Development of Bayesian hierarchical models of genetic diversity and adaptive evolution of micro-organisms in the extreme environments

• Project/Area Number: 16300086
• 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, Graduate School of Agricultural and Life Sciences, Professor, 大学院・農学生命科学研究科, 教授 (00141987)
• Co-Investigator(Kenkyū-buntansha): TAE-KUN Eo The University of Tokyo, Graduate School of Agricultural and Life Sciences, Assistant Professor, 大学院・農学生命科学研究科, 特任助手 (60401189) ; KITAZOE Yasuhiro Kochi Medical School, Center of Medical Information Science, Professor, 医学情報センター, 教授 (90112010) ; WATABE Teruaki Kochi Medical School, Center of Medical Information Science, Assistant, 医学情報センター, 助手 (90325415)
• Project Period (FY): 2004 – 2006
• Project Status: Completed (Fiscal Year 2006)
• Budget Amount: ¥13,600,000 (Direct Cost: ¥13,600,000); Fiscal Year 2006: ¥3,800,000 (Direct Cost: ¥3,800,000); Fiscal Year 2005: ¥5,500,000 (Direct Cost: ¥5,500,000); Fiscal Year 2004: ¥4,300,000 (Direct Cost: ¥4,300,000)
• Keywords: viral evolution / adaptation to the host / sequence and structure / population structure and history / recombination / Bayesian hierarchical model / convergent evolution / quasispecies

Research Abstract

Micro-organisms such as virus and bacteria adapt promptly to the strong selection pressures. Focusing mostly on viral evolution, we developed Bayesian hierarchical models and procedures to detect events of molecular evolution which play essential role on their adaptive evolution.
The theory of population genetics suggests that endangered populations under strong selection pressure have higher rate of sequence evolution. To see if accelerated sequence evolution leads to higher chance of structural evolution of its corresponding protein, we analyzed the V3-loop of HIV -1 during the asymptomatic period in the patients. Since it is impossible to measure the variation of protein structure experimentally, we developed an index of sequence-structure fitness. Based on the database of protein structures, the index is described as a likelihood of a sequence given a template structure. Structural variation is implied by the declining trend of the likelihood after infection. By extending this index, we developed an index of binding ability between two proteins in the form of likelihood ratio which contrasts the proteins as a complex to independent pair. By analyzing the long term trend of influenza virus HA, we observed that the escape from the antibodies bound to the binding region to the receptor of the host cell is stronger than the escape from those bound to the region neighbor to the binding sites.
Finally, we developed a Bayesian hierarchical model to detect recombination. If recombination occurs during the evolutionary history, the extant sequences have different phylogenetic relation (topology) between regions of the genomes. We developed an algorithm to calculate the recombination distance between a pair of topologies. By introducing a prior on the distances between the topologies of neighboring regions, it became possible to estimate the number of recombination and recombination break points reliably. We also developed a procedure to detect convergent evolution.

Research Products

• [Journal Article] Robust time estimation reconciles views of the antiquity of placental mammals. (2007)
  • Author(s): Kitazoe.Y., Kishino.H., Waddell, P.J., Nakajima, N., Okabayashi, T., Watabe, T., Okuhara, Y.
  • Journal Title: PLoS ONE 4
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies. (2007)
  • Author(s): Watabe.T., Kishino, H., Martins, L.O., Kitazoe.Y.
  • Journal Title: Molecular Biology and Evolution. (accepted)
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Population genetics without intraspecific data. (2007)
  • Author(s): Thorne, J.L., Choi, S.C., Yu, J., Kishino.H.
  • Journal Title: Molecular Biology and Evolution. (accepted)
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Quantifying the impact of protein tertiary structure on molecular evolution. (2007)
  • Author(s): Choi, S.C., Hobolth, A., Douglas M., Robinson, D.M., Kishino, H., Thorne, J.L.
  • Journal Title: Molecular Biology and Evolution. (accepted)
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies. (2007)
  • Author(s): Watabe, T., Kishino, H., Martins, L.0., Kitazoe, Y.
  • Journal Title: Molecular Biology and Evolution. (accepted)
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Population genetics without intraspecific data. (2007)
  • Author(s): Thorne, J.L, Choi, S.C., Yu, J., Fishing, H.
  • Journal Title: Molecular Biology and Evolution. (accepted)
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Quantifying the impact of protein tertiary structure on molecular evolution. (2007)
  • Author(s): Choi, S.C., Hobolth, A., Douglas M.Robinson, D.M., Kishino, H., Thorne, J.L
  • Journal Title: Molecular Biology and Evolution. (accepted)
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Fold recognition of the HIV-1 V3 loop and flexibility of its crown structure during the course of adaptation to a host. (2006)
  • Author(s): Watabe.T., Kishino.H., Okuhara.Y., Kitazoe.Y.
  • Journal Title: Genetics. 172 Pages: 1379-1383
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Core set approach to reduce uncertainty of gene trees (2006)
  • Author(s): Okabayashi, T., Kitazoe, Y., Kishino, H., Watabe, T., Nakajima, N., Okuhara, Y., O'Loughlin, S., Walton, C.
  • Journal Title: BMC Evolutionary Biology. 6 Pages: 41-41
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas. (2006)
  • Author(s): Kakizawa, S., Oshima, K., Jung, H-Y., Suzuki, S, Nishigawa, H., Arashida, R., Miyata, S., Ugaki, M., Kishino, H., Namba, S.
  • Journal Title: Journal of Bacteriology. 188 Pages: 3424-3428
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scyllaparamamosain) in Japan. (2006)
  • Author(s): Kitakado, T., Kitada, S., Obata, Y., Kishino, H.
  • Journal Title: Genetics. 173 Pages: 2063-2072
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] An integrated likelihood method for estimating genetic differentiation between populations. (2006)
  • Author(s): Kitakado, T., Kitada, S., Kishino, H., Skaug, H.J.
  • Journal Title: Genetics. 173 Pages: 2073-2082
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Phylogenetic methodology for detecting protein interactions. (2006)
  • Author(s): Waddell, P.J., Kishino.H., Ota, R.
  • Journal Title: Molecular Biology and Evolution. 24 Pages: 650-659
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Fold recognition of the HIV-1 V3 loop and flexibility of its crown structure during the course of adaptation to a host. (2006)
  • Author(s): Watabe, T., Kishino, H., Okuhara, Y., Kitazoe, Y.
  • Journal Title: Genetics. 172 Pages: 1379-1383
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Core set approach to reduce uncertainty of gene trees. (2006)
  • Author(s): Okabayashi, T., Kitazoe, Y., Kishino, H., Watabe.T., Nakajima, N., Okuhara, Y., O'Loughlin, S., Walton, C.
  • Journal Title: BMC Evolutionary Biology. 6 Pages: 41-41
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas. (2006)
  • Author(s): Kakizawa, S., Oshima, K, Jung, H-Y., Suzuki, S, Nishigawa, H., Arashida, R., Miyata, S., Ugaki, M., Kishino, H., Namba, S.
  • Journal Title: Journal of Bacteriology. 188 Pages: 3424-3428
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan. (2006)
  • Author(s): Kitakado, T., Kitada, S., Obata, Y., Kishino, H.
  • Journal Title: Genetics. 173 Pages: 2063-2072
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Phylogenetic methodology for detecting protein interactions. (2006)
  • Author(s): Waddell, P.J., Kishino, H., Ota, R.
  • Journal Title: Molecular Biology and Evolution. 24 Pages: 650-659
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Core set approach to reduce uncertainty of gene trees. (2006)
  • Author(s): Okabayashi, T., Kitazoe, Y., Kishino, H., Watabe, T., Nakajima, N., Okuhara, Y., O'Loughlin, S., Walton,C.
  • Journal Title: BMC Evolutionary Biology 6:41. Pages: 1-17
• [Journal Article] Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas. (2006)
  • Author(s): Kakizawa, S., Oshima, K., Jung, H-Y., Suzuki, S., Nishigawa, H., Arashida, R., Miyata, S., Ugaki, M., Kishino, H., Namba,S.
  • Journal Title: Journal of Bacteriology 188 Pages: 3424-3428
• [Journal Article] Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan. (2006)
