cultivation across the Japanese archipelago (2012)
  • Author(s): Katsumura, T., Oda, S., Tsukamoto, K., Sekiya, Y., Yamashita, T., Aso, M., Hata, M., Nonaka, M., Mano, S., Ishida, H., Mitani, H., Kawamura, S., Oota, H.
  • Journal Title: Anthropological Science Volume: 120 Issue: 1 Pages: 81-89
  • DOI: 10.1537/ase.110525
  • NAID: 10030738530
  • ISSN: 0918-7960, 1348-8570
  • Peer Reviewed
• [Journal Article] 古DNA分析：クオリティー検査法と考古学への応用 (2012)
  • Author(s): 太田博樹
  • Journal Title: 月刊 考古学ジャーナル Volume: 630 Pages: 22-26
• [Presentation] 遺伝学と生物医学における集団のラベリング/Population Descripors in Genetics andBiomedicine (2012)
  • Author(s): 竹沢泰子、加藤和人、太田博樹
  • Organizer: 京都大学人文科学研究所科研基盤(S)「人種表象の日本型グローバル研究」第2回 Knowledge-科学と社会の共生産
  • Place of Presentation: 京都
  • Year and Date: 2012-12-15
• [Presentation] 保美貝塚出土人骨・獣骨の分析 (2012)
  • Author(s): 米田穣、太田博樹、日下宗一郎、覚張隆史、小山荘太郎
  • Organizer: 日本考古学協会、第78会総会研究発表プログラム
  • Place of Presentation: 大正大学大崎キャンパス、東京
  • Year and Date: 2012-05-27
• [Presentation] ゲノムワイド SNPデータに基づく琉球列島の人々の集団構造 (2012)
  • Author(s): 佐藤丈寛、川口亮、石田肇、山口徹太郎、山本健、河村正二、中込滋樹、間野修平、埴原恒彦、太田博樹、渡辺千晶、山口今日子、木村亮介
  • Organizer: 第66回日本人類学会大会
  • Place of Presentation: 神奈川
• [Presentation] 琉球諸島と北部九州におけるクローン病の遺伝と環境の相互作用に関する人類学的考察 (2012)
  • Author(s): 中込滋樹、知念寛、竹山康章、Said H.S.、須田亙、木村亮介、石田肇、埴原恒彦、Kidd J.R.、Kidd K.K.、河村正 二、森田英利、服部正平、間野修平、太田博樹
  • Organizer: 第66回日本人類学会大会
  • Place of Presentation: 神奈川
• [Presentation] 現代日本人の寒冷適応能とミトコンドリアハプログループの関係について (2012)
  • Author(s): 西村貴孝、本井碧、星良和、近藤隆一郎、太田博樹、綿貫茂喜
  • Organizer: 第66回日本人類学会大会
  • Place of Presentation: 神奈川
• [Presentation] ヒトとメダカ共通に観察された地域集団間の性的二型の程度の違いに関与する遺伝的多型 (2012)
  • Author(s): 勝村啓史、尾田正二、三谷啓志、埴原恒彦、河村正二、太田博樹
  • Organizer: 第66回日本人類学会大会
  • Place of Presentation: 神奈川
• [Presentation] 米田穣動物遺存体および化石における古代 DNA分析の新たなプレスクリーニング法 (2012)
  • Author(s): 覚張隆史、太田博樹、大谷進
  • Organizer: 第66回日本人類学会大会
  • Place of Presentation: 神奈川
• [Presentation] ゲノムワイドSPNデータに基づく琉球列島の人々の集団構造 (2012)
  • Author(s): 佐藤丈寛
  • Organizer: 第66回日本人類学会大会
  • Place of Presentation: 神奈川
• [Presentation] A population genetic study and phylogenetic reconstruction of medaka migration across the Japanese archipelago based on nucleotide sequences of the mitochondrial genome D-loop region (2012)
  • Author(s): T. Katsumura
  • Organizer: 小型魚類研究会 第18回大会
  • Place of Presentation: 京都
• [Presentation] 沖縄人が大和人より酒に強い理由-遺伝子を調べてわかったこと- (2011)
  • Author(s): 太田博樹
  • Organizer: 第65回日本人類学会公開シンポジウム「琉球弧とヒトの適応戦略」
  • Place of Presentation: 那覇
  • Year and Date: 2011-11-06
• [Presentation] How do physical anthropolo- gists have-committed themselves on genome medicine? Changing Representations of Indige- nous and Migrant Groups in Globali- zing Japan Genes,Bones, and Cultures (2011)
  • Author(s): H.Oota
  • Organizer: IUAES/AAS/ASAANZ Conference 2011
  • Place of Presentation: Perth,Australia
  • Year and Date: 2011-07-05
• [Presentation] 環境要因と遺伝的多型と多 様な表現型との関係/Environmental factors and relationship between genetic polymorphisms and various phenotypes (2011)
  • Author(s): 太田博樹
  • Organizer: 第64回日本生理人類学会シンポジウム「環境及び遺伝の要因と生理的多型との関係」
