Statistical modeling of highly-resolved phylogeography based on molecular data of new generation

• Project/Area Number: 16H02788
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Statistical science
• Research Institution: The University of Tokyo
• Principal Investigator: KISHINO Hirohisa 東京大学, 大学院農学生命科学研究科(農学部), 教授 (00141987)
• Co-Investigator(Kenkyū-buntansha): 北田 修一 東京海洋大学, 学術研究院, 名誉教授 (10262338)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000); Fiscal Year 2018: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2017: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2016: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
• Keywords: ゲノムビッグデータ / 要約統計量 / 分子進化の中立説 / アレル頻度スペクトル / 多遺伝子系統樹 / 分散分析 / 統計科学 / ゲノム / 進化 / 生態学

Outline of Final Research Achievements

New-generation molecular data enables to represent the intra-species polymorphism and inter-species diversity seamlessly, and with high resolution. By extending classical theory of population genetics and molecular evolution, we developed a statistical model to express the summary statistics such as allele frequencies spectra and multi-gene phylogenetic trees. The population genomic study of Spodoptera litura, a polyphagous insect widely distributed in East Asia, identified a high gene flow along a South India-South China-Japan axis. We developed a novel method of ancestral state reconstruction of life history traits that associates the variation of trait values with the variation of molecular evolutionary rates. It inferred, consistent with fossils, that placentals were insectivores before Cretaceous-Paleogene boundary (65mya) and only nocturnal animals survived over the Eocene-Oligocene transition (EOT, 33.9 mya). These studies show clearly the validity of our approach.

Academic Significance and Societal Importance of the Research Achievements

本研究は、人の構築した集団遺伝と分子進化の理論を拡張し、要約統計量を統計的にモデリングするというアプローチを開発した。多遺伝子分子進化速度の分散分析により分子進化と表現型進化を橋渡しするアプローチは、ゲノムと表現型の種間比較の新たな方法を提供する。ハスモンヨトウの分析で観察された広範囲に及ぶ遺伝子流動は、害虫管理方策の策定に有用な情報を提供する。また、哺乳類の生活史の分析から得られた、社会性や一夫一婦制では全般に機能的な制約が緩むこと、社会性については脳や神経系に携わる遺伝子が予測因子として抽出されるなどの結果は、行動の遺伝的背景を理解する上でも示唆を与えるものと思われる。

