Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila

Reproductive isolation is a key component of speciation. In many insects, a major driver of this isolation is cuticular hydrocarbon pheromones, which help to identify potential intraspecific mates [1–3]. When the distributions of related species overlap, there may be strong selection on mate choice for intraspecific partners [4–9] because interspecific hybridization carries significant fitness costs [10]. Drosophila has been a key model for the investigation of reproductive isolation; although both male and female mate choices have been extensively investigated [6, 11–16], the genes underlying species recognition remain largely unknown. To explore the molecular mechanisms underlying Drosophila speciation, we measured tissue-specific cis-regulatory divergence using RNA sequencing (RNA-seq) in D. simulans × D. sechellia hybrids. By focusing on cis-regulatory changes specific to female oenocytes, the tissue that produces cuticular hydrocarbons, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects the hydrocarbons present on D. sechellia and D. melanogaster females, as well as the propensity of D. simulans males to mate with them. Therefore, cis-regulatory changes in eloF may be a major driver in the sexual isolation of D. simulans from multiple other species. Our RNA-seq approach proved to be far more efficient than quantitative trait locus (QTL) mapping in identifying candidate genes; the same framework can be used to pinpoint candidate drivers of cis-regulatory divergence in traits differing between any interfertile species. •RNA-seq on Drosophila hybrids identifies tissue-specific cis-regulatory changes•eloF, a fatty acid elongase, is a major determinant of hydrocarbon pheromones•Ablation of eloF increases interspecies mating nearly to intraspecies levels•This approach can be applied broadly to rapidly pinpoint key evolutionary drivers Combs et al. use RNA-seq in hybrid Drosophila to identify genes related to cuticular hydrocarbon (CHC) differences, including eloF. Ablation of eloF alters CHC profiles and increases interspecies mating nearly to intraspecies levels. This approach can be applied broadly to rapidly pinpoint key evolutionary drivers in a wide range of species.