UCE target enrichment of Nomada_ruficornis_quadrimaculata_BLX1471_GATTCAGC+ACTCCATC [Raw reads]
DNA was extracted from pinned specimens using non-destructive methods and Zymo Quick-DNA Miniprep Plus Kits (Zymo Research, Irvine, CA, USA). We used a bee-ant specific probe set  (Grab et al., 2019), which is just a subset version of the principal (Branstetter et al., 2017), to enrich 2,545 UCE loci. The probes are synthesized and available through Arbor Biosciences (Ann Arbor, MI, USA). Extracted samples were first sheared to fragment sizes of ~400-600 bp using a Qsonica sonicator (Q800R2; Qsonica, Newton, CT, USA). Older samples were not sheared due to their already degraded status; all other samples were sonicated for either 30, 60, or 90 seconds depending on their quality. Illumina libraries were generated using KAPA HyperPrep kits (Roche Sequencing, Pleasanton, CA, USA) and custom dual-indexing adapters (Glenn et al., 2019). Fragmented DNA was purified and concentrated using an in house paramagnetic-bead solution (Rohland & Reich, 2012). Once the final bead cleaning was complete, sample DNA concentration was measured using a Qubit 3 fluorometer and then pooled into 12 groups containing 9-10 samples of equimolar concentrations. Enrichment of the samples followed protocols from both Arbor Biosciences (v4 protocol; day1) and a standard UCE protocol (Blumenstiel et al., 2010; day 2) split over two consecutive days. After enrichment, each pool was quantified using qPCR, combined into one sample and then sent off for sequencing. For trimming raw reads, use i7:GATCGGAAGAGCACACGTCTGAACTCCAGTCAC*ATCTCGTATGCCGTCTTCTGCTTG and i5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT*GTGTAGATCTCGGTGGTCGCCGTATCATT where * indicates the index sequence.