Research Products

• [Journal Article] Stochastic variational inference for Bayesian phylogenetics: A case of CAT model (2019)
  • Author(s): Dang, T. T. and Kishino, H.
  • Journal Title: Molecular Biology and Evolution Volume: 36 Issue: 4 Pages: 825-833
  • DOI: 10.1093/molbev/msz020
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat (2019)
  • Author(s): Kitada, S., Nakajima, K., Hamasaki, K., Shishidou, H., Waples, R. S., & Kishino, H.
  • Journal Title: Scientific Reports Volume: 9 Issue: 1 Pages: 5292-5292
  • DOI: 10.1038/s41598-019-39050-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A new approach for comprehensively describing heterogametic sex chromosomes (2018)
  • Author(s): Li, S., Ajimura, M., Chen, Z., Liu, J., Chen, E., Guo, H., Tadapatri, V., Reddy, C. G., Zhang, J., Kishino, H., Abe, H., Xia, Q., Arunkumar, K. P., and Mita, K.
  • Journal Title: DNA Research Volume: 25 Issue: 4 Pages: 375-382
  • DOI: 10.1093/dnares/dsy010
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The empirical Bayes estimators of fine-scale population structure in high gene flow species. (2017)
  • Author(s): Kitada, S., Nakamichi, R., and Kishino, H.
  • Journal Title: Molecular Ecology Resources Volume: accepted Issue: 6 Pages: 1210-1222
  • DOI: 10.1111/1755-0998.12663
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest (2017)
  • Author(s): Cheng, T, Wu, J. et al
  • Journal Title: Nature Ecology and Evolution Volume: 1 Issue: 11 Pages: 1747-1756
  • DOI: 10.1038/s41559-017-0314-4
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Rates of molecular evolution suggest natural history of life history traits and a post-K-Pg nocturnal bottleneck of Placentals (2017)
  • Author(s): Wu, J., Yonezawa, T., and Kishino, H.
  • Journal Title: Current Biology Volume: 27 Issue: 19 Pages: 3025-3033
  • DOI: 10.1016/j.cub.2017.08.043
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Population structure and persistence of Pacific herring following the Great Tohoku earthquake. (2017)
  • Author(s): Kitada, S., Yoshida, R., Fujita, T., Hamasaki, K., Nakamichi, R., and Kishino, H.
  • Journal Title: Conservation Genetics Volume: 18 Issue: 2 Pages: 423-437
  • DOI: 10.1007/s10592-016-0918-2
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Expression map of a complete set of gustatory receptor genes in chemosensory organs of Bombyx mori (2017)
  • Author(s): Guo, H., Cheng, T., Chen, Z., Jiang, L., Guo, Y., Liu, J., Li, S., Taniai, K., Asaoka, K., Kadono-Okuda, K., Arunkumar, K. P., Wu, J., Kishino, H., Zhang, H., Seth, R. K., Gopinathan, K. P., Montagne, N., Jacquin-Joly, E., Goldsmith, M. R., Xia, Q., and Mita, K.
  • Journal Title: Insect Biochem. Mol. Biol. Volume: 82 Pages: 74-82
  • DOI: 10.1016/j.ibmb.2017.02.001
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Phylogenomics and morphology of extinct paleognaths reveal the origin and evolution of the ratites (2017)
  • Author(s): Takahiro Yonezawa, Takahiro Segawa, Hiroshi Mori, Paula F. Campos, Yuichi Hongoh et al.,
  • Journal Title: Current Biology Volume: 27 Issue: 1 Pages: 68-77
  • DOI: 10.1016/j.cub.2016.10.029
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Bridging molecular evolution and phenotypic evolution (2018)
  • Author(s): Kishino, H.
  • Organizer: University of Linz
  • Invited
• [Presentation] Stochastic variational inference of mixture models in phylogenetics. (2018)
  • Author(s): Dang, T. and Kishino, H.
  • Organizer: 統計関連学会連合大会.
• [Presentation] Stochastic Variational Inference of Mixture Models in Phylogenetics (2018)
  • Author(s): Dang, T. and Kishino, H.
  • Organizer: 日本進化学会
