Abstract
Relatively few genome-wide population studies of field-acquired insecticide resistance have been carried out on agricultural pests. We utilized the navel orangeworm (Amyelois transitella), the main insect pest of almond orchards in California, to study the short and long-terms effects of heavy insecticide usage in the population genomic landscape of insects. We re-sequenced the genomes of three contemporary A. transitella natural populations differing in resistance status and characterized its population genetics parameters. We detected an exceptionally large selective sweep present in all populations. This sweep has virtually no polymorphisms and extends up to 1.3 Mb (spanning 43 genes) in the resistant population. We analyzed the possible causes of this unusually strong population genetic signature, and find genes in the sweep that are associated with DDT and pyrethroid resistance. Moreover, we found that the sequence along the sweep is nearly identical in the genome assembled from a strain founded in 1966, suggesting that the underpinning for insecticide resistance may have been laid a half-century ago when the California Central Valley experienced massive use of DDT, or that DDT residues in the soil may still be at play as a selective pressure. Our findings show the effects of insecticide applications in genomes of agricultural pest. We show that insecticide application in this species has probably evolved as a stacking of selective pressures that started decades ago and which effectively reduced variation in a region that includes several genes that confer resistance to insecticides that share a mechanism of action.