Development of statistical genetic models and hierarchical Bayes procedures to predict emergence and dynamics of resistant alleles

• Project/Area Number: 19300094
• 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 The University of Tokyo, 大学院・農学生命科学研究科, 教授 (00141987)
• Co-Investigator(Kenkyū-buntansha): 渡部 輝明 高知大学, 医, 講師 (90325415) ; 北添 康弘 高知大学, 医, 名誉教授 (90112010)
• Research Collaborator: THORNE Jeffrey l. ノースカロライナ州立大学, バイオインフォマティクス研究センター, 教授 ; DE OLIVEIRA MARTINS Leonardo ヴィゴ大学, 生化遺伝, ポスドク ; DE SOUZA LEAL Elcio パラ連合大学, バイオテクノロジー, 教授
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000); Fiscal Year 2009: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2008: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2007: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
• Keywords: MCMC / 立体構造データベースと尤度 / 配列進化と構造進化 / 分子系統樹 / ベイズ階層モデル / 統計遣伝学 / 適応度ランドスケープ / ゲノム組換え / 統計遺伝学 / 立体構造データベース / 銃計遣伝学

Research Abstract

Setting a virus as a main target of the research, we developed new statistical models and procedures to estimate its genetic diversity and to predict the emergence of resistant alleles. Our hierarchical Bayes model detects inconsistency of phylogenetic relation between the segments of the genomes and estimates the recombination history. By our knowledge-based measure of the binding ability of a protein complex, it became possible to predict the change in the values of the coefficients that specify a population dynamic model. As a result, it became possible to predict the types and timing of new resistant alleles that are likely to be fixed among host population.

Research Products

• [Journal Article] Structural considerations in the fitness landscape of a virus (2010)
  • Author(s): Watabe, T., Kishino, H.
  • Journal Title: Molecular Biology and Evolution (in press)
  • Peer Reviewed
• [Journal Article] Estimation of the size of genetic bottlenecks in cell-to-cell movement of Soil-borne wheat mosaic virus (SBWMV) and the possible role of the bottlenecks in speeding up selection on variation in trans-acting genes or elements (2010)
  • Author(s): Miyashita, S., Kishino, H.
  • Journal Title: Journal of Virology 84 Pages: 1828-1837
  • Peer Reviewed
• [Journal Article] Structural considerations in the fitness landscape of a virus. (2010)
  • Author(s): Watabe, T., Kishino, H.
  • Journal Title: Molecular Biology and Evolution. (in press.)
  • Peer Reviewed
• [Journal Article] Lineage-specific positive selection at the merozoite surface protein 1(msp1)locus of Plasmodium vivax and related simian malaria parasites. (2010)
  • Author(s): Sawai, H., Otani, H., Arisue, N., Palacpac, N., de Oliveira Martins, L., Pathirana, S., Handunnetti, S., Kawai, S., Kishino, H., Horii, T., Tanabe, K.
  • Journal Title: BMC Evolutionary Biology. 10 Pages: 52-52
  • Peer Reviewed
• [Journal Article] Estimation of the size of genetic bottlenecks in cell-to-cell movement of Soilborne wheat mosaic virus(SBWMV)and the possible role of the bottlenecks in speeding up selection on variation in trans-acting genes or elements. (2010)
  • Author(s): Miyashita, S., Kishino, H.
  • Journal Title: Journal of Virology. 84 Pages: 1828-1837
  • Peer Reviewed
• [Journal Article] Distribution of distances between topologies and its effect on detection of phylogenetic recombination. (2010)
  • Author(s): de Oliveira Martins, L., Kishino, H.
  • Journal Title: Annals of the Institute of Statistical Mathematics. 62 Pages: 145-159
  • NAID: 40016969856
  • Peer Reviewed
• [Journal Article] Distribution of distances between topologies and its effect on detection of phylogenetic recombination (2009)
  • Author(s): de Oliveira Martins, L., Kishino, H.
  • Journal Title: Annals of the Institute of Statistical Mathematics 62 Pages: 145-159
  • NAID: 40016969856
  • Peer Reviewed
• [Journal Article] Statistical comparison of nucleotide-, amino-acid- (2009)
  • Author(s): Seo, T. -K., Kishino, H.
