Local Effects of Limited Recombination in Drosophila

Recent years have witnessed the integration of theoretical advances in population genetics with large-scale analyses of complete genomes. As a result, a growing number of studies suggest the frequent occurrence of deleterious as well as adaptive mutations. Given the evidence for the widespread occurrence of selection, the finite sizes of natural populations, and the limited recombination in every genome, mutations under selection are expected to alter the fate of genetically linked mutations. The consequences of this non-independent behavior of mutations can be described by the Hill-Robertson effect in terms of the reduction in the effective population size (Ne). Reduction in the effective population size has two effects: 1) a reduction in levels of genetic variation and 2) a reduction in the effectiveness of selection that is manifested in an increased probability of fixation of deleterious mutations and a reduced probability of fixation of advantageous mutations. Changes in Ne that have previously been frequently associated with changes in recombination rate can also occur locally, in association with changes in the number of sites under selection even when the recombination rate remains uniform. The main objective of the work presented in this thesis is to investigate these local effects of the non-independent behavior of mutations on patterns of polymorphism and divergence in Drosophila using computer simulation and experimental approaches. A computer simulation approach is developed to investigate the local consequences of linked selection on estimates of selection and the proportion of adaptive substitutions using the McDonald-Kreitman framework. The results suggest that even a high level of recombination is unlikely to remove all the effects of linked selection.