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Title: Patterns of Genome Evolution and Habitat Adaptation in Tetraploid Arabidopsis arenosa
Abstract: Polyploidy occurs throughout eukaryotes, and is particularly prevalent among plants. Nearly 40\% of all vascular plant species are thought to be recent polyploids, including a number of invasive species and familiar crops. Despite the high incidence of polyploidy, most studies of its genetic attributes are based on crop and model systems that do not represent natural evolutionary models. Here, we make use of the natural diploid / autotetraploid system offered by Arabidopsis arenosa to narrow this gap in the evolutionary study of polyploids. In chapter 1, I compare one railway and one mountain population of tetraploid A. arenosa to investigate the genetic mechanisms underlying the adaptation to the railway habitat, using transcriptome sequencing, genome scans for selection, and stress tolerance assays. In chapter 2, I examine a broader array of mountain and railway populations to confirm the trends observed in chapter 1 through transcriptomic, genomic, and trait mapping approaches. By examining an independent railway colonization, I find evidence of long-distance gene flow between railway populations; this introgression provides railway haplotypes that may have facilitated this colonization event. In chapter 3, I include both diploid and tetraploid populations in a combined genomic and transcriptomic analysis to determine the patterns of genome evolution associated with autopolyploidy. The results suggest that there is relaxed purifying selection and reduced frequencies of positive selection events in tetraploid populations relative to their diploid counterparts. Overall, from the results of this study, there is no evidence that autopolyploidy confers evolutionary advantages. Autotetraploids as a group are not globally tolerant of ruderal habitats, and they also suffer from increased genetic load.