title: RAD-Seq of Cataglyphis israelensis worker
design: All the DNA for this analysis was extracted using Qiagen blood and tissue DNA extraction kit following the standard protocol. We used a modified protocol  to constructed double-digest RAD libraries. Changes were as follows: Added dual-index barcoding to allow multiplexing >96 samples per library. The Y-adapter for MseI from Peterson et al. (ddRAD) was used to prevent amplification of MseI-MseI fragments. Simplified restriction and ligation mixes using CutSmart buffer. Purification post-ligation was done using Agencourt AMPure beads. PCR using Q5 Hot Start Polymerase (New England BioLabs). PCR modified to decrease number of cycles by increasingnumber of replicates and starting DNA volume. Addition of primers and dNTPs for a final thermal cycle, in order to reduce production of single-stranded or heteroduplex PCR products. Final cleanup and size selection were carried out with AMPure beads. Three samples were omitted from the final results due to poor sequencing yield. All samples were multiplexed and sequenced by single-end 100 bp reads on 2 lanes of an Illumina HiSeq4000 sequencer.