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

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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.