GBS of Oncorhynchus sp.
Genomic DNA was extracted from fish fin tissue clips according to the manufacturer's instrucitons using Qiagen DNeasy Blood and Tissue Kits and a QIAcube robot (Qiagen, Inc.). Reduced-complexity genomic libraries were then prepared according to the genotyping-by-sequencing protocol outlined by Parchmen et al., (2012). DNA was first fragmented with EcoRI and MseI restriction enzymes, and fragments from each individual fish were then ligated to a unique 8 to 10 base pair nucleotide identificaiton barcode. After barcode ligation, individual samples were multiplexed and amplified by PCR. We pooled 192 to 248 individuals per library and each library was sequenced on one Illumina HiSeq 4000 lane. Prior to sequencing, libraries were size-selected using BluePippin (Sage Science) to retain only fragments 350-450 base pairs in length. DNA sequencing of the 2016 libraries (EGM samples) was completed at the University of Texas Genome Seqeuncing and Analysis Facility, Austin, Texas and at the the Genomics and Cell Characterization Core Facility at the University of Oregon for 2020 libraries (WR samples).