ddRADseq of Cepphus grylle
Purified DNA samples were sent to lInstitut de biologie integrative et des systmes (IBIS) de LUniversit Laval, Quebec for ddRADseq library construction. The restriction enzymes SbfI and MspI were used to cut the DNA into fragments. Fragments were then ligated to two adapters, one of which was a DNA barcode unique to each individual and one that was a common adapter (Davey and Blaxter 2010). Fragments were size-selected using a BluePippin bioanalyzer (Sage Science) and the resulting RADseq libraries were sequenced either on a HiSeq 2000 using single-read 100 bp sequencing (Batches 1 and 2) at the Genome Quebec Innovation Center (McGill University, Montreal, Quebec), or on a HiSeq 2500, using single-read 100 bp sequencing (Batch 3) at The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children, Ontario. Raw data was demultiplexed using process_radtags in Stacks (process_radtags -i gzfastq -f input_file -o output_file -b barcode_file --renz_1 sbfI --renz_2 mspI -r -D).