Chromosome Number Evolution, Phylogeography, and the Effects of Climate Change on Species Distributions in Polyploid Plant Systems

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number using likelihood-based methods. The best-fit model of chromosome evolution showed that chromosome transitions within Allium occurred through the constant gains and losses of single chromosomes as well as demi-polyploidization events, with the rate of chromosome gain events being approximately 2.5 to 4.5 times more likely to occur than demi-polyploidization and loss events, respectively. In the second chapter, I used nuclear and chloroplast DNA sequences generated from eight populations in the North American Coastal Plain (NACP) biodiversity hotspot and one nearby population in Kansas to examine genetic diversity and population structure of A. canadense var. canadense, a polyploid species that exhibits vegetative reproduction which may lead to low genetic diversity within extant populations. A total of 12 ITS ribosomal and 10 chloroplast DNA haplotypes were identified, and significant genetic subdivision among populations was detected across all populations by analysis of molecular variance. In the third chapter, I used ecological niche modeling to evaluate the differences in niche identity among diploid and polyploid plants endemic to the NACP at the generic level using current bioclimatic variables, then niche overlap and habitat suitability using future climate change scenarios were assessed. I found that congeneric ploidy level pairs differed significantly in niche identity, and niche overlap varied across genera. I also identified 11 genera that showed greater than 100% increases in habitat suitability and six genera that showed almost no remaining suitable habitat in at least one future climate scenario. Based on these results, I provide future directions for continued studies in the NACP