  • Journal Title: and codon-substitution models for the evolutionary analysis of protein-coding sequences. Systematic Biology 58 Pages: 199-210
  • Peer Reviewed
• [Journal Article] Major contribution of dominant inheritance to autism spectrum disorder(ASD)in populationbased families. (2009)
  • Author(s): Nishiyama, T., Notohara, M., Sumi, S., Takami, S., Kishino, H.
  • Journal Title: Journal of Human Genetics. 54 Pages: 721-726
  • Peer Reviewed
• [Journal Article] The small heat shock protein(sHSP)genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes. (2009)
  • Author(s): Li, Z-W., Li, X., Yu, Q-Y., Xiang, Z-H., Kishino, H., Zhang, Z.
  • Journal Title: BMC Evolutionary Biology. 9 Pages: 215-215
  • Peer Reviewed
• [Journal Article] Statistical comparison of nucleotide-, amino-acid-, and codon-substitution models for the evolutionary analysis of protein-coding sequences. (2009)
  • Author(s): Seo, T.-K., Kishino, H.
  • Journal Title: Systematic Biology. 58 Pages: 199-210
  • Peer Reviewed
• [Journal Article] Observation subarea decision and population density estimation by space scale-invariance. (2009)
  • Author(s): Koyano, H., Kishino, H.
  • Journal Title: J.Japanese Statistical Society. 39 Pages: 77-88
  • NAID: 10025991911
  • Peer Reviewed
• [Journal Article] Genetic effects of long-term stock enhancement programs. (2009)
  • Author(s): Kitada, S., Shishidou, H., Sugaya, T., Kitakado, T., Hamasaki, K., Kishino, H.
  • Journal Title: Aquaculture. 290 Pages: 69-79
  • Peer Reviewed
• [Journal Article] Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. (2009)
  • Author(s): Choi, S.C., Stone, E.A., Kishino, H., Thorne, J.L.
  • Journal Title: Gene. 441 Pages: 45-52
  • Peer Reviewed
• [Journal Article] Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci. (2009)
  • Author(s): Choi, S. C., Stone, E. A., Kishino, H., and Thorne, J. L.
  • Journal Title: Gene (In press)
  • Peer Reviewed
• [Journal Article] Phylogenetic detection of recombination with a Bayesian prior on the distance between trees (2008)
  • Author(s): de Oliveira Martins, L., Leal, E., Kishino, H.
  • Journal Title: PloS ONE 3(7)
  • Peer Reviewed
• [Journal Article] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins (2008)
  • Author(s): Seo, T. -K., Kishino, H
  • Journal Title: Systematic Biology 57 Pages: 367-377
  • Peer Reviewed
• [Journal Article] Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. (2008)
  • Author(s): de Oliveira Martins, L., Leal, E. and Kishino, H.
  • Journal Title: PLoS ONE. 3
  • Peer Reviewed
• [Journal Article] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins. (2008)
  • Author(s): Seo, T.-K. and Kishino, H.
  • Journal Title: Systematic Biology 57 Pages: 367-377
  • Peer Reviewed
• [Journal Article] Bombyx small RNAs: Genomic defense system against transposons in the silkworm Bombyx mori (2008)
  • Author(s): Kawaoka. S., Hayashi, N., Katsuma, S., Kishino, H., Kohara, Y., Mita, K., and Shimada, T.
  • Journal Title: Insect Biochem. Mol. Biol. 38 Pages: 1058-1065
  • Peer Reviewed
• [Journal Article] Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates. (2008)
  • Author(s): Kitazoe, Y., Kishino, H., Hasegawa, M., Nakajima, N., Thorne, J. L., and Tanaka M
  • Journal Title: PLoS ONE. 3
  • Peer Reviewed
• [Journal Article] Complex population history of two forest-dependent Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change. (2008)
  • Author(s): 0' Loughlin, S. M., Okabayashi, T., Honda, M., Kitazoe, Y., Kishino, H., Somboon, P., Sochantha, T., Nambanya, S., Saikia, P. K., Dev, V., and Walton C
  • Journal Title: Journal of Evolutionary Biology. 21 Pages: 1555-1559
  • Peer Reviewed
• [Journal Article] Statistical comparison of nucleotide-, amino-acid-, and codon-substitution models for the evolutionary analysis of protein-coding sequences. (2008)
  • Author(s): Seo, T,-K. and Kishino, H.
