title: UCE sequences of Crematogaster_alafara_CASENT0492850
design: We extracted DNA destructively or non-destructively (specimen retained after extraction) from worker ants or pupae using the DNeasy Blood and TissueKit (Qiagen, Valencia, CA, USA). We quantified genomic DNA for each sample using a Qubit fluorometer (High sensitivity kit, Life Technologies, Inc.) and sheared between <5ng and 300 ng for 1060 secs (amp=25, pulse=10) to a target size of approximately 500600 bp by sonication (Q800, Qsonica Inc.). This sheared DNA was used as the input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that incorporated with-bead cleanup steps (Fisher et al. 2011) and a generic SPRI substitute (Rohland and Reich 2012, speedbeads hereafter), as described by Faircloth et al. (2015). We used TruSeq-style adapters during adapter ligation (Faircloth and Glenn 2012), and combined groups of nine to ten libraries at equimolar ratios into enrichment pools having final concentrations of 84.7-160 ng/L. We enriched each pool using a set of custom-designed probes (MYcroarray, Inc., now ArborBiosciences) targeting 2590 UCE loci in ants (Branstetter et al. 2017c). We followed target enrichment procedures for the MYcroarray MYBaits kit (Blumenstiel et al. 2010), except we used a 0.2X concentration of the standard MYBaits concentration, and added 0.7 L of 500 M custom blocking oligos designed against our custom sequence tags. We ran the hybridization reaction for 24 h at 65 C, subsequently bound all pools to streptavidin beads (Dynabeads MyOne Streptavidin T1; Life Technologies) and washed bound libraries according to a standard target capture protocol (Blumenstiel et al. 2010). We used the with-bead approach for PCR recovery of enriched libraries as described in Faircloth et al. (2015). We performed qPCR library quantification and combined libraries at equimolar concentrations into two final pools based on the estimated size-adjusted concentrations. We size-selected these final pools for 250800 bp with a BluePippin (SageScience). For a more detailed description of library and enrichment protocols used refer to Blaimer et al. (2016a; 2016b).