Data from: Landscape genomics of Colorado potato beetle provides evidence of polygenic adaptation to insecticides

The ability of insect pests to rapidly and repeatedly adapt to insecticides has long challenged entomologists and evolutionary biologists. Since Crow's seminal paper on insecticide resistance in 1957, new data and insights continue to emerge that are relevant to the old questions about how insecticide resistance evolves: such as whether it is predominantly mono- or polygenic, and evolving from standing vs. de novo genetic variation. Many studies support the monogenic hypothesis, and current management recommendations assume single- or two-locus models. But inferences could be improved by integrating data from a broader sample of pest populations and genomes. Here we generate evidence relevant to these questions by applying a landscape genomics framework to the study of insecticide resistance in a major agricultural pest, Colorado potato beetle, Leptinotarsa decemlineata (Say). Genome-environment association tests using genomic variation from 16 populations spanning gradients of landscape variables associated with insecticide exposure over time revealed 42 strong candidate insecticide resistance genes, with potentially overlapping roles in multiple resistance mechanisms. Measurements of resistance to a widely-used insecticide, imidacloprid, among 47 L. decemlineata populations revealed heterogeneity at a small (2 km) scale and no spatial signature of origin or spread throughout the landscape. Analysis of nucleotide diversity suggested candidate resistance loci have undergone varying degrees of selective sweeps, often maintaining similar levels of nucleotide diversity to neutral loci. This study suggests that many genes are involved in insecticide resistance in L. decemlineata and that resistance likely evolves from both de novo and standing genetic variation.WI Leptinotarsa decemlineata SNP genotype matrixCurated SNP x individual genotype matrix for 16 Lepinotarsa decemlineata populations in Wisconsin, USA. Genotypes are encoded in a {0,1,2} format. Contains genotypes for 160 individuals at 34,186 SNPs.b33_mark3WI_poly_bgl2.txtMidwest Leptinotarsa decemlineata SNP genotype matrixCurated SNP x individual genotype matrix for 24 Lepinotarsa decemlineata populations in the Midwest, USA. Genotypes are encoded in a {0,1,2} format. Contains genotypes for 188 individuals at 34,186 SNPs.b33_mark3_poly_bgl2.txtEnvironmental variablesValues of potato intensification and percent non-forest habitat associated with 16 Leptinotarsa decemlineata populations in Wisconsin, USA.PI&NFdata.txtImidacloprid LC50 dataCoordinates and imidacloprid LC50 estimates for 47 Leptinotarsa decemlineata populations in Wisconsin, USALC50data.txtCPB1 barcode keyfileBarcodes used to demultiplex "CPB1" GBS library deposited in the NCBI Short Read Archive: https://www.ncbi.nlm.nih.gov/biosample/6295597CPB1_abrv_barcodes.txtCPB2 barcode keyfileBarcodes used to demultiplex "CPB2" GBS library deposited in the NCBI Short Read Archive: https://www.ncbi.nlm.nih.gov/biosample/6295598CPB2_abrv_barcodes.txtCPB3 barcode keyfileBarcodes used to demultiplex "CPB2" GBS library deposited in the NCBI Short Read Archive: https://www.ncbi.nlm.nih.gov/biosample/6295599CPB3_abrv_barcodes.tx