  • Journal Title: Systematic Biology (In press )
  • Peer Reviewed
• [Journal Article] Genetic effects of long-term stock enhancement programs. (2008)
  • Author(s): Kitada, S., Shishidou, H., Sugaya, T., Kitakado, T., Hamasaki, K., and Kishino, H.
  • Journal Title: Aquaculture. (accepted)
  • Peer Reviewed
• [Journal Article] 遺伝子型の分子進化と表現型の適応進化 (2008)
  • Author(s): 渡部輝明,徐泰健,岸野洋久
  • Journal Title: 統計数理 56 Pages: 37-54
  • NAID: 120006019009
  • Peer Reviewed
• [Journal Article] コドンモデルを用いた分岐年代のベイズ推定. (2008)
  • Author(s): 徐泰健,岸野洋久,Je岱ey L. Thorne
  • Journal Title: 統計数理 56 Pages: 19-36
  • NAID: 120006019013
  • Peer Reviewed
• [Journal Article] Empirical Bayes inference of pairwise FST and its distribution in the genome (2007)
  • Author(s): Kitada, S., Kitakado, T., Kishino, H.
  • Journal Title: Genetics 177 Pages: 861-873
  • Peer Reviewed
• [Journal Article] Recent independent evolution of mspl polymorphism in Plasmodium vivax and related simian malaria parasites (2007)
  • Author(s): Tanabe, K., Escalante, A., Sakihama, N., Honda, M., Arisue, N., Horii, T., Culleton, R., Hayakawa, T., Hashimoto, T., Longacre, S., Pathirana, S., Handunnetti, S., Kishino, H.
  • Journal Title: Molecular & Biochemical Parasitology 156 Pages: 74-79
  • Peer Reviewed
• [Journal Article] Population genetics without intraspecific data (2007)
  • Author(s): Thorne, J. L., Choi, S. C., Yu, J., Higgs, P. G., Kishino, H.
  • Journal Title: Molecular Biology and Evolution 24 Pages: 1667-1677
  • Peer Reviewed
• [Journal Article] A likelihoodbased index of protein-protein binding affinities with application to influenza HA escape from antibodies (2007)
  • Author(s): Watabe, T., Kishino, H., de Oliveira Martins, L., Kitazoe, Y.
  • Journal Title: Molecular Biology and Evolution 24 Pages: 1627-1638
  • Peer Reviewed
• [Journal Article] A likelihood-based index of protein-protein binding affnities with application to influenza HA escape from antibodies (2007)
  • Author(s): Watabe, T., Kishino, H., Martins, L.O., and Kitazoe, Y.
  • Journal Title: Molecular Biology and Evolution 24 Pages: 1627-1638
  • Peer Reviewed
• [Journal Article] Recent independent evolution of mspl polymorphism in Plasmodium vivax and related simian malaria parasites (2007)
  • Author(s): Tanabe, K., Escalante, A., Sukihama, N., Hondac, M., Arisue, N., Horii, T., Culleton, R., Huyakawa, T., Hashimoto, T., Longacre, S., Pathirana, S., Handunnetti, S., and Kishino, H.
  • Journal Title: Molecular & Biochemical Parasitology 156 Pages: 74-79
  • Peer Reviewed
• [Journal Article] Empirical Bayes inference of pairwise FST and its distribution in the genome (2007)
  • Author(s): Kitada, S., Kitakado, T., and Kishino, H.
  • Journal Title: Genetics 177 Pages: 861-873
  • Peer Reviewed
• [Presentation] Co-evolution of proteins and covariation of evolutionary rate. (2009)
  • Author(s): Kishino, H. (代表)
  • Organizer: 生物物理学会
  • Place of Presentation: 徳島文理大学
  • Year and Date: 2009-10-30
• [Presentation] Co-evolution of proteins and covariation of evolutionary rate. (2009)
  • Author(s): 岸野洋久
  • Organizer: 生物物理学会.
