Inferring Species Phylogenies Under the Coalescent Model with Hybridization

了解物种之间的进化关系是进化生物学中最基本的目标之一。DNA测序技术的进步导致了使用多个基因来推断这种系统发育历史的转变。随着这种转变，人们认识到基因组中的每个基因都有自己的历史，这可能与物种的整体进化历史不同。在这个项目中，两个已知的导致基因和物种历史不和谐的过程将被统计建模。第一种，被称为“不完全谱系分类”，导致个体基因进化的实质性差异，几乎发生在所有生物体中。第二种，杂交——来自两个不同物种的个体交配并产生可存活的后代——被认为发生在多达25%的植物和10%的动物身上。该项目将开发统计方法，同时整合这两个过程，以重建生物之间进化关系的历史。结合这两个过程的统计上合理的系统发育模型的发展将允许两个基本的生物学问题得到解决：(1)估计物种对之间的历史杂交程度；(2)考虑到这两个过程导致的基因间变异时，对真正的系统发育历史的推断。其结果将使我们更准确地了解当今物种之间的进化关系。此外，研究者参与了nsf资助的本科生数学生物学项目，因此本科研究人员将参与该研究的某些方面。

Understanding evolutionary relationships among a collection of species is one of the most fundamental objectives in evolutionary biology. Advances in DNA sequencing technology have resulted in a shift toward the use of multiple genes to infer such phylogenetic histories. With this shift has come the realization that each gene in the genome has its own history, which may differ from the overall evolutionary history of the species. In this project, two processes known to cause discord between gene and species histories will be modeled statistically. The first, termed "incomplete lineage sorting," leads to substantial differences in the evolution of individual genes and occurs in virtually all organisms. The second, hybridization - the mating of individuals from two distinct species with the production of viable offspring - is believed to occur for as many as 25% of plants and 10% of animals. This project will develop statistical methods that integrate both of these processes simultaneously to reconstruct the history of evolutionary relationships among organisms. Development of statistically-sound phylogenetic models incorporating both processes will allow two fundamental biological issues to be addressed: (1) estimation of the extent of historical hybridization between pairs of species; and (2) inference of the true phylogenetic history when gene-by-gene variation due to both processes is taken into account. The result will be more accurate understanding of the evolutionary relationships among present-day species. In addition, the investigator is involved in an NSF-funded program in mathematical biology for undergraduates, and thus undergraduate researchers will participate in some aspects of this research.