Two major-effect loci influence interspecific mating in females of the sibling species, Drosophila simulans and D. sechellia.

Secondary contact between incompletely isolated species can produce a wide variety of outcomes. The vinegar flies Drosophila simulans and D. sechellia diverged on islands in the Indian Ocean and are currently separated by partial pre- and postzygotic barriers. The recent discovery of hybridization between D. simulans and D. sechellia in the wild presents an opportunity to monitor the prevalence of alleles that influence hybridization between these sibling species. We therefore sought to identify those loci in females that affect interspecific mating, and we adapted a two-choice assay to capture female mate choice and female attractiveness simultaneously. We used shotgun sequencing to genotype female progeny of reciprocal F1 backcrosses at high resolution and performed QTL analysis. We found 2 major-effect QTL in both backcrosses, one on either arm of the third chromosome that each account for 32-37% of the difference in phenotype between species. The QTL of both backcrosses overlap and may each be alternate alleles of the same locus. Genotypes at these 2 loci followed an assortative mating pattern with D. simulans males but not D. sechellia males, which mated most frequently with females that were hybrid at both loci. These data reveal how different allele combinations at 2 major loci may promote isolation and hybridization in the same species pair. Identification of these QTLs is an important step toward understanding how the genetic architecture of mate selection may shape the outcome of secondary contact.