  • Author(s): Kitakado, T., Kitada, S., Obata, Y., Kishino,H.
  • Journal Title: Genetics 173 Pages: 2063-2072
• [Journal Article] An integrated likelihood method for estimating genetic differentiation between populations. (2006)
  • Author(s): Kitakado, T., Kitada, S., Kishino, H., Skaug, H.J.
  • Journal Title: Genetics 173 Pages: 2073-2082
• [Journal Article] Phylogenetic methodology for detecting protein interactions. (2006)
  • Author(s): Waddell, P.J., Kishino, H., Ota, R.
  • Journal Title: Molecular Biology and Evolution 24 Pages: 650-659
• [Journal Article] Fold recognition of the HIV-1 V3 loop and flexibility of its crown structure during the course of adaptation to a host. (2006)
  • Author(s): Watabe, T., Kishino, H., Okuhara, Y., Kitazoe, Y.
  • Journal Title: Genetics. (in press)
• [Journal Article] Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. (2005)
  • Author(s): Seo, T.-K., Kishino.H., Thorne, J.L.
  • Journal Title: Proceedings of National Academy of Sciences, USA. 102 Pages: 4436-4441
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Multidimensional vector space representation for correlated evolution and molecular phylogeny. (2005)
  • Author(s): Kitazoe, Y., Kishino.H., Okabayashi, T., Watabe, T., Nakajima, N., Okuhara, Y., Kurihara, Y.
  • Journal Title: Molecular Biology and Evolution. 22 Pages: 704-715
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Inheritance of song and stridulatory peg number divergence between Chorthippus brunneus and C. jacobsi, two naturally hybridising grasshopper species (Orthoptera : Acrididae). (2005)
  • Author(s): Saldamando C.I., Miyaguchi, S., Tatsuta, H., Kishino.H., Bridle, J.R., R.K.Butlin.
  • Journal Title: Journal of Evolutionary Biology. 18 Pages: 703-712
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Divergence pattern of duplicate genes in protein-protein interactions follows the power law. (2005)
  • Author(s): Zhang, Z., Luo, Z., Kishino.H., Kearsey, M.J.
  • Journal Title: Molecular Biology and Evolution. 22 Pages: 501-505
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. (2005)
  • Author(s): Seo, T.-K., Kishino, H., Thorne, J.L
  • Journal Title: Proceedings of National Academy of Sciences, USA. 102 Pages: 4436-4441
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Multidimensional vector space representation for correlated evolution and molecular phylogeny. (2005)
  • Author(s): Kitazoe, Y., Kishino, H., Okabayashi, T., Watabe, T., Nakajima, N., Okuhara, Y., Kurihara, Y.
  • Journal Title: Molecular Biology and Evolution. 22 Pages: 704-715
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Inheritance of song and stridulatory peg number divergence between Chorthippus brunneus and C. jacobsi, two naturally hybridising grasshopper species (Orthoptera : Acrididae). (2005)
  • Author(s): Saldamando C.I., Miyaguchi, S., Tatsuta, H., Kishino, H., Bridle, J.R., R.K Butlin.
  • Journal Title: Journal of Evolutionary Biology 18 Pages: 703-712
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Divergence pattern of duplicate genes in protein-protein interactions follows the power law. (2005)
  • Author(s): Zhang, Z., Luo, Z., Kishino, H., Kearsey, M.J.
  • Journal Title: Molecular Biology and Evolution. 22 Pages: 501-505
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Inheritance of song and stridulatory peg number divergence between Chorthippus brunneus and C.jacobsi, two naturally hybridising grasshopper species (Orthoptera : Acrididae). (2005)
  • Author(s): Saldamando C.I., Miyaguchi, S., Tatsuta, H., Kishino, H., Bridle, J.R., Butlin, R.K.
  • Journal Title: Journal of Evolutionary Biology 18 Pages: 703-712
• [Journal Article] Multidimensional vector space representation for correlated evolution and molecular phylogeny (2005)
  • Author(s): Kitazoe Y, H Kishino, T Okabayashi, T Watabe, N Nakajima, Y Okuhara
  • Journal Title: Molecular Biology and Evolution. 22 Pages: 704-715
• [Journal Article] Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. (2005)
  • Author(s): Seo T-K, H Kishino, JL Thorne
  • Journal Title: Proceedings of National Academy of Sciences, USA. 102 Pages: 4436-4441
• [Journal Article] Simultaneous detection of linkage disequilibrium and genetic differentiation of subdivided populations. (2004)
  • Author(s): Kitada S, H Kishino
  • Journal Title: Genetics. 167 Pages: 2003-2013
• [Journal Article] Divergence pattern of duplicate genes in protein-protein interactions follows the power law. (2003)
  • Author(s): Zhang Z, Z Luo, H Kishino, MJ Kearsey
  • Journal Title: Molecular Biology and Evolution. 22 Pages: 501-505
• [Journal Article] Robust time estimation reconciles views of the antiquity of placental mammals.
  • Author(s): Kitazoe, Y., Kishino, H., Waddell, P.J., Nakajima, N., Okabayashi, T., Watabe, T., Okuhara, Y.
  • Journal Title: PLoS ONE 4
  • Description: 「研究成果報告書概要(欧文)」より
• [Book] ゲノム進化の読解法 (2006)
  • Author(s): 岸野洋久
  • Total Pages: 106
  • Publisher: 岩波書店
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 進化系統樹のモデルヴァリデーション.(モデルヴァリデーション(北川源四郎・岸野洋久・樋口知之・山下智志・川崎能典)) (2005)
  • Author(s): 岸野洋久
  • Total Pages: 49
  • Publisher: 共立出版