Comparative genomics of human populations in the Ryukyu islands and northern Kyushu; and its relevance for the origin of modern Japanese and their adaptation

• Project/Area Number: 24370099
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• 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): KIMURA Ryosuke 琉球大学, 医学系研究科, 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): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥18,850,000 (Direct Cost: ¥14,500,000、Indirect Cost: ¥4,350,000); Fiscal Year 2014: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2013: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2012: ¥8,970,000 (Direct Cost: ¥6,900,000、Indirect Cost: ¥2,070,000)
• Keywords: ヒト / 日本列島 / ゲノム / 混血 / 琉球 / 北部九州 / 縄文 / 弥生 / ゲノム網羅的SNPデータ / 琉球諸島 / 先島諸島 / 北海道アイヌ / 本州日本 / 分集団構造 / 二重構造モデル / 沖縄本島 / 宮古島 / 石垣島 / 縄文人 / 弥生人 / 集団遺伝学 / 移住

Outline of Final Research Achievements

To investing the biological origin of Japanese, we conducted well-planned samplings and genome analyses. The data showed the sub-population structure of Japanese in fine resolution.
[Details]1.Genome-wide SNP analysis for the Ryukyu islanders showed, ①the cluster of the islanders differ from that of main-island Japanese. ②current habitants in the islands seemed to have no relationship with the 17,000 year-old skeletal remain that was recently found in the Ishigaki island (Sato et al. 2014). 2.Using the genome-wide SNP data of Ainu, Han Chinese, and main-island Japanese, three demographic models, (1) transformation, (2) replacement, (3) hybridization, were compared by Kernel approximate Bayesian computation (ABC), and the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively (Nakagome et al. in press).

