GBS of Oncorhynchus sp.
Genomic DNA was extracted from fin tissue using Qiagen DNeasy Blood and Tissue kits and a QIAcube robot according to the manufacturers instructions (Qiagen, Inc.). We prepared reduced complexity genomic libraries for high throughput DNA sequencing using a genotyping-by-sequencing protocol (Parchman et al. 2012). DNA was initially fragmented using restriction enzymes EcoRI and MseI and fragments from each individual fishs DNA were ligated to a unique 8-10 base pair nucleotide barcode. Following the ligation of the identification barcodes, individual samples were multiplexed and amplified by PCR. 192--248 individuals were pooled per library and each library was sequenced on one Illumina HiSeq 4000 lane to produce approximately 1.5 billion 150 base pair single-end sequence reads. Prior to sequencing, each library was size-selected using BluePippin (Sage Science) to retain only fragments 350-450 base pairs in length. DNA sequencing of all 11 libraries was completed at the Genomics and Cell Characterization Core Facility at the University of Oregon.