  • Place of Presentation: 徳島文理大学
  • Year and Date: 2009-10-30
• [Presentation] 感染症研究における統計遺伝学的アプローチの可能性 (2009)
  • Author(s): 岸野洋久 (代表)
  • Organizer: 統計関連学会
  • Place of Presentation: 同志社大学
  • Year and Date: 2009-09-07
• [Presentation] 感染症研究における統計遺伝学的アプローチの可能性. (2009)
  • Author(s): 岸野洋久
  • Organizer: 統計関連学会.
  • Place of Presentation: 同志社大学
  • Year and Date: 2009-09-07
• [Presentation] マラリア原虫(Plasmodium falciparum)大陸間の集団分化と遺伝的交流、集団履歴の推定 (2009)
  • Author(s): 堀部舜, 岸野洋久, 田邉和裄
  • Organizer: 日本進化学会
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-09-03
• [Presentation] Statistical Comparison of nucleotide-, amino-acid-, and codon-substitution models for evolutionary analysis of protein-coding sequences. Evolution 20009 (2009)
  • Author(s): Seo, T. -K. (代表), Kishino, H.
  • Organizer: the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN)
  • Place of Presentation: University of Idaho
  • Year and Date: 2009-06-16
• [Presentation] Statistical comparison of nucleotide-, amino-acid-, and codon-substitution models for evolutionary analysis of protein-coding sequences. (2009)
  • Author(s): Seo, T.-K., Kishino, H.
  • Organizer: Evolution 20009, the joint annual meeting of the Society for the Study of Evolution(SSE), the Society of Systematic Biologists(SSB), and the American Society of Naturalists(ASN).
  • Place of Presentation: University of Idaho USA
  • Year and Date: 2009-06-16
• [Presentation] Structural consideration on the fitness-landscape of virus (2009)
  • Author(s): Watabe. T. (代表), Kishino, H.
  • Organizer: Society for Molecular Biology and Evolution
  • Place of Presentation: University of Iowa
  • Year and Date: 2009-06-07
• [Presentation] Structural consideration on the fitness-landscape of virus. (2009)
  • Author(s): Watabe, T., Kishino, H.
  • Organizer: Society for Molecular Biology and Evolution.
  • Place of Presentation: University of Iowa USA
  • Year and Date: 2009-06-07
• [Presentation] Modeling sequence evolution and diversity (2008)
  • Author(s): Hirohisa Kishino
  • Organizer: Southwest University (special talk)
  • Place of Presentation: Chongqing, China
  • Year and Date: 2008-12-29
• [Presentation] Modeling sequence evolution, structural adaptation, and diversity (2008)
  • Author(s): Hirohisa Kishino
  • Organizer: Chongqing University (special talk)
  • Place of Presentation: Chongqing, China
  • Year and Date: 2008-12-29
• [Presentation] Measuring diversity and evolution through statistical modeling (2008)
  • Author(s): Kishino. H. (代表)
  • Organizer: Workshop on Measuring Evolution
  • Place of Presentation: ノルウェイ科学アカデミー, Oslo, Norway
  • Year and Date: 2008-10-03
• [Presentation] Measuring diversity and evolution through statistical modeling (2008)
  • Author(s): Hirohisa Kishino
  • Organizer: Workshop on Measuring Evolution
  • Place of Presentation: Oslo, Norway
  • Year and Date: 2008-10-03
• [Presentation] 構造データベースに基づく複合体結合能の予測とウイルス適応度マップの構成 (2008)
  • Author(s): 渡部輝明、岸野洋久
  • Organizer: 日本統計関連学会
  • Place of Presentation: 慶応義塾大学
  • Year and Date: 2008-09-09
• [Presentation] Bayesian Estimation of Two Risk Components in Autism Spectrum Disorders(ASD) (2008)
  • Author(s): 西山毅、高橋邦彦、鷲見聡、谷合弘子、岸野洋久、丹後俊郎
  • Organizer: 日本統計関連学会
  • Place of Presentation: 慶応義塾大学
  • Year and Date: 2008-09-09
• [Presentation] 構造データベースに基づく複合体結合能の予測とウイルス適応度マップの構成 (2008)
