title: RAD-Seq analysis of Chylismia brevipes
design: Total genomic DNA was extracted at California Botanic Garden (Claremont CA) from 10 mg of silica dried plant leaf tissue per sample using a modified CTAB method, where the main modification included the addition of a pectinase step. Gel electrophoresis and Qubit 2.0 Fluorometer (Invitrogen) assays indicated high quality of all DNA samples. Restriction-site Associated DNA Sequencing (RADseq) libraries were prepared and sequenced by Floragenex (9590 Southwest Gemini Drive, Beaverton, OR, 97008), with SbfI as the single-digest restriction enzyme. Samples were barcoded and multiplexed in two libraries (380 samples per library), and single-end sequencing was run on a 1 100 bp Illumina HiSeq4000 platform. Lanes were 100% allocated, and samples were run in replicate to improve depth of coverage. Raw sequences were trimmed of restriction site sequence, demultiplexed, and binned into individual sample files. The read data from the two replicate runs were then merged to a single data file for each individual.