FASTA mtDNA alignment, 12,248 bp assembly of resequencing data from heliothine species

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). 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 sequence reads obtained from whole genome sequencing were aligned to the H. armigera mitochondrial genome using BBMap v. 33.43 (http://sourceforge.net/projects/bbmap/), permitting a minimum identity of 0.6 and allowing for a minimum quality threshold equivalent to Q10 over two consecutive bases before reads were trimmed. Reads were assembled using mira v. 4 (Chevreux et al. 2004) before mitobim v. 1.7 (Hahn et al. 2013) was used to iteratively map and assemble whole mitochondrial sequences. Heterozygous bases were removed, sequences were aligned using MAFFT v. 7.017 (Katoh 2002) and sequences were trimmed using the Gblocks v. 0.91b online server (http://molevol.cmima.csic.es/castresana/Gblocks_server.html) (Talavera & Castresana 2007).