vcf file of all heliothine individuals that have undergone whole genome sequencing aligned to B3 and B1/B2 BAC

Chromosome "1" contains the B3 BAC, Chromsome "B1_B2" contains the B1/B2 BAC. Heliothine moths were collected between 2004 and 2014 from 16 different countries around the world across various climatic zones and altitudes (Tables S1 and S2), many of which are described in Behere et al. (2007); and Tay et al. (2013). Samples were collected as larvae from wild and crop host plants, as adult moths via light/pheromone traps, or as larvae after bioassay, and preserved in ethanol (>95%) or RNAlater, or stored at -20°C prior to DNA extraction. DNA was extracted from samples using DNeasy blood and tissue kits (Qiagen), before being quantified with a Qubit 2.0. Nextera libraries were produced following the manufacturer’s instructions and sequence was generated as 100 bp PE reads (Illumina HiSeq 2000, Biological Resources Facility, Australian National University, Canberra, Australia, as well as at Beijing Genomics Institute, Hong Kong). Sample and sequencing data are included in the supplementary material (Table S2). Raw reads were aligned to BAC sequences, originally derived from H. armigera and available on NCBI (accessions in supplementary document), using BBMap. Reads were trimmed when quality in at least 2 bases fell below Q10. Only uniquely aligning reads were included in the analysis, to prevent spuriously inferring evolutionary processes occurring independently on each BAC. Outputted BAM files were sorted before duplicate reads were removed and files were annotated with read groups using Picard v. 1.138 (http://picard.sourceforge.net). BAC reference sequences were indexed using Samtools v. 1.1.0 (Li et al. 2009). UnifiedGenotyper in GATK v. 3.3-0 (McKenna et al. 2010) was used to estimate genotypes across all individuals simultaneously, implementing a heterozygosity value of 0.01. Variant call format files containing SNP calls were reformatted into Plink format using VCFtools v. 0.1.12b (Danecek et al. 2011). When linkage disequilibrium (LD)-based pruning was necessary, Plink v. 1.07 (Purcell et al. 2007) was used to filter one of a pair of SNPs using a pairwise LD threshold (r2=0.5) within windows of 50 SNPs, moving forwards 5 SNPs per iteration.