Research Products

• [Journal Article] Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data (2015)
  • Author(s): S. Nakagome, T. SAto, H. Ishida, T. Hanihara, T. Yamaguchi, R. Kimura, S. Mano, S. Kawamura, H. Oota
  • Journal Title: Molecular Biology and Evolution Volume: 印刷中
  • Peer Reviewed
• [Journal Article] Genome-WideSNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago (2014)
  • Author(s): T. Sato, S. Nakagome, C. Watanabe, K. Yamaguchi, A. Kawaguchi, K. Koganebuchi, K. Haneji, T. Yamaguchi, T. Hanihara, K. Yamamoto, H. Ishida, S. Mano, R. Kimura, H. Oota
  • Journal Title: Molecular Biology and Evolution Volume: 31(11) Pages: 2929-2940
  • Peer Reviewed / Open Access
• [Journal Article] Correspondence: Human genetic research, race, ethnicity and the labeling of populations: recommendations based on an interdisciplinary workshop in Japan (2014)
  • Author(s): Takezawa, Y., Kato, K., Oota. H., Caulfield, T., Fujimoto, A., Honda, F., Kamatani, N., Kawamura, S., Kawashima, K., Kimura, R., Matsumae, H., Saito, A., Savage, P. E., Seguchi, N., Shimizu, K., Terao, S., Yamaguchi-Kabata, Y., Yasukouchi, A., Yoneda, M. and Tokunaga, K.
  • Journal Title: BMC Medical Ethics Volume: 15 Issue: 1 Pages: 33-33
  • DOI: 10.1186/1472-6939-15-33
  • Peer Reviewed / Open Access
• [Journal Article] Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers (2014)
  • Author(s): Heba S. Said
  • Journal Title: DNA Research Volume: 21(1) Issue: 1 Pages: 15-25
  • DOI: 10.1093/dnares/dst037
  • Peer Reviewed / Open Access
• [Journal Article] 古人類のゲノム解析～ネアンデルタール人とデニソワ人/Paleogenomics on extinct hominins- Neanderthal and Denisovan (2014)
  • Author(s): 太田博樹
  • Journal Title: 生物科学 Volume: Vol.65No.4 Pages: 226-235
  • 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] 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] 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
• [Presentation] 人類学の視点からヒトの「遺伝」・「多様性」をどう考えるか 日本人類学会の取り組み (2015)
  • Author(s): 太田博樹
  • Organizer: 東京都生物学教育連合会
  • Place of Presentation: 日本医科大学病院棟（東京都文京区）
  • Year and Date: 2015-01-12
• [Presentation] Challenges to Ancient DNA Analysis in Japan: bioarcheological remains from high temperature, high humidity and an acidic soil environment (2014)
  • Author(s): H. Matsumae, T. Gakuhari, T. Katsumura, R. Schmidt, K. Koganebuchi, H. Oota
  • Organizer: 6th International Symposium on Biomolecular Archaeology
  • Place of Presentation: Basel, Switzerland
  • Year and Date: 2014-08-27 – 2014-08-30
• [Presentation] 化石標本とライフサイエンスデータを統合する進化史研究の基盤データベースの開発 (2014)
  • Author(s): 松前ひろみ、仲里猛留、大田達郎、太田博樹
  • Organizer: 日本進化学会第16回大阪大会
  • Place of Presentation: 高槻現代劇場（大阪府高槻市）
  • Year and Date: 2014-08-21 – 2014-08-24
• [Presentation] 日本列島ヒト集団におけるモヤモヤ病感受性遺伝子RNF213の遺伝的多様性の検討 (2014)
  • Author(s): 小金渕佳江、石崎直也、河村正二、木村亮介、石田肇、城圭一郎、副島英伸、藤本一真、佐藤公彦、安井美江、隈部俊宏、藤井清隆、秋山辰穂、埴原恒彦、太田博樹
  • Organizer: 日本進化学会第16回大阪大会
  • Place of Presentation: 大高槻現代劇場（大阪府高槻市）
  • Year and Date: 2014-08-21 – 2014-08-24
• [Presentation] 遺跡出土のヒトのDNA分析最先端科学で明らかになる古代人のルーツ (2014)
  • Author(s): 太田博樹
  • Organizer: 公益財団法人・群馬県埋蔵文化財調査事業団主催の一般向け講座である埋蔵文化財講座「ぐんま発掘玉手箱」第2回
  • Place of Presentation: 群馬県埋蔵文化財調査センター発掘情報館（群馬県渋川市）
  • Year and Date: 2014-07-13
• [Presentation] メラトニン抑制に関する生理的多型と時計遺伝子PERIOD2 多型との関係及びその適応的意義の考察 (2014)
  • Author(s): 秋山辰穂、勝村啓史、中込滋樹、城圭一郎、副島英伸、木村亮介、石田肇、埴原恒彦、樋口重和、太田博樹
  • Organizer: 第70回日本生理人類学会大会
  • Place of Presentation: 九州大学大橋キャンパス（福岡県福岡市）
  • Year and Date: 2014-06-21 – 2014-06-22
• [Presentation] Association between the PERIOD2 gene polymorphism and the physiological polytypism for light sensitivity in humans (2014)
