DISSERTATION RESEARCH: Stochastic modeling approaches to evaluate the evolution of chromosome number and genome size in plants

DNA为生命提供了遗传指令，但人们对为什么基因组中的DNA含量在不同物种之间存在巨大差异却知之甚少。在开花植物中，基因组的大小和组成可以通过全基因组复制而发生巨大变化，这与生态适应和物种多样性比率的变化有关。该项目采用跨学科的方法，结合植物学、遗传学和统计学等不同领域的见解和方法，研究全基因组复制在产生和维持物种间基因组大小和染色体数量变异方面的作用。具体地说，该项目将开发和实施新的数学模型，以衡量与复制相关的不同进化机制对开花植物基因组大小变异的影响。该项目开发的软件和方法将帮助科学家以统计严格的方式测试基因组进化中的许多问题，该项目还将为研究生提供跨学科培训。全基因组复制(WGD)是被子植物中一个反复出现的基因组过程，与遗传创新、生态适应和多样化比率的变化有关。然而，WGD在产生和维持物种间基因组大小和染色体数量变异方面的作用仍在很大程度上是未知的。该项目的目标是开发新的染色体数量和基因组大小变化的随机模型，使科学家能够推断导致基因组大小变化的进化机制的速度，以及能够估计这种进化过程的频率的推断程序。具体地说，该项目将(1)使用正式的模拟方法估计基因组缩减和约束对WGD的相对影响；(2)提出一个新的包含二倍化的倍性变化的随机模型；(3)提出一个新的基因组大小变化的随机模型，该模型包括基因组缩减和针对WGD的大基因组分类群的选择。该项目还将为科学界提供新的方法和开放源码软件，并为研究生提供跨学科培训。

DNA provides the genetic instructions for life, yet very little is known about why the amount of DNA in a genome varies tremendously across species. In flowering plants, the size and composition of genomes can change drastically through whole genome duplications, which are associated with ecological adaptation and shifts in species diversification rates. This project takes an interdisciplinary approach, combining insights and approaches from disparate fields, such as Botany, Genetics, and Statistics, to examine the role of whole genome duplication in generating and maintaining variation in genome size and chromosome number among species. Specifically, this project will develop and implement new mathematical models to measure the effect of different evolutionary mechanisms associated with duplications on genome size variation in flowering plants. The software and methods developed by this project will help scientists test many questions in genome evolution in a statistically rigorous manner, and the project also will provide interdisciplinary training to graduate students.Whole genome duplication (WGD) is a recurrent genomic process in angiosperms that has been linked to genetic innovation, ecological adaptation, and shifts in diversification rates. However, the role of WGD in generating and maintaining variation in genome size and chromosome number among species is still largely unknown. The goal of this project is to develop new stochastic models of chromosome number and genome size change that will enable scientists to infer the speed of evolutionary mechanisms responsible for the variation in genome size as well as an inferential procedure that will allow estimation of the frequency of such evolutionary processes. Specifically, this project will (1) estimate the relative influence of genome downsizing and constraints against WGD using a formal simulation approach; (2) propose a new stochastic model for ploidy change that includes diploidization; and (3) propose a new stochastic model for genome size change that includes genome downsizing and selection against WGD for taxa with large genomes. The project will also provide new methods and open source software for the scientific community and will provide interdisciplinary training for graduate students.