UCE target enrichment of Crematogaster_degeeri_CASENT0122383_BBX179_GCTTCTTG+AACGCCTT [Raw reads]
We performed non-destructive DNA extraction from pinned material available in the California Academy of Sciences collection (see Table S2.3 for detailed information on DNA input and sequencing output). We then proceeded with sample QC using a Qubit fluorometer (High sensitivity kit, Life Technologies, Inc.), DNA fragmentation (400600 bp) by sonication (QSonica), library preparation (Kapa Hyper Prep Library Kit, Kapa Biosystems) that incorporated with-bead cleanup steps (Fisher et al., 2011), and used iTruSeq-style adapters during adapter ligation (Faircloth & Glenn, 2012), and library pooling (equimolar pools of 10 samples). Pooled libraries were enriched for UCEs using an ant-customized bait set (myBaits UCE Hymenoptera 2.5Kv2A; ArborBiosciences, MI) that includes 9,898 baits targeting 2,524 UCE loci shared across Hymenoptera (Branstetter, Longino, Ward, Faircloth, & Price, 2017). Finally, we performed qPCR quantification of enriched library pools using a SYBR FAST qPCR kit (Kapa Biosystems) with a Bio-Rad CFX Connect Real-Time PCR Detection System. This study was part of a larger sequencing effort, and sequencing was performed on an Illumina HiSeq 2500 instrument (2x125 bp v4 chemistry; Illumina Inc., San Diego, CA) by the University of Utah and the University of North Carolina at Chapel Hill genomics core facilities. For trimming raw reads, use i7:GATCGGAAGAGCACACGTCTGAACTCCAGTCAC*ATCTCGTATGCCGTCTTCTGCTTG and i5:AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT*GTGTAGATCTCGGTGGTCGCCGTATCATT, where * indicates the index sequence.