Lib5_Run1_Index12_S4_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 12; Read 2Lib5_Run1_Index12_S4_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 12; Read 1Lib5_Run1_Index6_S3_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 6; Read 2Lib5_Run1_Index6_S3_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 6; Read 1Lib5_Run1_Index2_S2_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 2; Read 2Lib5_Run1_Index2_S2_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 2; Read 1Lib5_Run1_Index1_S1_L001_R2_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (first run); Index 1; Read 2Lib5_Run1_Index1_S1_L001_R1_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (first run); Index 1; Read 1Lib5_Run2_Index12_S4_L001_R2_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 12; Read 2Lib5_Run2_Index12_S4_L001_R1_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 12; Read 1Lib5_Run2_Index6_S3_L001_R2_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 6; Read 2Lib5_Run2_Index6_S3_L001_R1_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 6; Read 1Lib5_Run2_Index2_S2_L001_R2_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 2; Read 2Lib5_Run2_Index2_S2_L001_R1_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 2; Read 1Lib5_Run2_Index1_S1_L001_R2_001.fastqgzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 1; Read 2Lib8_Index12_S4_L001_R2_001.fastqgzipped file containing Illumina sequencing data from: Library 8; Index 12; Read 2Lib8_Index12_S4_L001_R1_001.fastqgzipped file containing Illumina sequencing data from: Library 8; Index 12; Read 1Lib8_Index6_S3_L001_R2_001.fastqgzipped file containing Illumina sequence data from: Library 8; Index 6; Read 2Lib8_Index6_S3_L001_R1_001.fastqgzipped file containing Illumina sequence data from: Library 8; Index 6; Read 1.Lib8_Index1_S1_L001_R2_001.fastqgzipped file containing Illumina sequence data from: Library 8; Index 1; Read 2Lib8_Index1_S1_L001_R1_001.fastqgzipped file containing Illumina sequence data from: Library 8; Index 1; Read 1Lib8_Index2_S2_L001_R2_001.fastqgzipped file containing Illumina sequencing data from: Library 8; Index 2; Read 2Lib8_Index2_S2_L001_R1_001.fastqgzipped file containing Illumina sequencing data from: Library 8; Index 2; Read 1Lib7_Index12_S4_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index 12; Read 2Lib7_Index12_S4_L001_R1_001.fastqgzipped tar file containing Illumina sequencing data from: Library 7; Index 12; Read 1Lib7_Index6_S3_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index 6; Read 2Lib7_Index6_S3_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index 6; Read 1Lib7_Index2_S2_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index 2; Read 2Lib7_Index2_S2_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index 2; Read 1Lib7_Index1_S1_L001_R2_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index1; Read 2Lib7_Index1_S1_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 7; Index 1; Read 1Lib5_Run2_Index1_S1_L001_R1_001.fastqgzipped tar file containing Illumina sequence data from: Library 5 (second run); Index 1; Read 1Sample Information for demultiplexingA text file containing the following columns: Library number, Index number, barcode, sample name. Those sample names with a trailing "_1" or "_2" indicate the same individual that was incorporated more than once into the prepared libraries. Each of these sample replicates was run with distinct barcodes, but the resulting fastq files were eventually combined for downstream population genomic analysis.

Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other hosts, or 3) loss of resistance to previously used management practices including insecticides. Here we begin to address whether such changes occurred in H. virescens populations between 1997-2012, as Bt cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD-seq enabled genome scan to identify loci with significant allele frequency changes over the 15 year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan, and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.