With the advent of QTL mapping in the late 1980s, evolutionary geneticists have actively dissected the genetic basis of adaptive phenotypes. In recent times, advances in whole genome sequencing have allowed for finer scale mapping of traits that have diverged due to natural selection. These relatively inexpensive sequencing technologies have also greatly facilitated adaptive trait dissection in non-model species that exhibit especially interesting patterns of adaptation. One class of trait that

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... has largely escaped the attention of the next generation ecological and evolutionary genomics research programme, are sexually-selected traits. Sexual selection is a strong form of directional selection in nature and is thought to be responsible for the evolution of elaborate sexual ornaments and armaments. However we still know comparatively little of the genetic basis of such traits. The cuticular hydrocarbons (CHCs) of Drosophila serrata provide an opportunity for dissecting the divergence of sexually selected traits. Populations along the eastern Australian coast exhibit latitudinal variation in these traits in association with climatic factors and consistent with the action of divergent natural selection. Under experimental settings, divergent sexual as well as natural selection has been implicated in the evolution of CHCs. Natural populations of D. serrata along the northern part of the Eastern Australian coast have recently been observed to exhibit a polymorphism in three of their CHC compounds representing the shortest carbon chains; 5,9-tetracosadiene (5,9-C 24 ), 5,9-pentacosadiene (5,9-C 25 ) and 9-pentacosene (9-C 25 ). One class of phenotype only expresses these three compounds in trace amounts ('low' phenotype) whereas the other has normal levels ('high' phenotype). These short-chained CHCs also exhibit strong genetically-based latitudinal clines up to, but not beyond, 20 degrees south of the equator. Based on both traditional QTL and modern sequence-based genomic mapping approaches, the aim of this study was to dissect the genetic basis of the polymorphism in D. serrata CHCs and to examine its adaptive significance within the context of sexual and natural selection. Through F2 QTL mapping based on a cross between two inbred lines, from the opposite ends of the D. serrata CHC cline, one a 'low' phenotype and the other a 'high' phenotype, the genetic basis of all CHCs in this species was mapped to twenty two overlapping QTLs on chromosomes 2 and 3. The short-chain CHC polymorphism was traced to two major effect recessive QTLs on the right arm of chromosome 3, which including their interaction, accounted for more than 70% of the variance in the polymorphism (Chapter 2). Fine mapping of this major polymorphism was then conducted using next generation DNA sequencing and bulk segregant analysis of an advanced F60 cross of the same founding lines. Bulk segregant analysis revealed a single peak of genetic differentiation on chromosome 3R (~20kb), harbouring three adjacent fatty acyl-CoA reductase ii genes (Chapter 3). Other candidate genes already reported in the literature as underlying CHC variation in Drosophila were also detected nearby the reductases but appear unlikely responsible for the polymorphism. An analysis of genome sequences for nine independent wild-derived inbred lines, fixed for either the 'low' or 'high' phenotype, replicated the results of the bulk segregant analysis and uncovered a hotspot of fixed nucleotide differences within three adjacent reductase genes, particularly in gene CG17560. This gene has recently been confirmed to be expressed in D. serrata oenocytes in both CTN42 and FORS4 lines (Chapter 4). In an attempt to identify the likely sources of natural and sexual selection acting on and maintaining this polymorphism, I assayed desiccation resistance and heat stress survival on multiple lines of contrasting phenotype from a single population of flies in Cooktown, far north Queensland. I also assayed male and female mate choice on the same lines (Chapter 5). The fitness effects of the polymorphism appeared sex-specific. Natural selection seemed to operate on this polymorphism through females, with 'low' individuals being superior to 'high' ones in their survival to desiccation. By contrast, the effect of sexual selection on this polymorphism was evident in males but not females. 'Low' males were half as likely to succeed in copulation as their 'high' counterparts. This is the first study to trace the genetic basis of CHC variation to gene level in D. serrata and exposes a small genomic region where a polymorphism may be maintained by an antagonistic relationship between natural and sexual selection. Although complex traits are generally polygenic, mutations within specific segments of a biosynthetic pathway may have a pervasive effect on trait divergence if targeted by selection. Further tissue-specific gene expression analysis is likely to pinpoint the gene and ultimately the actual causal mutation(s) underlying this polymorphism. Combining traditional QTL and modern genomic approaches may greatly accelerate the fine-scale genetic dissection of adaptive trait divergence in non-model species. iii