Evolutionary Dynamics of a Multiple-Ploidy System in Arabidopsis Arenosa

Whole-genome duplication (WGD), which leads to polyploidy, has been implicated in speciation and biological novelty. In plants, many species have experienced historical bouts of WGD or exhibit extant ploidy variation, which is likely representative of an early stage in the evolution of new polyploid lineages. To elucidate the evolutionary dynamics of autopolyploids and species with multiple ploidy levels, I develop population genetic theory in Chapter 2 that I use in Chapter 4 to extract information about the evolutionary history of Arabidopsis arenosa, a European wildflower that has diploid and autotetraploid populations. Chapter 3 involves a separate project exploring the ascertainment bias in restriction site associated DNA sequencing (RADseq). In Chapter 2, I develop coalescent models for autotetraploid species with tetrasomic inheritance and show that the ancestral genetic process in a large population without recombination may be approximated using Kingman’s standard coalescent, with a coalescent effective population size 4N. Using this result, I was able to use existing coalescent simulation programs to show in Chapter 4 that, in A. arenosa, a widespread autotetraploid race arose from a single ancestral population. This autopolyploidization event was not accompanied by immediate reproductive isolation between diploids and tetraploids in this species, as I find evidence of extensive interploidy admixture between diploid and tetraploid populations that are geographically close. To draw these conclusions about population history in Chapter 4, I used a reduced representation genome-sequencing approach based on restriction digestion. However, I was bothered by the possibility that sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent-simulation framework in Chapter 3 to mimic the biased recovery of chromosomes in RAdseq experiments. We show that loci with missing haplotypes have estimated diversity statistic values that can deviate dramatically from true values and are also enriched for particular genealogical histories. These results urge caution when applying this technique to make population genetic inferences and helped me tailor analyses in Chapter 4 to accommodate for this particular method of DNA sequencing.Biology, Organismic and Evolutionar