Library Construction and Sequencing
For whole genome resequencing, libraries were built using unique in-line indexed adapters designed by Rohland & Reich, 2012. First, 100 ng of DNA per sample were sheared to 400bp on the Covaris E220 focused-ultrasonicator using recommended factory settings for 400bp. Library construction included blunt-end repair, adapter ligation, and adapter fill-in that followed the protocol by Rohland & Reich, 2012. The individual samples were then PCR amplified with Pre-hyb primers following Rohland et al., 2015 and PCR products were purified using bead purification and pooled (Rohland & Reich, 2012). Sample pools were reamplified with indexed Illumina-compatible primers and they were size selected for fragments between 400-1000 bp and sequenced at 2x150 on the Illumina NovaSeq 6000 at the Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida.