The goal of this research is to dissect the causative genes and mutations underlying a complex trait, and trace the stepwise process by which the identified causative alleles arose and spread through an isolated population to generate a fixed morphological phenotype. The species Drosophila santomea exhibits a recently evolved, drastic shift in its pigment patterns that represents an optimal model system in which to dissect complex polygenic traits. Our previous work identified the gene underlying one of four major QTL contributing to this trait. Analysis of multiple individuals in the population revealed that causative alleles of this gene arose several times in parallel in the D. santomea population (i.e. a soft sweep). Here, we propose to employ molecular genetic techniques (introgression mapping and transgenic complementation) to identify causative genes and mutations responsible for two additional QTL. Using a combination of molecular and genomic techniques (in situ hybridization, RNA-seq), we will then assess how these loci interact with each other, as well as how they impact the genome-wide profile of expression. Finally, we will survey population variation at these additional causative loci to assess whether a similar soft sweep occurred, and determine whether these genes exhibit signs of positive selection. This study will provide a rare vista of a complex morphological trait that integrates molecular studies of gene function with processes occurring at the population level.