Probability Questions in Phylogenetics

组装生命之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。许多关于过去进化事件的信息可以从现有物种收集的DNA序列数据分析中推断出来。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，随机性的数学研究，提供了关键的新见解，在分析统计方法的力量，以重建大规模遗传学的进化过程。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、实施和传播，这项研究将有助于推进进化生物学的知识水平。该项目旨在为系统发育研究为社会带来的众多益处做出贡献，例如保护生态系统免受入侵物种的侵害，识别新出现的疾病以及预测疾病爆发。研究与教育的结合是该项目的一个重要组成部分。除了为研究生提供研究培训外，还将结合这些活动编写教材，并广泛提供。在进化生物学中，一组有机体的物种形成历史是用一个物种发生图来表示的，也就是说，一棵有根的树，它的叶子代表现在的物种，它的分支代表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，并且开发了越来越强大的方法，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。传统的系统发育重建方法主要包括两个步骤：多序列比对和树估计。这种两步法引入了系统偏差，可能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提供新的数学见解比对方法及其对系统发育分析的影响，以及开发新的工具来分析方法，超越传统的两步法系统发育重建。这一目标将通过进一步发展概率论和数学遗传学之间富有成效的接口来实现。

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.