UCE sequences of Augochlorella striata
DNA for this sample was extracted with a QiaGen DNeasy Blood and Tissue Kit (Qiagen Inc.). We either soaked single whole specimens or individual legs in Proteinase-K extraction buffer and incubated overnight at 56C (~12 h). After incubation, whole specimens were washed in ethanol and mounted back on pins. We followed the extraction kit manufacturers protocol but eluted the DNA from the spin column with 120 l of purified H2O. After extraction, we assessed DNA fragmentation and concentration, and sheared fragments to a targeted size of 450-600 bp using a Q800R sonicator (Qsonica, LLC.). We used up to 100 ng of DNA per sample to prepare individual dual-indexed libraries with a KAPA HyperPrep kit (Roche Sequencing Systems, Inc.) and TruSeq adapters (Faircloth and Glenn 2012). We followed the pooled on-bead enrichment procedure outlined in Faircloth et al. (2015) and included the modifications from Blaimer et al. (2016b, 2016a).  We used the expanded Hymenoptera UCE bait set (ant-specific Hym-v2; Branstetter et al. 2017) for the enrichment procedure. After enrichment, we measured DNA quantity with a Qubit fluorometer (model 3.0, Thermo Fisher Scientific, Inc.) and assessed fragment distribution with an Agilent 2200 TapeStation and D1000 HS screen tapes (Agilent Technologies, Inc.). Based on our results, we combined pools at equimolar concentrations and size selected for a range of 250-600 bp with a Blue Pippin device (Sage Science, Inc.). Sequencing was carried out on an Illumina HiSeq 2500 platform with 150 bp read lengths. The index combination for this sample is: CACGTTGT+ACCGACAA.