  • Author(s): T. Akiyama, T. Katsumura, S. Nakagome, K. Joh, H. Soejima, K. Fujimoto, R. Kimura, H. Ishida, T. Hanihara, S. Higuchi, H. Oota
  • Organizer: Sokendai International Symposium "Modern Human Diversity on Gene and Culture: with special reference to Asia and Oceania"
  • Place of Presentation: Hayama, Japan
• [Presentation] Population structure of the Ryukyu Islanders revealed by genome-wide SNP genotyping (2014)
  • Author(s): T. Sato
  • Organizer: IUAES 2014 with JASCA
  • Place of Presentation: Makuhari Messe, Chiba, Japan
• [Presentation] A genetic polymorphism of the PER2 gene associates with physiological polytypisms for light sensitivity in humans (2014)
  • Author(s): T. Akiyama, S. Higuchi, H. Oota
  • Organizer: IUAES 2014 with JASCA
  • Place of Presentation: Makuhari Messe, Chiba, Japan
• [Presentation] Evolutionary insights into genetic and environmental factors for Crohn's disease in Ryuku and Nothern Kyushu (2013)
  • Author(s): S. Nakagome, H. Chinen, H. Said, W. Suda, A. Iraha, A. Hokama, F. Kinjo, J. Fujita, Y. Takeyama, S. Sakisaka, T. Matsui, J. R. Kidd, K. K. Kidd, S. Kawamura, T. Hanihara, R. Kimura, H. Ishida, H. Morita, M. Hattori, S. Mano, H. Oota
  • Organizer: American Society of Human Genetics 2013 Annual Meeting
  • Place of Presentation: Boston, USA
• [Presentation] アルコール代謝関連遺伝子群を用いた日本列島ヒト集団の遺伝的多様性の検証 (2013)
  • Author(s): 小金渕佳江、松草博隆、中込滋樹、石田肇、埴原恒彦、城圭一郎、副島英伸、藤本一眞、河村正二、太田博樹、アジア人DNAレポジトリーコンソーシアム
  • Organizer: 第26回北里大学バイオサイエンスフォーラム
  • Place of Presentation: 北里大学相模原キャンパス、相模原
• [Presentation] 光刺激応答の生理的多様性に関与する時計遺伝子多型の同定 (2013)
  • Author(s): 秋山辰穂、勝村啓史、樋口重和、安河内朗、藤本一眞、副島英伸、城圭一郎、中込滋樹、石田肇、埴原恒彦、太田博樹
  • Organizer: 第26回北里大学バイオサイエンスフォーラム
  • Place of Presentation: 北里大学相模原キャンパス、相模原
• [Presentation] ヒト色覚多型の起源解明を目指したL-Mオプシン遺伝子間塩基相違度のExon*intron 領域による違い方の集団間及び種間比較 (2013)
  • Author(s): 栗山友理子、石崎直也、白井裕介、福世裕貴子、Kenneth K. Kidd, 太田博樹、手島康介、河村正二
  • Organizer: 第67回日本人類学会大会
  • Place of Presentation: 茨城
• [Presentation] 時計遺伝子PERIOD2の多型と光刺激応答の生理的多様性の関係及びその人類学的考察 (2013)
  • Author(s): 秋山辰穂、勝村啓史、埴原恒彦、太田博樹、中込滋樹、藤本一眞、副島英伸、城圭一郎、木村亮介、石田肇、安河内朗、樋口重和
  • Organizer: 第67回日本人類学会大会
  • Place of Presentation: 茨城
• [Presentation] モヤモヤ病原因遺伝子RNF213の琉球諸島・北部九州ヒト集団における遺伝的多型 (2013)
  • Author(s): 小金渕佳江、中込滋樹、間野修平、石崎直也、河村正二、木村亮介、石田肇、城圭一郎、副島英伸、藤本一眞、佐藤公俊、安井美江、隈部俊宏、藤井清隆、秋山辰穂、埴原恒彦、太田博樹
  • Organizer: 第67回日本人類学会大会
  • Place of Presentation: 茨城
• [Presentation] 人類学の立場からパーソナルゲノムプロジェクトを考える (2013)
  • Author(s): 松前ひろみ、間野修平、太田博樹
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 兵庫
• [Presentation] Comparative Analysis of Salivary Microbiota of IBD Patients and Healthy Individuals using Barcoded Pyrosequencing (2012)
  • Author(s): H. S. Said, S. Wataru, N. Shigeki, H. Oota, H. Chinen, H. Morita, M. Hattori
  • Organizer: International Human Microbiome Congress
  • Place of Presentation: フランス、パリ(招待講演)
• [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、慶應義塾大学
• [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、慶應義塾大学
• [Book] 医学のあゆみ 249巻6号 (2014)
  • Author(s): 太田博樹 他
  • Publisher: 医歯薬出版株式会社
• [Book] 生命のビッグデータ利用の最前線 (2014)
  • Author(s): 松前ひろみ、間野修平、太田博樹、植田充美 他
  • Total Pages: 231
  • Publisher: 株式会社シーエムシー
• [Book] ヒトは病気とともに進化した シリーズ認知と文化 (2013)
  • Author(s): 太田博樹、長谷川眞理子
  • Total Pages: 232
  • Publisher: 勁草書房
• [Book] 生物の科学 遺伝５月号 (2013)
  • Author(s): 太田博樹 他
  • Total Pages: 412
  • Publisher: 株式会社エヌ・ティー・エス
• [Book] Evolutionary Insights into the "Population-Specificity" of the Genetic Factors Associated with Inflammatory Bowel Diseases. ppl-20. Ulcerative Colitis 2 (2012)
  • Author(s): S. Nakagome, H. Oota
  • Total Pages: 222
  • Publisher: InTech (Rijeka, Croatia)
• [Remarks] 北里大学医学部・太田研究室ホームページ
  • URL: http://www.med.kitasato-u.ac.jp/~anatomy-anthropology/oota_lab/index.php