Empirical approaches to detecting the action of natural selection in Drosophila

This dissertation examines two aspects of how natural selection shapes the amount and pattern of genetic variation within and between species: (1) the role of positively selected alleles in shaping the variation within and between subpopulations of a subdivided species and (2) the influence of epistatic selection operating on RNA secondary structures. First, the role of natural selection in shaping the pattern of variation within and between populations of the subdivided species Drosophila ananassae is investigated. To delimit the spread of positively selected alleles and characterize the role of natural selection in genetic differentiation, sequence data was collected from a locus in a region of low recombination for 13 populations, spanning a majority of the species range of D. ananassae. The migration behavior of this selected locus is compared to that of 10 independent neutrally evolving loci and tested against alternative models of natural selection. Second, nucleotide variation at the D. melanogaster bicoid locus is examined. The presence of a large, conserved secondary structure in the 3’ untranslated region enables the relationship between RNA secondary structure and patterns of standing variation in natural populations to be explored. Variation within this structure is analyzed with respect to models of compensatory evolution and recent improvements of these models. Evidence suggests that bicoid may be the result of a relatively recent gene duplication in the Dipteran lineage, thus, variation in the bicoid coding region is also analyzed with respect to the evolutionary processes that may be ongoing if this gene is still undergoing diversification and/or refining of its function. Finally, long-range compensatory interactions between the two ends of Drosophila alcohol dehydrogenase (Adh) mRNA are investigated by experimental manipulation. Site-directed mutations were introduced in the D. melanogaster Adh gene in an effort to explain why previous mutational analysis failed to fit Kimura’s classical model of compensatory evolution. The results of the mutational analysis indicate that a classical result was not observed due to the pleiotropic effect of changing a nucleotide involved in both long-range base pairing and the negative regulation of gene expression