UCE sequences of Acropyga_myops_ACR28
DNA was extracted destructively or non-destructively (specimen retained after extraction) from worker ants or pupae using a DNeasy Blood and TissueKit (Qiagen, Valencia, CA, USA). We quantified DNA for each sample using a Qubit fluorometer (High sensitivity kit, Life Technologies, Inc.) and sheared 1.8Đ245 ng (91 ng mean) DNA to a target size of approximately 500Đ600 bp by sonication (Q800 or Diagenode BioRuptor; Qsonica Inc.). The sheared DNA was used as input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that incorporated Ňwith-beadÓ cleanup steps (Fisher et al. 2011) and a generic SPRI substitute (Rohland and Reich 2012, ŇspeedbeadsÓ hereafter), as described by (Faircloth et al. 2015). We used TruSeq-style adapters during adapter ligation (Faircloth and Glenn 2012), and PCR amplified 50% of the resulting library volume (15 ľL) using a reaction mix of 25 ľL HiFi HotStart polymerase (Kapa Biosystems), 2.5 ľL each of Illumina TruSeq-style i5 and i7 primers (5 ľM each) and 5 ľL double-distilled water (ddH20). We used the following thermal protocol: 98 źC for 45 s; 13 cycles of 98 źC for 15 s, 65 źC for 30 s, 72 źC for 60 s, and final extension at 72 źC for 5 m. After rehydrating (in 23ľL pH 8 Elution Buffer (EB hereafter)) and purifying reactions using 1.0X speedbeads, we combined groups of eight libraries at equimolar ratios into enrichment pools having final concentrations of 74Đ156 ng/ľL.