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

极端环境下微生物遗传多样性和适应性进化的贝叶斯层次模型的发展

• 批准号: 16300086
• 负责人: KISHINO Hirohisa
• 金额: $ 8.7万
• 依托单位: THE UNIVERSITY OF TOKYO
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2004
• 资助国家: 日本
• 起止时间: 2004 至 2006
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16300086/
• 关键词: viral evolution; adaptation to the host; sequence and structure; population structure and history; recombination; Bayesian hierarchical model; convergent evolution; quasispecies

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.

病毒和细菌等微生物迅速适应强大的选择压力。我们主要针对病毒进化，建立了贝叶斯层次模型和程序，用于检测在病毒适应性进化中起重要作用的分子进化事件。为了了解加速的序列进化是否会导致其相应蛋白质结构进化的更高机会，我们分析了患者无症状期间HIV-1的V3环。由于不可能通过实验测量蛋白质结构的变化，我们开发了一个序列结构适应度指数。基于蛋白质结构的数据库，该索引被描述为给定模板结构的序列的可能性。感染后可能性的下降趋势暗示了结构变异。通过扩展这个指数，我们开发了一个指数的两个蛋白质之间的结合能力的似然比的形式，对比的蛋白质作为一个复杂的独立对。通过分析流感病毒HA的长期变化趋势，我们发现结合区抗体对宿主细胞受体的逃逸比结合区抗体对宿主细胞受体的逃逸更强，最后我们建立了一个贝叶斯分层模型来检测重组。如果重组发生在进化历史中，则现存序列在基因组的区域之间具有不同的系统发育关系（拓扑学）。我们开发了一个算法来计算一对拓扑之间的重组距离。通过引入相邻区域的拓扑结构之间的距离的先验，可以可靠地估计重组和重组断点的数量。我们还开发了一个检测收敛进化的程序。

项目成果

Robust time estimation reconciles views of the antiquity of placental mammals.

稳健的时间估计可以核对胎盘哺乳动物上古的观点。

• DOI: 10.1371/journal.pone.0000384
• 发表时间: 2007-04-18
• 期刊: PLOS ONE
• 影响因子: 3.7
• 作者: Kitazoe, Yasuhiro;Kishino, Hirohisa;Waddell, Peter J.;Nakajima, Noriaki;Okabayashi, Takahisa;Watabe, Teruaki;Okuhara, Yoshiyasu
• 通讯作者: Okuhara, Yoshiyasu

An integrated-likelihood method for estimating genetic differentiation between populations

• DOI: 10.1534/genetics.106.055350
• 发表时间: 2006-08-01
• 期刊: GENETICS
• 影响因子: 3.3
• 作者: Kitakado, Toshihide;Kitada, Shuichi;Skaug, Hans Julius
• 通讯作者: Skaug, Hans Julius

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))

进化系统发育树的模型验证（模型验证（Genshiro Kitakawa、Hirohisa Kishino、Tomoyuki Higuchi、Satoshi Yamashita、Yoshinori Kawasaki））

• 发表时间: 2005
• 作者: Amemiya;T.;岸野洋久
• 通讯作者: 岸野洋久

Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data.

• DOI: 10.1073/pnas.0408313102
• 发表时间: 2005-03
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Tae-Kun Seo;H. Kishino;J. Thorne

Population genetics without intraspecific data.

• DOI: 10.1093/molbev/msm085
• 发表时间: 2007-08
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: J. Thorne;S. Choi;Jiaye Yu;P. Higgs;H. Kishino