Drosophila ananassae and its relatives have many advantages as a model of genetic differentiation and speciation. In chapter I, I examined evolutionary relationships in the ananassae species subgroup using a multi-locus molecular data set. Analysis of Y-chromosomal and mitochondrial haplotypes suggests that these taxa represent a recent evolutionary radiation and may experience substantial gene flow. I discuss possible evolutionary histories of these species.;In Chapter II, I investigated the genetic basis of color pattern variation between two allopatric subspecies of D. malerkotliana, a widespread member of the ananassae species subgroup. In D. m. malerkotliana , the last three abdominal segments are darkly pigmented in males but not in females, while in D. m. pallens both sexes lack dark pigmentation. Composite interval mapping in F2 hybrid progeny shows that this difference is largely controlled by three quantitative trait loci (QTLs) located on the 2L chromosome arm, which is homologous to the 3R of D. melanogaster (Muller element E). Using highly recombinant introgression strains produced by repeated back-crossing and phenotypic selection, we showed that these QTLs do not correspond to any of the candidate genes known to be involved in pigment patterning and synthesis in Drosophila .;Drosophila males use their sex combs to grasp the females' abdomen and genitalia and to spread their wings prior to copulation. In Chapter III, to test the role of this structure in male mating success in Drosophila melanogaster, I genetically ablated the sex comb by expressing the female-specific isoform of the sex determination gene transformer in the tarsal segments of male legs. This technique does not remove the sex comb entirely, but simply restores the morphology of its constituent bristles to the ancestral condition found in Drosophila species that lack sex combs. Direct observations and differences in long-term insemination rates showed that the loss of the sex comb strongly reduces the ability of males to copulate with females. Detailed analysis of video recordings indicated that this effect is not due to changes in the males' courtship behavior.
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