UCE sequences of Crematogaster_sordidula_BBX1163
We extracted DNA from specimens using a Qiagen DNeasy Blood & Tissue kit (Qiagen, Valencia, CA). A slightly modified version of the manufacturers protocol was followed. We either extracted DNA destructively by pulverizing the entire ant (mostly used for pupae and in cases where multiple individuals from the same colony series were available) or non-destructively (mostly used for adults), enabling us to re-mount voucher specimens after extractions. The DNA quality was checked first by measuring DNA concentration with a Qubit fluorometer (High sensitivity kit, Life Technologies, Inc., Carlsbad, CA), and second by running 5 l of DNA eluate on a 1%-Agarose gel for 1 hour at 120 V. We used a Qsonica sonicator (Q800, Qsonica Inc., Newton, CT) to shear <5100 ng (64.6 ng mean) DNA to a target size of approximately 500600 bp from 090 seconds (amp=25, pulse=10), depending on prior DNA degradation. This sheared DNA was used as input for a modified genomic DNA library preparation protocol using a Kapa Hyper Prep Library Kit (Kapa Biosystems, Inc., Wilmington, MA) and incorporating bead-based cleanup steps (Fisher et al., 2011), a generic SPRI substitute (Rohland & Reich, 2012), and TruSeq-style adapters during adapter ligation (Faircloth & Glenn, 2012), following Faircloth et al. (2012). After 13 PCR cycles, we obtained post-library preparation DNA concentrations between 1.0442.7 ng/l (mean 15.89 ng/l), quantified using a Qubit fluorimeter (Broad range kit, Life Technologies, Inc.). We pooled libraries at equimolar concentrations containing eight to ten samples prior to target enrichment, aiming at total target DNA input of 500 ng. We enriched these pools using a published Hymenoptera bait set (myBaits UCE Hymenoptera 2.5Kv2P; Branstetter et al. (2017)), which targets 2,590 UCE loci shared among Hymenoptera and contains 31,829 unique baits. We followed an enrichment protocol by Blumenstiel et al. (2010), modified by Faircloth et al. (2012) and ArborBiosciences (MYbaits version 4.01). Finally, we performed qPCR quantification of enriched library pools to obtain accurate DNA concentrations of the pools using a SYBR FAST qPCR kit (Kapa Biosystems, Inc., Wilmington, MA) and a CFX Opus Real-Time PCR System (Bio-Rad Laboratories, Inc.). Sequencing was performed on an Illumina Novaseq 6000 instrument (Novogene, Cambridge, UK).