Evolutionary inference in the presence of gene tree discordance

存在基因树不一致时的进化推理

• 批准号: 1936187
• 负责人: Matthew Hahn
• 金额: $ 64万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-03-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1936187&HistoricalAwards=false
• 关键词: Evolutionary; inference; presence; gene; tree

Large DNA sequencing projects have revealed that there is not just one way that species are related. Genes and pieces of the same genome can have different relationships. Sometimes these relationships differ because of ancient mating between species called hybridization. When hybridization occurs, important traits can be shared between unrelated species. This project will develop new methods to determine the history of traits shared between unrelated species. It also will develop methods to more accurately determine the relationships among species. The research will allow researchers to identify cases where key traits, such as insecticide resistance, arise once and are passed between species. The research combines mathematical modeling with new statistical approaches. These will be combined to produce open-source software for carrying out the analyses. The software will ensure that all scientists will be able to take advantage of the tools developed by the research, adding to the national infrastructure by enabling new biological discoveries. This work also will improve and accelerate biological research with multiple societal benefits, including helping to identify genes controlling important traits. This project will support the training of a postdoctoral researcher, graduate students, and undergraduates from groups that are underrepresented in science and technology careers. Workshops will be developed to provide training in the use of the software developed by this project.Species trees make it possible to understand the evolutionary history of traits. Previous work has documented how gene trees that are discordant with the species tree lead to inaccurate inferences about the timing and direction of trait transitions, the number of trait transitions, how often such changes are thought to be driven by adaptive evolution, and even the species tree itself. This research goes beyond documenting the problems of gene tree discordance, providing solutions to these problems. The theoretical approach used will make it possible to incorporate the multiple causes of discordance—including introgression—into a single framework, allowing researchers to make statistically rigorous inferences about evolutionary processes in the presence of discordance. Integrating these results into a single software package enables these insights and methods to be applied widely, for both binary and continuous traits.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

大型DNA测序项目表明，不仅有一种相关物种的方式。同一基因组的基因和部分可以具有不同的关系。有时，这些关系是由于称为杂交的物种之间的古老交配而有所不同。当发生杂交时，无关物种之间可以共享重要的特征。该项目将开发新的方法来确定无关物种之间共享特征的历史。它还将开发方法以更准确地确定物种之间的关系。这项研究将使研究人员能够确定一个关键特征（例如绝缘耐药性）在物种之间传递的案例。该研究将数学建模与新的统计方法结合在一起。这些将合并以生产开源软件以进行分析。该软件将确保所有科学家都能够利用研究开发的工具，从而通过实现新的生物学发现来增加国家基础设施。这项工作还将通过多种社会利益改善和加速生物学研究，包括帮助识别控制重要特征的基因。该项目将支持博士后研究人员，研究生和本科生的培训，这些群体在科学和技术职业中的人数不足。将开发研讨会，以提供有关该项目开发的软件的培训。种类树使您可以了解特征的进化历史。先前的工作已经记录了与物种树的基因树如何导致有关性状过渡的时机和方向，性状过渡的数量，认为这种变化的频率被认为是由适应性进化驱动的，甚至物种树本身都无法驱动这种变化的信息。这项研究不仅仅记录了基因树不一致的问题，还为这些问题提供了解决方案。所使用的理论方法将使结合单个框架的多种不和谐原因（包括渗入），从而使研究人员能够在存在不一致的情况下对进化过程进行统计上的严格信息。将这些结果集成到单个软件包中，可以广泛应用这些见解和方法，以适用于二进制和连续特征。该奖项反映了NSF的法定任务，并通过使用基金会的知识分子优点和更广泛的影响评估标准来通过评估来获得支持。

项目成果

The Frequency and Topology of Pseudoorthologs

伪同系物的频率和拓扑

• DOI: 10.1093/sysbio/syab097
• 发表时间: 2021
• 期刊: Systematic Biology
• 影响因子: 6.5
• 作者: Smith, Megan L.;Hahn, Matthew W.;Smith, ed., Stephen
• 通讯作者: Smith, ed., Stephen

New Methods to Calculate Concordance Factors for Phylogenomic Datasets

• DOI: 10.1093/molbev/msaa106
• 发表时间: 2020-09-01
• 期刊: MOLECULAR BIOLOGY AND EVOLUTION
• 影响因子: 10.7
• 作者: Bui Quang Minh;Hahn, Matthew W.;Lanfear, Robert
• 通讯作者: Lanfear, Robert

New Approaches for Inferring Phylogenies in the Presence of Paralogs

存在旁系同源物时推断系统发育的新方法

• DOI: 10.1016/j.tig.2020.08.012
• 发表时间: 2021
• 期刊: Trends in Genetics
• 影响因子: 11.4
• 作者: Smith, Megan L.;Hahn, Matthew W.
• 通讯作者: Hahn, Matthew W.