DISSERTATION RESEARCH: Developing a toolbox for evolutionary inferences in polyploids: new methods of analysis applied to the plant genus Penstemon (Plantaginaceae)

全基因组复制，或称多倍体，是许多植物中所有染色体加倍的普遍现象。研究具有重复基因组的物种的一个主要挑战是，额外的基因拷贝使重建它们的进化关系变得极其困难。该项目的目标是开发和应用新的统计工具，利用现代DNA测序技术来研究多倍体生物。然后，这些工具将用于研究一组复杂的多倍体杂交模式和全基因组复制，这些多倍体是一种来自Penstemon属的植物。除了为研究生提供实验室和生物信息学技术培训的机会外，该项目还将制作并免费分发软件代码，供进化生物学家使用。虽然多倍体在许多真核生物谱系的历史中发挥了重要作用，但在当代时间尺度上研究和理解其遗传历史的工具很少。造成这种情况的两个主要原因是：(1)由于等位基因拷贝数的不确定性导致的基因型不明确；(2)等位基因遗传的复杂模式可能在基因组的不同位点上发生变化。提出的工作通过开发一个统计框架来从高通量测序数据推断遗传模式，同时考虑基因型的不确定性来解决这些问题。它将开发一个模型，然后将用于测试关于同种六倍体垂花物种复合体起源的假设，该复合体包含四个区域品种，每个品种都有不同的假定亲本物种。双消化酶切位点相关DNA测序将用于收集该模型的全基因组单核苷酸多态性（SNP）数据，并将使用渗入测试评估异源多倍体起源的假设。该统计模型将有助于其他非模式生物多倍体的研究。

Whole genome duplication, or polyploidy, is a common phenomenon in many plants wherein all chromosomes are doubled. A major challenge for working with species with duplicated genomes is that the extra gene copies make it extremely difficult to reconstruct their evolutionary relationships. The goal of this project is to develop and apply new statistical tools that take advantage of modern DNA sequencing technologies to enable the study of polyploid organisms. These tools will then be used to study patterns of hybridization and whole genome duplication in a complex group of polyploids in beardtongues, plants from the genus Penstemon. In addition to providing opportunities for graduate student training in laboratory and bioinformatics techniques, this project will produce and freely distribute software code for use by evolutionary biologists. Although polyploidy has played an important role in the history of many eukaryotic lineages, there are few tools for studying and understanding their genetic history at contemporary timescales. Two of the main reasons for this are (1) ambiguous genotypes due to uncertainty in allele copy number and (2) complex patterns of allelic inheritance that can vary at different loci across the genome. The proposed work addresses these issues by developing a statistical framework to infer inheritance patterns from high throughput sequencing data while simultaneously accounting for genotype uncertainty. It will develop a model that will then be used to test hypotheses regarding the origins of the allohexaploid Penstemon attenuatus species complex, which contains four regional varieties each with different putative parental species. Double digest restriction site associated DNA sequencing will be employed to gather genome-wide Single Nucleotide Polymorphism (SNP) data for the model, and hypotheses of allopolyploid origin will be evaluated using tests for introgression. The statistical model will facilitate the study of polyploidy in other non-model organisms.