ddRADseq data of Gambelia copeii tissue from tail-tip
We collected ddRADseq data using the Peterson et al. 2012 protocol. We digested genomic DNA with SbfI and MspI in a single reaction. Fragments were purified with Agencourt AMPure beads before ligation of barcoded Illumina adaptors onto the fragments. Libraries were size-selected (between 415 and 515 bp after accounting for adapter length) on a Blue Pippin Prep automatic size fractionator (Sage Science). The final library amplification used proofreading Taq and Illumina's indexed primers. The fragment size distribution and concentration of each pool was determined on an Agilent 2200 TapeStation and qPCR was performed to determine library concentrations. Sequencing was conducted on a single Illumina HiSeq 2500 lane (50-bp, single-end run) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. We processed raw Illumina reads using the program pyRAD v.3.0.5 (Eaton 2014), which included the use of VSEARCH to cluster the filtered reads by similarity and MUSCLE to align the sequences. We de-multiplexed samples using their unique barcode and adapter sequences, and sites with Phred quality scores under 99% were considered ambiguous (i.e., turned into an "N" code), and reads with > 10% ambiguous bases were discarded.