RAD-seq of European hake
Genomic DNA of specimens was extracted from preserved fin clips using the DNeasy Blood & Tissue kit (Qiagen). The quality and concentration were checked using a Qubit fluorometer (Invitrogen) and a Nanodrop followed by gel electrophoresis prior to the preparation of single-digested RAD-seq libraries, following the protocol of Etter et al. (2011). Briefly, approximately 1 g of DNA per sample was digested with the restriction endonuclease SbfI (CCTGCA|GG recognition site) (NEB) and ligated to modified Illumina P1 adapters containing 5 bp sample-specific barcodes to allow sample multiplexing. Pools of 48 individuals were sheared with a Q800R3 Sonicator (Qsonica) and size-selected for fragments spanning 300500 bp via agarose gel electrophoresis. Purifications between steps were performed with QIAquick columns (Qiagen). Following the ligation of the Illumina P2 adapters, each genomic library was amplified using 12 PCR cycles and quality checked by a 2100 Bioanalyzer using a DNA 1000 chip (Agilent technologies). A step-by step protocol for library construction can be found at https://digital.csic.es/handle/10261/297272.