DOI: 10.5061/dryad.4k40j
title: Data from: Contemporary evolution of a Lepidopteran species, Heliothis virescens, in response to modern agricultural practices

description: 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.
description: 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.