UCE target enrichment of ammodramus-savannarum-JFBM-43678 muscle tissue
We extracted genomic DNA from vouchered bird tissues using Qiagen DNeasy Blood & Tissue Kits (Qiagen Inc.), and we prepared sequencing libraries for Illumina sequencing using Nextera XT Library Preparation Kits (Illumina, Inc.). We generally followed the sequence capture workflow for Nextera-prepared libraries detailed in Faircloth et al. (2012), but we modified this protocol by using 1/4 aliquots of the required Nextera kit reagents and genomic DNA, and we pooled indexed libraries into groups of eight libraries, prior to enrichment. We enriched each pool using a set of 5,472 custom-designed probes (MYbaits, MYcroarray, Inc.) targeting 5,060 UCE loci (Faircloth et al. 2012) following an open-source protocol (see www.ultraconserved.org for the full protocol). Following enrichment and an 18 cycle PCR-recovery, we combined pooled libraries together in equimolar ratios to a final concentration of 10 然, and we sent the pooled libraries to the UCLA Genoseq Facility for 250 base-pair paired-end sequencing using two runs of an Illumina MiSeq.