title: UCE target enrichment of Prionurus_laticlavius_23 muscle tissue
design: For each sample, approximately 0.51ug of DNA was sonicated to approximately 600bp using an Episonic 1000E sonicator with 15 second pulse intervals. Fragmentation was verified on a 1% agarose gel, and the process was repeated as necessary. Library preparation was conducted using a KAPA Hyper Library Prep Kit (KAPA Biosciences) using 10bp TruSeq-style oligonucleotide dual-indexing barcodes (Faircloth & Glenn 2012). Library preparation followed manufacturers protocols, with the exception that reaction sizes were scaled to 0.5x. Pre-amplification and post-library amplification values were quantified before equimolar pooling of samples in batches of eight. A target capture approach was then used to amplify ultra-conserved elements (UCEs; Faircloth et al. 2012). Pooled libraries were enriched for 1,300 UCE loci using a custom probe set (Arbor Biosciences) originally designed by McGee et al. (2016), following manufacturers protocols. Pools were then amplified and cleaned using 16-18 PCR cycles following procedures outlined in Faircloth et al. (2013). These pools were then combined in equimolar ratios and paired-end fragments of 150bp were sequenced on a single lane of an Illumina HiSeq Sequencer at the University of Oklahoma Medical Research Institute.