Molecular evolution in a genomic context: Patterns and processes

My research has focused on the role of background substitutions in generating heterogeneities in patterns of molecular evolution both within and between genomes. The first chapter of my thesis addresses the role of insertion and deletion substitutions in genome size evolution, and specifically tests the mutational equilibrium model. To do so, I characterized the small-scale indel spectrum in several insect lineages. My results suggest that deletion biases may play a role in genome size evolution, and thus provide further support for the mutational equilibrium model. This model also predicts that organisms with rapid DNA loss should have high rates of sequence turnover at unconstrained loci. I investigated this question in Drosophila melanogaster, a species with rapid DNA loss. My results indicate that unconstrained sequence content can change dramatically, reflecting an equilibrium between persistent DNA loss and periodic DNA gain.; Chapter two of my dissertation focuses on the evolution of base composition, which varies within and among genomes. I quantified rates of single nucleotide substitutions among different regions of the Drosophila melanogaster genome, as well as in the D. saltans and willistoni groups. My results provide evidence in support of a recombination-associated substitutional bias towards increased GC in D. melanogaster, and document a slight shift in substitutional patterns towards increased AT relative to D. melanogaster in D. saltans and willistoni. The implications of these biases are discussed with respect to the evolution of both coding and noncoding sequences in these species.; The final chapter in my thesis compares molecular evolutionary patterns between the X chromosome and the autosomes. Because rates and patterns of molecular evolution are affected by population genetic parameters such as effective population size and mutation rate, as well as the strength and frequency of selective events, this comparison provides insight into the relative roles of different evolutionary forces in producing genetic changes. My examination of the evolution of codon bias in D. melanogaster and C. elegans suggests that weak selection is more effective on the X chromosome. My follow-up study indicates that this stronger selection is likely due to higher variance in reproductive success among males.