Copy Number Variation and Transposable Elements Feature in Recent, Ongoing Adaptation at the Cyp6g1 Locus

Abstract

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.

Evolutionary Toxicogenomics: Diversification of the Cyp12d1 and Cyp12d3 Genes in Drosophila Species

“…While the link between gene amplification and insecticide resistance is commonly encountered for esterases and glutathione Significance levels are indicated by two asterisks (P \ 0.0001), one asterisk (P \ 0.001) or pound sign (P = 0.0016) S-transferases, gene duplication is often less associated with insecticide resistance and cytochrome P450 monooxygenases, though some cases have been documented (Bass and Field 2011). In D. melanogaster, Cyp6g1 has been found as a duplication in wild populations throughout Europe, Asia, and the United States, but increased transcription of Cyp6g1 cannot be dissociated from the presence of a transposable element within the 5 0 promoter region, a common mechanism of overexpression of P450 genes (Schmidt et al 2010). Overexpression of Cyp12d1 in a transgenic fly system resulted in flies with tolerance to DDT, ostensibly due to the increased metabolism of the compound, but other P450 genes associated with DDT resistance (Cyp6a2, Cyp6a8) do not seem to increase DDT metabolism (Daborn et al 2001).…”

“…The Cyp12d1 duplication has been estimated to occur within *80 % of the individuals within a wild population, but the proportion of individuals carrying the duplication was not different between unexposed field populations and survivors of DDT exposure (Schmidt et al 2010). If the Cyp12d1 duplication does not seem to increase detoxification activity toward DDT, as posited by the positive dosage model (Kondrashov et al 2002), then why does it seem to be so prevalent in the wild?…”

Gene duplication in the major insecticide target site,Rdl, inDrosophila melanogaster

“…In D. melanogaster, an allelic series at the cytochrome P450 Cyp6g1 locus involves a gene duplication and a variety of transposable element (TE) insertions. The most derived alleles are correlated with increased enzyme production and multiinsecticide resistance, including dichlorodiphenyltrichloroethane (DDT) (24).…”

“…For the Rdl duplicated lines, our data suggest ectopic recombination in neighboring Roo TEs initiated the genome rearrangement. TEs and genome rearrangements have previously been implicated in adaptation to environmental pressures such as insecticide resistance (24,37,38). TEs contribute substantially to adaptive evolution and have the capacity to generate deletions, duplications, and regulatory changes with wide-ranging phenotypic effects that cannot be achieved by point mutations (39).…”

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

“…Like Drosophila, most host genomes are occupied by multiple TE families, which are defined by sequence similarity (homology) and by replication and transposition mechanisms. Even though incidences of potentially adaptive individual TE insertions with high population frequencies have been reported (Daborn et al 2002; Aminetzach et al 2005;González et al 2008;Schmidt et al 2010), the mutagenic effects of TE insertions are typically deleterious because they disrupt gene structure and function (Finnegan 1992) and can lead to deleterious chromosomal rearrangement (Montgomery et al 1987(Montgomery et al , 1991Langley et al 1988). Supporting this, TEs in natural populations of Drosophila are generally found in intergenic regions (Aquadro et al 1986;Kaminker et al 2002; Bergman et al 2006) Because of these deleterious fitness impacts of TEs on their hosts, the interaction between host and TEs has been suggested to be analogous to an arms race between host and other more familiar pathogens (Kidwell and Lisch 2001;Aravin et al 2007;Siomi et al 2008;Obbard et al 2009a;Blumenstiel 2011).…”