III: Small: RUI: Finding Best Representative Phylogenetic Tree Reconciliations

III：小：RUI：寻找最佳代表性系统发育树协调

基本信息

批准号：
2231150
负责人：
Ran Libeskind-Hadas
金额：
$ 49.85万
依托单位：
Claremont McKenna College
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2022
资助国家：
美国
起止时间：
2022-05-01 至 2024-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2231150&HistoricalAwards=false
关键词：
III Small RUI Finding Best

项目摘要

This project will develop new techniques and software tools to aid biologists in studying the relationships between groups such as parasites and their host organisms. These methods and tools will allow life scientists to better understand the origins of viral and bacterial diseases, parasites that attack crops, and other pairs of co-evolving groups. The project will involve the design and analysis of new algorithms, systematic validation of these algorithms on large biological datasets, and the development of a software tool that will be broadly disseminated. This work will be conducted at an undergraduate college and will prepare approximately 25 students to engage in research. The work will also result in teaching materials and outreach activities for high school and college students.The work under this award will explore the problem of reconciling pairs of phylogenetic trees representing taxa such as hosts and parasites or genes and species. Given a pair of phylogenetic trees and the associations between their leaves, maximum parsimony reconciliation seeks to map one tree (e.g., the parasite tree) onto the other (e.g., the host species tree) to minimize the number of biological events required to explain their discordance. In general, the number of such maximum parsimony reconciliations can grow exponentially with the size of the trees. Consequently, it can be difficult or impossible to identify one, or a small number, of best representative reconciliations. This work will develop efficient algorithms to find best representative reconciliations in order to make more robust conclusions about the evolutionary histories of the pairs of taxa. These algorithms will be implemented in a new software tool for life science researchers.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.

该项目将开发新技术和软件工具，以帮助生物学家研究寄生虫及其寄主生物等群体之间的关系。这些方法和工具将使生活科学家能够更好地了解病毒和细菌疾病的起源，攻击作物的寄生虫以及其他共同发展的群体。该项目将涉及新算法的设计和分析，对大型生物数据集的这些算法的系统验证以及将广泛传播的软件工具的开发。这项工作将在一所本科学院进行，并准备大约25名学生从事研究。这项工作还将为高中和大学生提供教材和外展活动。该奖项下的工作将探讨与代表寄主，寄生虫或基因或物种等分类单元的系统发育树对齐的问题。给定一对系统发育树和叶子之间的关联，最大的简约和解试图将一棵树（例如寄生虫树）映射到另一棵树（例如寄生虫树（例如宿主物种树）上，以最大程度地减少解释其不和谐所需的生物学事件的数量。通常，这种最大简约对帐的数量随树的大小而成倍增长。因此，很难或不可能识别一个或少数最佳代表性对帐。这项工作将开发有效的算法来找到最佳的代表性对帐，以便对分类群的进化历史得出更强大的结论。这些算法将在生命科学研究人员的新软件工具中实施。该奖项反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响审查标准，被认为值得通过评估来获得支持。