SNP data in plink bed format from GBS analysis of Helicoverpa armigera, H. zea and H. punctigera

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.GBS library preparation and sequencing was performed by the Genomic Diversity Facility, Cornell University, NY, USA. Information regarding the samples used and sequencing output is recorded in the supplementary material (Table S1). Briefly, 50 ng of gDNA was digested using PstI, before library construction as in Elshire et al. (2011) and sequencing using an Illumina Hiseq. A negative control was included with each plate. Raw data were assessed for quality and processed using Stacks v. 1.30 (Catchen et al. 2013b). Briefly, process_radtags was used to demultiplex samples, trim to 90 bp and assess the quality of reads before being forwarded to denovo_map, which was run using default settings. The Populations module was then run, limiting the output to loci existing in at least 5% of samples from each sampling location, with at least 5x coverage. The Populations module was used to output SNP data in Plink format.