  • Author(s): 渡部輝明、岸野洋久
  • Organizer: 日本進化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2008-08-22
• [Presentation] AMEVA: Analysis of Metagenomic Variance (2008)
  • Author(s): 小谷野仁、岸野洋久
  • Organizer: 日本進化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2008-08-22
• [Presentation] 真猿類におけるミトコンドリア蛋白質の膜貫通領域でのスレオニンの増加と寿命の関係. (2008)
  • Author(s): 北添康弘、岸野洋久、長谷川政美、中島典昭、Jefferey Thorne,田中雅嗣
  • Organizer: 日本進化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2008-08-22
• [Presentation] Species Leverage: assessing species-induced incongruities in phylogenetic inference (2008)
  • Author(s): Mahendra Mariadassou, AvnerBar-Hen,岸野洋久
  • Organizer: 日本進化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2008-08-22
• [Presentation] Statistical comparison of nucleotide-, amino acid-, and codon-substitution models (2008)
  • Author(s): Tae-Kun Seo, Hirohisa Kishino
  • Organizer: 日本進化学会
  • Place of Presentation: 東京大学
  • Year and Date: 2008-08-22
• [Presentation] Population history of malaria and population dynamics of virus (2008)
  • Author(s): Hirohisa Kishino
  • Organizer: Southwest University (special talk)
  • Place of Presentation: Chongqing, China
  • Year and Date: 2008-07-07
• [Presentation] ゲノム進化と変異の統計解析 (2008)
  • Author(s): 岸野洋久. (代表)
  • Organizer: 応用統計学会
  • Place of Presentation: 筑波大学
  • Year and Date: 2008-06-07
• [Presentation] ゲノム進化と変異の統計解析 (2008)
  • Author(s): 岸野洋久
  • Organizer: 応用統計学会(特別講演)
  • Place of Presentation: 筑波大学
  • Year and Date: 2008-06-07
• [Presentation] Statistical comparison of nucleotide-, amino acid-, and codon-substitution models (2008)
  • Author(s): Tae-KUn Seo and Hirohisa Kishir.
  • Organizer: Society for Molecular Biology and Evolution
  • Place of Presentation: Barcelona, Spain
  • Year and Date: 2008-06-06
• [Presentation] アレル頻度分布に基づくマラリア原虫(Plasnmodium falciparum)集団履歴の推定 (2008)
  • Author(s): 堀部舜、岸野洋久、田邉和桁
  • Organizer: 計量生物学会
  • Place of Presentation: 筑波大学
  • Year and Date: 2008-06-04
• [Presentation] Using a database and a prior for the estimation of structural evolution and recombination (2008)
  • Author(s): Kishino, H., (代表)
  • Organizer: Phylogenetic workshop at the 15th HIV Evolution and Dynamics meeting
  • Place of Presentation: Los Alamos 国立研究所, Santa Fe, U.S.A.
  • Year and Date: 2008-04-27
• [Presentation] Using a database and a prior for the estimation of structural evolution and reconibi (2008)
  • Author(s): Hirohisa Kishino
  • Organizer: Phylogenetic workshop at the 15th HIV Evolution and Dynamicsmeeting(invited talk)
  • Place of Presentation: Santa Fe, USA
  • Year and Date: 2008-04-27
• [Presentation] Estimation of the population history based on the allele frequency distribution (2008)
  • Author(s): 岸野 洋久
  • Organizer: Colloquium on malaria infection, genetics and evolution(寄生虫学会)
  • Place of Presentation: 千里ライフサイエンスセンター
  • Year and Date: 2008-02-09
• [Presentation] ウィルススパイク蛋白質の受容体結合vs抗体結合の最適バランスと適応進化の予測 (2007)
  • Author(s): 渡部 輝明, 岸野 洋久
  • Organizer: 統計関連学会
  • Place of Presentation: 神戸大学
  • Year and Date: 2007-09-09
• [Presentation] 系統樹間の距離とゲノム組換えのベイズ推定 (2007)
  • Author(s): de Oliveira Martins, L., (代表), Leal, E. S., 岸野洋久
  • Organizer: 統計関連学会
  • Place of Presentation: 神戸大学
  • Year and Date: 2007-09-07
• [Book] 分子準化の統計科学.(21世紀の統計科学II:自然・生物・健康の統計科学(小西貞則・国友直人編)) (2008)
  • Author(s): 岸野洋久
  • Total Pages: 26
  • Publisher: 東京大学出版会