III: Small: RUI: Algorithms and Tools for Phylogenetic Tree Reconciliation

III：小：RUI：系统发育树协调的算法和工具

• 批准号: 1419739
• 负责人: Ran Libeskind-Hadas
• 金额: $ 33.13万
• 依托单位: Harvey Mudd College
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-01 至 2018-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1419739&HistoricalAwards=false
• 关键词: III; Small; RUI; Algorithms; Tools

Reconciliation analysis is a fundamental method in the study of species and genes, hosts and parasites, and geographical areas and species. While these applications are different, the underlying mathematical and computational problems are analogous. Genes and species interact through complex evolutionary processes such as gene duplication, horizontal gene transfer, and gene loss. Parasites and their hosts coevolve through processes including both contemporaneous and independent speciation, host switch, and extinction. And, species and their geographical habitats interact over geological time scales through vicariance, sympatric speciation, dispersal, and extinction. Consequently, the phylogenetic trees for genes and species, parasites and hosts, and species and their geographic regions are inherently incongruent. This research will develop new algorithms, visualization methods, and software tools for studying the evolutionary histories of pairs of entities such as genes and species, hosts and parasites, and species and their geographical habitats and also help to train the next generation of researchers.Genes and species interact through complex evolutionary processes such as gene duplication, horizontal gene transfer, and gene loss. Parasites and their hosts coevolve through processes including both contemporaneous and independent speciation, host switch, and extinction. And, species and their geographical habitats interact over geological time scales through vicariance, sympatric speciation, dispersal, and extinction. Consequently, the phylogenetic trees for genes and species, parasites and hosts, and species and their geographic regions are inherently incongruent. Phylogenetic tree reconciliation seeks to reconstruct the evolutionary histories of pairs of related entities by positing the evolutionary events that explain their incongruence. Traditional maximum parsimony methods for tree reconciliation require the user to select costs for each type of evolutionary event. These cost parameters are notoriously difficult to estimate and their values can substantially affect the results and conclusions. This approach uses a Pareto-optimal methodology that does not require the user to select event costs a priori, thereby providing a systematic view of the set of all possible optimal reconciliations. This work will ultimately result in software tools with applications across the life sciences including genomics, parasitology, virology, and biogeography. In addition, this project will involve a substantial number of undergraduates, thereby helping prepare the next generation of researchers in computational biology.

调和分析是研究物种与基因、寄主与寄生虫、地理区域与物种的基本方法。虽然这些应用是不同的，但基本的数学和计算问题是相似的。 基因和物种通过复杂的进化过程相互作用，如基因复制，水平基因转移和基因丢失。寄生虫和它们的宿主共同进化的过程包括同时和独立的物种形成，主机转换，灭绝。而且，物种和它们的地理栖息地在地质时间尺度上通过地理分隔、同域物种形成、扩散和灭绝相互作用。因此，基因与物种、寄生虫与宿主、物种与其地理区域的系统发育树本质上是不一致的。 该研究将开发新的算法、可视化方法和软件工具，用于研究基因和物种、宿主和寄生虫、物种及其地理栖息地等成对实体的进化历史，并有助于培养下一代研究人员。基因和物种通过基因复制、水平基因转移和基因丢失等复杂的进化过程相互作用。寄生虫和它们的宿主共同进化的过程包括同时和独立的物种形成，主机转换，灭绝。而且，物种和它们的地理栖息地在地质时间尺度上通过地理分隔、同域物种形成、扩散和灭绝相互作用。因此，基因与物种、寄生虫与宿主、物种与其地理区域的系统发育树本质上是不一致的。 系统发生树和解试图通过假设解释其不一致性的进化事件来重建相关实体对的进化历史。 传统的最大简约树和解方法需要用户选择每种类型的进化事件的成本。 众所周知，这些成本参数很难估计，它们的值会对结果和结论产生重大影响。 这一方法采用帕累托最优方法，不要求用户事先选择事件成本，从而提供了一套所有可能的最佳调节的系统视图。 这项工作最终将产生软件工具，应用于整个生命科学，包括基因组学，寄生虫学，病毒学和昆虫学。 此外，该项目将涉及大量的本科生，从而帮助准备计算生物学的下一代研究人员。