Quantifying Positive and Negative Selection in Natural Populations

The strength and direction of natural selection are key parameters that are predicted to influence the maintenance of genetic variation, genome structure, and the long-term evolutionary fate of populations. New technologies now allow us to estimate these quantities across the entire genomes of organisms, and to examine the variation in selection across the genome and across species. In chapter two we review the state of knowledge about selection on plant genomes and discusses the key factors that may drive differences across species in the strength and direction of selection. In my third chapter I infer the strength and extent of positive and negative selection across the genome of an outcrossing plant, with emphasis on comparing selective differences between coding and noncoding DNA. I find evidence that both positive and negative selection are widespread in protein coding regions, but primarily restricted to a subset of highly conserved sites in noncoding DNA. In my chapter four I investigate the extent to which a shift to asexuality within a single diploid plant species affects the accumulation of deleterious alleles across the genome. I find evidence for a significant increase in the numbers of deleterious mutations in the asexual haplotypes, consistent with a reduced efficacy of selection in asexual populations due to selective interference. My final chapter focuses on the effects of a strong demographic event on the efficacy of selection in a pathogenic fungus. The patterns show evidence for a severe loss of neutral diversity and a weakening of purifying selection following this colonization bottleneck. My results reveal an important contrast in the nature of selective constraint in plant genomes relative to animal taxa, provide genomic evidence for the advantage of sexual reproduction, and show how rapid shifts in the efficacy of selection can arise in non-equilibrium populations.Ph.D