In situ hybridization to polytene chromosomes of Drosophila melanogaster and other dipteran species

Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ∼16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

The study of insecticide resistance has greatly enriched our understanding of the genetic basis of adaptation, because it represents some of the most intense selection pressures acting on any natural population of eukaryote. Thus it can inform us about the limits of natural selection, both in terms of the number and type of mutations that can arise and also in terms of the rate at which these spread throughout populations. Fifty years ago, studies in Drosophila melanogaster indicated that many genes contributed to DDT resistance. Subsequent research into the Hikone-R strain indicated much of the resistance in this particular strain could be attributed to a single gene known as Cyp6g1. Here we show that there have been successive DDT resistance mutations occurring at the Cyp6g1 locus. They include an increase in gene copy number and the insertion of transposable elements into the regulatory regions of the Cyp6g1 gene. These mutations have swept to high frequencies in natural populations since World War II, when insecticides were first used. D. melanogaster is not a pest and has not been targeted by insecticides, and yet profound changes are occurring within its genome in response to man-made chemicals in the environment.