RADseq of Pacific hake (Merluccius productus)
Genomic DNA was extracted from fin clips stored in 95% ethanol or dried fin punches using the Qiagen DNAeasy Blood & Tissue 96 extraction kit and then quantified using a BioTek FLX800 Microplate Fluorescence Reader. We dropped samples with extractions yielding <5 ng/l, resulting in 2008 samples suitable for sequencing library preparation. Individual DNA concentrations were then normalized to 125 ng in 10 ul for samples with concentrations >12.5 ng/ul and to 50 ng in 10 ul for samples with > 5ng/ul & < 12.5 ng/ul. We used the RADseq protocol of Ali et al. (2016) to construct libraries with the following specific details: 1) genomic DNA from each sample was digested with the restriction enzyme SbfI; 2) libraries were sheared to 300 - 500 bp using a Qsonica sonicator; 3) low-concentration library (5ng/ul) preparations were modified at several steps (contact corresponding author for details); and, 4) 100 bp paired-end sequencing was conducted in 20 lanes using a HiSeq 4000 at the University of Oregon Genomics and Cell Characterization Core Facility.