ddRAD-seq
Around 200ng of gDNA was incubated for digestion with 4U EcoRI and 2U Mse1 (NEB) enzymes at 37¡ C for 3 hrs.11. Adapters were ligated and size selected on 2% agarose gel (400-500bp) and purified using Qiaquick gel extraction kit. The paired-end sequencing (2x101 nts) of ddRAD libraries were sequenced using HiSeq 1000. However, 5 bases of internal barcode sequences were trimmed to retain 96 bases in R1.