Probability Questions in Phylogenetics

系统发育学中的概率问题

• 批准号: 1614242
• 负责人: Sebastien Roch
• 金额: $ 19.4万
• 依托单位: University of Wisconsin-Madison
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2020-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1614242&HistoricalAwards=false
• 关键词: Probability; Questions; Phylogenetics

Assembling the Tree of Life is a fundamental problem in biology that is providing insights into evolution, adaptation, and speciation. Much information about past evolutionary events can be inferred from the analysis of DNA sequence data collected from existing species. A notable feature of the evolution of molecular sequences is the significant role played by chance. In recent years, probability theory, the mathematical study of randomness, has provided key new insights in analyzing the power of statistical methods to reconstruct evolutionary processes in large-scale phylogenetics. The overall goal of this research project is to further investigate these connections. Through the development, analysis, implementation, and dissemination of algorithms for the alignment of molecular sequences and the reconstruction of evolutionary trees, this research will help advance the state of knowledge in evolutionary biology. The project aims to contribute to the numerous benefits to society of phylogenetic research such as the protection of ecosystems from invasive species, the identification of emerging diseases, and the prediction of disease outbreaks. Integration of research and education is a major component of this project. In addition to providing research training for graduate students, course materials will be developed in conjunction with the activities and made widely available. In evolutionary biology, the speciation history of a group of organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves represent current species and whose branchings indicate past speciation events. Phylogenies are commonly estimated from molecular sequences collected from the species of interest. Despite breathtaking advances in sequencing technologies and the development of increasingly more powerful methods, phylogenetic reconstruction remains a challenging problem, and many evolutionary relationships continue to be the source of controversy. Most traditional phylogenetic reconstruction methods involve two steps: multiple sequence alignment and tree estimation. This two-step approach introduces systematic biases that can adversely affect the final tree estimate and other downstream analyses. The general objective of this project is to provide new mathematical insights on alignment methods and their effects on phylogenetic analyses as well as to develop new tools to analyze methodologies that go beyond the traditional two-step approach to phylogenetic reconstruction. This objective will be achieved by further developing the fruitful interface between probability theory and mathematical phylogenetics.

组装生命树是生物学中的一个基本问题，它提供了对进化、适应和物种形成的见解。通过对从现有物种收集的DNA序列数据的分析，可以推断出许多关于过去进化事件的信息。分子序列进化的一个显著特征是偶然性所起的重要作用。近年来，概率论，即对随机性的数学研究，在分析统计方法重建大规模系统发育进化过程的能力方面提供了关键的新见解。本研究项目的总体目标是进一步研究这些联系。通过分子序列比对和进化树重建算法的开发、分析、实现和传播，这项研究将有助于推进进化生物学的知识状态。该项目旨在促进系统发育研究给社会带来的诸多好处，例如保护生态系统免受入侵物种的侵袭，识别新出现的疾病，以及预测疾病暴发。研究和教育的融合是这个项目的一个主要组成部分。除了为研究生提供研究培训外，还将结合活动编写课程材料，并广泛提供。在进化生物学中，一组生物的物种形成历史由系统发育图来表示，即有根的树，其叶子代表当前物种，其分支表明过去的物种形成事件。系统发育通常是根据从感兴趣的物种收集的分子序列来估计的。尽管测序技术取得了惊人的进步，方法也越来越强大，但系统发育重建仍然是一个具有挑战性的问题，许多进化关系仍然是争议的来源。大多数传统的系统发育重建方法涉及两个步骤：多序列比对和树估计。这种分两步走的方法引入了系统性偏差，这可能会对最终的树木估计和其他下游分析产生不利影响。该项目的总体目标是就比对方法及其对系统发生分析的影响提供新的数学见解，并开发新的工具来分析超越传统两步法重建系统发生的方法。这一目标将通过进一步发展概率论和数学系统发育学之间卓有成效的接口来实现。