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Adaptation of insect phenotypes for survival after exposure to xenobiotics can result from selection at multiple loci with additive genetic effects. To the authors’ knowledge, no selective sweep analysis has been performed to identify such loci in highly dichlorodiphenyltrichloroethane (DDT) resistant insects. Here we compared a highly DDT resistant phenotype in the  Drosophila melanogaster  ( Drosophila) 91-R  strain to the DDT susceptible  91-C  strain, both of common origin. Whole genome re-sequencing data from pools of individuals was generated separately for  91-R  and  91-C , and mapped to the reference  Drosophila  genome assembly (v. 5.72). Thirteen major and three minor effect chromosome intervals with reduced nucleotide diversity ( π ) were identified only in the  91-R  population. Estimates of Tajima's D ( D ) showed corresponding evidence of directional selection in these same genome regions of  91-R , however, no similar reductions in π or  D  estimates were detected in  91-C . An overabundance of non-synonymous proteins coding to synonymous changes were identified in putative open reading frames associated with  91-R . Except for  NinaC  and  Cyp4g1 , none of the identified genes were the ‘usual suspects’ previously observed to be associated with DDT resistance. Additionally, up-regulated ATP-binding cassette transporters have been previously associated with DDT resistance; however, here we identified a structurally altered  MDR49  candidate resistance gene. The remaining fourteen genes have not previously been shown to be associated with DDT resistance. These results suggest hitherto unknown mechanisms of DDT resistance, most of which have been overlooked in previous transcriptional studies, with some genes having orthologs in mammals.

plos one

Selective Sweep Analysis in the Genomes of the 91-R and 91-C Drosophila melanogaster Strains Reveals Few of the ‘Usual Suspects’ in Dichlorodiphenyltrichloroethane (DDT) Resistance