UCE sequences of  Crematogaster_lucayana_D1890
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). This product served as input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that included SPRI bead cleanup using a generic substitute (Rohland & Reich, 2012) and custom dual-indexing barcodes (Glenn et al., 2016). For UCE enrichment, 9-10 libraries were combined at equimolar ratios and adjusted to a final pool concentration of 147 ng/ml. Each pool was enriched using a set of custom-designed probes, hym-v2-ants (MYcroarray, Inc., now ArborBiosciences, Ann Arbor, MI) targeting 2,524 UCE loci in ants (Branstetter et al. 2017), following a standardized in-solution protocol (Blaimer et al. 2018; Ward & Branstetter 2017). The DNA concentration of enriched pools was quantified with qPCR, and these values were used to make an equimolar pool-of-pools, which was submitted for sequencing on an Illumina HiSeq 4000 at Novogene (Novogene Corporation, Sacramento, CA). For 22 of the samples, library preparation, enrichment, and sequencing were carried out by RAPiD Genomics (Gainesville, FL), using similar protocols.