DNA was isolated from 100–300 µl of packed animals using the Blood and Tissue DNA isolation kit (QIAGEN, Valencia, CA). The provided protocol was followed with the addition of RNase (4 µl of 100 mg/ml) following the initial lysis for 2 min at room temperature (RT). DNA concentration was determined using the Qubit dsDNA Broad Range Assay Kit (Invitrogen, Carlsbad, CA). Libraries were generated using the Illumina Nextera Sample Prep Kit and indexed using the Nextera Index Kit. A total of 24 uniquely-indexed samples were pooled by mixing 100 ng of each sample. The pooled material was size selected by electrophoresing the DNA on a 2% agarose gel and excising the fragments ranging from 300 to 500 bp. The sample was purified using the QIAGEN MinElute Kit and eluted in 11 µl of Buffer EB. The concentration of the purified sample was determined using the Qubit dsDNA High Sensitivity Assay Kit. Sequencing was performed on the Illumina HiSeq 2500 platform. To increase coverage of some strains, we incorporated data from two separate studies of wild strains (Thompson et al. 2013 (link); Noble et al. 2015 (link)).