ddRAD data were generated using the quaddRAD approach. Genomic DNA was digested double-digested using restriction enzymes PstI and MspI. Each sample was dual-indexed through ligation with adapters containgin a 6 bp barcode and 4 degenerate bases. After cleaning, samples were combined in pools of 12 samples each and each pool was indexed by PCR with the addition of Illumina adapters. Products were cleaned and size selected and combined equimolarly into two libraries, which were size-selected and then sequenced in two MiSeq runs using v3 150 cycle kits. PCR duplicates were removed using the Stacks 2.68 module clone_filter. Reads were then demulitplexed to sample, using the combination of the two 6 bp barcodes, with Stacks 2.68 process_radtags. The enzyme cutsites were removed and additional filtering was performed using the -c, -r and -q arguments.