  • Place of Presentation: 福岡
  • Year and Date: 2011-06-11
• [Presentation] 人類の形態、生理・代謝、疾患の進化に関するゲノム多様性研究 (2011)
  • Author(s): 太田博樹
  • Organizer: 統数研研究集会、統計数理学研究所
  • Place of Presentation: 立川
• [Presentation] Populations specific susceptibility To Crohn's disease and signals of natural selection on standing vari- Populations specific susceptibility To Crohn's disease and signals of natural selection on standing vari- ation (Poster) (2011)
  • Author(s): S. Nakagome, S. Mano, L. Kozlowski, J. M. Bujnicki, H. Shibata, Y. Fukumaki, J. R. Kidd, K. K. Kidd, S. Kawamura, H. Oota
  • Organizer: The 12th ICHG/The 61th Annual Meeting of The American Society of Human Genetics
  • Place of Presentation: Montreal, Canada
• [Presentation] Toward understanding evolutionary force behind color vision poly- morphism in humans (2011)
  • Author(s): 石崎直也、白井裕介、福世裕貴子、石田 肇、K.K.Kidd、太田博樹、河村正二
  • Organizer: 第13回日本進化学会
  • Place of Presentation: 京都大学百周年時計台記念館、京都
• [Presentation] Population specific distri- bution of Crohn's disease risk alleles on the NOD2locus and natu- ral selection on standing variation (Oral) (2011)
  • Author(s): S. Nakagome, S. Mano, L. Kozowski, J. M. Bujnicki, H. Shibata, Y. Fukumaki, J. R. Kidd, K. K. Kidd, S. Kawamura, H. Oota
  • Organizer: The Society for Molecular Biology and Evolution Annual Meeting
  • Place of Presentation: kyoto,Japan
• [Presentation] Toward Understanding Evolutionary Force behind Color Vision Polymorphism in Humans(Poster) (2011)
  • Author(s): N. Ishizaiki, Y. Shirai, Y. Fukuyo, H. Ishida, K. K. Kidd, H. Oota, S. Kawamura
  • Organizer: The Society for Molecular Biology and Evolution, Annual Meeting
  • Place of Presentation: Kyoto,Japan
• [Presentation] An evolutionary study of human complex diseases (Invited) (2011)
  • Author(s): S. Nakagome, S. Mano, L. Kozlowski, J. M. Bujnicki, J. R. Kidd, S. Kawamura, H. Oota
  • Organizer: Workshop on Evolutioary Analysis and Applications
  • Place of Presentation: Xi'an and Lhasa, China
• [Presentation] 人類の形態、生理・代謝、疾患の進化に関するゲノム多様性研究 (2011)
  • Author(s): 太田博樹
  • Organizer: 統数研研究集会
  • Place of Presentation: 統計数理学研究所（立川）
• [Presentation] 保美貝塚出土人骨・獣骨の分析
  • Author(s): 米田穣
  • Organizer: 日本考古学協会、第78回総会研究発表プログラム
  • Place of Presentation: 東京
• [Book] Evolutioary Insights into the "Population- Specificity"of the Genetic FactorsAssociated with Inflammatory BowelDiseases (2012)
  • Author(s): S.Nakagome,H.Oota
  • Total Pages: 222
• [Book] Ulcerative Colitis 2 (2012)
  • Author(s): S. Nakagome
  • Total Pages: 222
  • Publisher: Evolutionary Insights into the “Population-Specificity” of the Genetic Factors Associated with Inflammatory Bowel Diseases.
• [Book] Effects of Human Migration on Genome Diversity in East Asia (2011)
  • Author(s): H.Oota, M.Stoneking
  • Total Pages: 252
• [Remarks] 北里大学医学部解剖学・人類学研究室
  • URL: http://www.med.kitasato-u.ac.jp/~anatomy-anthropology/
• [Remarks] 解剖学（埴原単位）ゲノム人類学研究室
  • URL: http://www.med.kitasato-u.ac.jp/~anatomy-anthropology/oota_lab/index.php