design: DNA was extracted from single ants, either adults or pupae, using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), and quantified with a Qubit fluorometer (HS Assay Kit, Life Technologies Inc., Carlsbad, CA). We sheared 5-50 ng input DNA to a target size of ~600 bp using either a Diagenode BioRuptor (Diagenode Inc., Denville, NJ) or QSonica Q800R3-110 (Qsonica Inc., Newtown, CT). Sheared DNA was input into a modified library prep procedure utilizing Kapa Hyper Prep kits (Roche Sequencing, Kapa Biosystems, Wilmington, MA) and custom dual-indexing adapters (Glenn et al. 2019). All library preparation steps were performed at quarter volume except for PCR, which was done at full volume. We cleaned libraries using 1.0x SPRI beads and quantified the cleaned products with Qubit. Enrichment of UCE loci was carried out using taxon-specific versions of the Hymenoptera v2 UCE probeset (Branstetter et al. 2017), which targets up to 2,590 UCE loci in Hymenoptera. Most taxa were enriched using the ant-specific version of the probe set, but three samples were enriched using a bee-ant-specific version (Grab et al. 2019). The probes and enrichment kit were purchased from Arbor Biosciences (Ann Arbor, MI). Enrichment was performed following either a standard UCE protocol (enrichment protocol v1.5 available at ultraconserved.org), based on Blumenstiel et al. (2010), or by using a modified protocol in which we followed Arbor Biosciences v3.02 protocol for enrichment day 1, and the standard UCE protocol for day 2. For the procedure we combined up to 10 samples into equimolar enrichment pools and used 500 ng of DNA for the hybridization reaction, which was carried out over 24 hours at 65C. Following enrichment, each pool was quantified via qPCR and then pooled into a final sequencing pool of 100 to 110 samples. Sequencing pools were sent to either the University of Utah Genomics Core for sequencing on an Illumina HiSeq 2500 or Novogene (Novogene Inc., Sacramento, CA) for sequencing on an Illumina HiSeq X.