UC Davis

This dissertation explores the ecology and evolution of polyploid species, or organismswith multiple sets of chromosomes from whole genome duplication (WGD). Polyploidy is a widespread phenomenon across the tree of life, significantly impacting both animal and plant evolution. Recent advancements in genomics technology has made the study of polyploid species substantially more feasible, but the complexity of polyploid biology is still limiting. As a result, many questions on the evolutionary role of polyploidy remain unanswered. Here, I study the origin and ecological role of polyploidy in Andropogon gerardi Vitman, a mixedploidy and ecologically dominant prairie grass, using a novel reference genome and whole genome sequencing data. We found mixed-ploidy in A. gerardi is a result of recurrent polyploid formation, or happy little accidents. Further, we found WGD in A. gerardi confers immediate adaptive phenotypic changes. In the course of this research, we fortuitously assembled a reference genome for Poa pratensis, an economically valuable and popular turfgrass, instead of a second A. gerardi genome. Finally, I synthesize the challenges of variant calling in polyploids due to extensive genomic diversity and a lack of genomic resources and I propose a variant calling pipeline to addresses key challenges. Overall, this dissertation enhances our understanding of polyploidy’s role in plant evolution and environmental adaptation.