• [Presentation] Fast approximate inference for phylogenetic reconstruction via stochastic variational inference in large data sets (2018)
  • Author(s): Dang, T. and Kishino, H.
  • Organizer: Society of Molecular Biology and Evolution.
  • Int'l Joint Research
• [Presentation] Rates of molecular evolution suggest life history and a post-K-Pg nocturnal bottleneck of Placentals (2018)
  • Author(s): Wu, J., Yonezawa, T., and Kishino, H.
  • Organizer: Society of Molecular Biology and Evolution.
  • Int'l Joint Research
• [Presentation] 分子進化速度が語るもの (2018)
  • Author(s): 岸野洋久
  • Organizer: 日本計量生物学会
  • Invited
• [Presentation] 分子系統と地誌から辿る日本の淡水魚類相の形成過程とそれに関与した大陸産魚種 (2017)
  • Author(s): 岡崎登志夫, 谷口昇志, 指田昌樹, 田祥麟, 岸野洋久
  • Organizer: 日本生態学会
  • Place of Presentation: 早稲田大学, 東京都新宿区
  • Year and Date: 2017-03-14
• [Presentation] 大陸からの侵入淡水魚による置き換りの推定: 分子系統地理的前向きシミュレーションによるアプローチ (2017)
  • Author(s): 谷口昇志, 指田昌樹, 岡崎登志夫, 田祥麟, Bertl, J., Futschik, A., 岸野洋久
  • Organizer: 日本生態学会
  • Place of Presentation: 早稲田大学, 東京都新宿区
  • Year and Date: 2017-03-14
• [Presentation] 大陸からの侵入時期の魚種間共通性と個別性：分子進化速度の種間分布によるアプローチ (2017)
  • Author(s): 指田昌樹, 岡崎登志夫, 谷口昇志, 田祥麟, 岸野洋久
  • Organizer: 日本生態学会
  • Place of Presentation: 早稲田大学, 東京都新宿区
  • Year and Date: 2017-03-14
• [Presentation] Gene-by-branch analysis of evolutionary rates predict times, traits and genes of ecological importance (2017)
  • Author(s): 呉佳齊, 岸野洋久
  • Organizer: 日本生態学会
  • Place of Presentation: 早稲田大学, 東京都新宿区
  • Year and Date: 2017-03-14
• [Presentation] Spatio-temporal modeling to measure viral adaptation and community diversity (2017)
  • Author(s): Kishino, H.
  • Organizer: International Conference on Bioinformatics and Biostatistics for Agriculture
  • Place of Presentation: University of Rajshahi, Rajshahi, Bangladesh
  • Year and Date: 2017-01-20
  • Int'l Joint Research / Invited
• [Presentation] Natural history of life history traits and a post-K-Pg nocturnal bo8leneck of Placentals implicated by neutral theory (2017)
  • Author(s): Wu, J., Yonezawa, T., and Kishino, H.
  • Organizer: EMBL Conference Mammalian Genetics and Genomics
  • Int'l Joint Research
• [Presentation] Natural history of life history traits and a post-K-Pg nocturnal bo8leneck of Placentals implicated by neutral theory (2017)
  • Author(s): 呉佳齊, 米澤隆弘, 岸野洋久
  • Organizer: 統計関連学会連合大会
• [Presentation] 分子進化速度が語る動物行動の進化 (2017)
  • Author(s): 呉佳齊, 米澤隆弘, 岸野洋久
  • Organizer: 日本行動計量学会
• [Presentation] Natural history of life history traits and a post-KPg nocturnal bottleneck of Placentals: Implications from neutral theory (2017)
  • Author(s): 呉佳齊, 米澤隆弘, 岸野洋久
  • Organizer: 日本進化学会
• [Presentation] 同一種内の淡水魚の個体群間の置き換わりで生じる地理的分断の検出 (2017)
  • Author(s): 谷口昇志, 岡崎登志夫, Bertl, J., Futschik, A., 岸野洋久
  • Organizer: 日本進化学会
• [Presentation] Inter-specific genome wide association study and prediction of ecotype (2016)
  • Author(s): 呉佳齊, 岸野洋久
  • Organizer: 統計関連学会連合大会
  • Place of Presentation: 金沢大学. 石川県金沢市
  • Year and Date: 2016-09-04
• [Presentation] 分子系統と地誌から見る淡水魚の大陸から日本への侵入パターンと国内での拡散・置き換り (2016)
  • Author(s): 岡崎登志夫, 谷口昇志, 田祥麟, 岸野洋久
  • Organizer: 日本進化学会
  • Place of Presentation: 東京工業大学, 東京都目黒区
  • Year and Date: 2016-08-25
• [Presentation] 淡水魚の侵入、拡散、置き換りの推定; ベイズ法及びシミュレーションをベースとしたアプローチ (2016)
  • Author(s): 谷口昇志, 岡崎登志夫, Jeon, S.-R., Bertl, J., Futschik, A., 岸野洋久
  • Organizer: 日本進化学会
  • Place of Presentation: 東京工業大学, 東京都目黒区
  • Year and Date: 2016-08-25
• [Book] Tree Evaluation and Robustness Testing. In Encyclopedia of Bioinformatics and Computational Biology (edited by Ranganathan, S., Nakai, K., Schönbach, C., and Gribskov, M.). Pp. 736-745 (2019)
  • Author(s): Mariadassou, M, Bar-Hen, A. and Kishino, H.
  • Total Pages: 3284
  • Publisher: Academic Press
  • ISBN: 0128114142