Justin Conover - Final Oral Exam
Molecular evolution following allopolyploidization in Gossypium
Abstract: Whole genome duplication (polyploidy) is an important mechanism of speciation and generator of novel genetic and phenotypic diversity, particularly in plants. While over 400 polyploidy events have been identified throughout the angiosperm phylogeny, many crops also have a recent episode of whole genome duplication, indicating that polyploidy plays an important role in modern agriculture. Additionally, the timing of many ancient polyploidy events can be placed near the K-Pg boundary, coinciding with the extinction of nearly 70% of all plant and animal life, including all non-avian dinosaurs, suggesting that polyploidy has important adaptive potential and may play a vital role in determining success following the human-mediated mass extinction event currently underway due to climate change. Hence, understanding the consequences of polyploidy events at the genic and genomic level is important for further understanding why polyploidy is so important in plant evolution. In this dissertation, I use the cotton genus (Gossypium) as a model system to better understand several aspects of molecular evolution following polyploidization. Specifically, in chapter 2, I use genomic and transcriptomic data from representatives of eight of the nine subfamilies in the mallow family (Malvaceae) to better characterize an ancient 5X or 6X whole genome multiplication event at the base of the family. In chapter 3, I develop a novel method for inferring orthologs between species of any ploidy level using conserved gene order (synteny), and demonstrate that it performs better than other similar methods, especially when polyploid species are involved in the analysis. In chapter 4, I show that deleterious mutations accumulate faster in allopolyploid than in diploid cotton species due to the masking effect of duplicated genes with shared functions, and discuss the possible implications of this finding for several other aspects of polyploid genome evolution. I introduce the concept of “homoeologous epistatic dominance” to describe this masking effect between homoeologous loci. Finally, in chapter 5, I explore how selection acts differently between subgenomes of six allopolyploid species and their respective diploid progenitors, with a special focus on nuclear genes encoding proteins that are transported to and utilized in the mitochondria and chloroplasts. Overall, this dissertation explores several of the unique ways in which natural selection acts on polyploids and furthers our understanding of why polyploidy may be such an important and widespread evolutionary phenomenon in plants.