title: UCE target enrichment of Triopasites_penniger_EX094_AACGGTCA+AACCGAAC [Raw reads]
design: We used a targeted UCE approach to generate sequence data following previous literature (Faircloth et al. 2012, 2015). The protocols used followed those outlined in Branstetter et al. (2017) and were carried out at the USDA-ARS bee research lab in Logan, Utah, USA. We targeted a set of 2,527 UCE loci and additional legacy loci using baits based on the Hymenoptera v2 probe set outlined by Branstetter et al. (2017), with ant-bee specific probes as described in Grab et al. (2019). Probes were synthesized by Arbor Biosciences, previously MYcroarray. First, extracted DNA samples were sheared to reduce the average fragment size to a target of ~400-600 bp. Older or more degraded samples were not sheared, while other samples were sheared in a Q800R3 sonicator (Qsonica) for 30, 60, or 90 seconds depending on sample quality and predicted size distribution. Mean final DNA input mass for all samples was 102 ng but ranged from <1 ng  1,630 ng. Library preparation involved the use of a KAPA HyperPrep kit (Roche Sequencing Systems) for enzymatic steps including repair of fragment ends and addition of A-tails, and Illumina TruSeq-style adapters (Glenn et al. 2019) for dual-indexing with redundantly unique sequences. DNA-binding magnetic beads were made following an in-house protocol based on Rohland and Reich (2012) and were used to clean and concentrate samples at various steps in the process. After the final bead cleaning, samples were measured for DNA concentration with a Qubit 3 fluorometer and pooled in groups of 8-10 at equimolar concentrations. These pooled samples were enriched following a protocol from Arbor Biosciences (v4) for the first day of UCE enrichment, and a standard UCE protocol for the second day (enrichment protocol v1.5 available at ultraconserved.org, based on Blumenstiel et al. (2010)). Post-enrichment samples were measured on a TapeStation machine for fragment size distributions and size selected with a Blue Pippin machine (Sage Science) for a range of 200-700 base pairs, if necessary. Finally, pooled libraries were quantified with an Applied Biosystems qPCR machine and KAPA reagents, pooled together, and sent off for sequencing.