A primary goal of population genetics is to determine the genetic basis of natural trait variation. We could significantly advance this goal by developing comprehensive genome-wide approaches to link genotype and phenotype in model organisms. Here we combine artificial selection with population-based resequencing to investigate the genetic basis of variation in the interpulse interval (IPI) of Drosophila melanogaster courtship song. We performed divergent selection on replicate populations for only 14 generations, but had considerable power to differentiate alleles that evolved due to selection from those that evolved stochastically. We identified a large number of variants that changed frequency in response to selection for this simple behavior, and they are highly underrepresented on the X chromosome. Though our power was adequate using this experimental technique, the ability to differentiate causal variants from those affected by linked selection requires further development.

There has been considerable recent interest in using Drosophila melanogaster to investigate the molecular basis of decision-making behavior. Deciding where to place eggs is likely one of the most important decisions for a female fly, as eggs are vulnerable and larvae have limited motility. Here, we show that many natural genotypes of D. melanogaster prefer to lay eggs near nutritious substrate, rather than in nutritious substrate. These preferences are highly polymorphic in both degree and direction, with considerable heritability (0.488) and evolvability.Relative preferences are modulated by the distance between options and the overall concentration of ethanol, suggesting Drosophila integrate many environmental factors when making oviposition decisions. As oviposition-related decisions can be efficiently assessed by simply counting eggs, oviposition behavior is an excellent model for understanding information processing in insects. Associating natural genetic polymorphisms with decision-making variation will shed light on the molecular basis of host choice behavior, the evolutionary maintenance of genetic variation, and the mechanistic nature of preference variation in general.

Little is currently known about the genetic complexity of quantitative behavioral variation, the types of genes involved, or their effects on intermediate phenotypes. Here, we conduct a genome-wide association study of Drosophila melanogaster courtship song variation using 168 sequenced inbred lines, and fail to find highly significant associations. However, by combining these data with results from a well-powered Evolve and Resequence (E&R) study on the same trait, we provide statistical evidence that some power to associate genotype and phenotype is available. Genes that are significant in both analyses are enriched for expression in the nervous system, and affect neural development and synaptic growth when perturbed. Quantitative complementation at one of these loci, Syntrophin-like 1, supports a hypothesis that variation at this locus affects variation in the inter-pulse interval of courtship song. These results suggest that experimental evolution may provide an approach for genome-scale replication in Drosophila.

The heritability of genome‐wide fitness that is expected in finite populations is poorly understood, both theoretically and empirically, despite its relevance to many fundamental concepts in evolutionary biology. In this study, we used two independent methods of estimating the heritability of lifetime female fecundity (the predominant female fitness component in this population) in a large, outbred population of Drosophila melanogaster that had adapted to the laboratory environment for over 400 generations. Despite strong directional selection on adult female fecundity, we uncovered high heritability for this trait that cannot be explained by antagonistic pleiotropy with juvenile fitness. The evolutionary significance of this high heritability of lifetime fecundity is discussed.

In female heterogamous (ZW) species, sex-linked genes coding for maternal products that are packaged into the egg open a unique arena for genetic conflict that does not occur in male heterogamous (XY) species. Z-linked maternal-effect alleles that help sons and harm daughters are expected to go to fixation, as are W-linked alleles that help daughters and harm sons. This conflict differs from known cases of meiotic drive, because sex-specific ontogeny, physiology, and gene expression greatly simplify the genetic interactions that lead to sexual conflict. Selection on maternal-effect genes may substantially alter the evolution of ZW compared with XY systems.