title: RADseq of wild solanum
design: We used fresh or silica-dried leaf tissues for DNA extraction with the CTAB method.  Quality and quantity of extracted DNA were measured with a NanoDrop2000 and Qubit.   Restriction-site-associated DNA sequence (RADseq) libraries containing uniquely barcoded DNA samples were created using a single PstI enzymatic digestion of sample DNA following the protocol of Elshire et al. (2011).   We checked the quality of individual RADseq samples on an Agilent 4200 Tape Station system and samples were combined in equimolar concentrations into sequencing libraries at the the DNA Services facility within the Research Resources Center at the University of Illinois at Chicago.   Libraries were then sequenced with Illumina HiSeq2500 technology to generate 100bp paired-end reads at the Roy J. Carver Biotechnology Center at the University of Illinois.  We de-multiplexed and trimmed adaptor and barcode sequences from raw reads using Sabre ({\texttt https://github.com/najoshi/sabre}).  Reads were then cleaned using the SLIDINGWINDOW setting in Trimmomatic and clipped when the average Phred score fell below 15 within a four base pair sliding window.  The resulting reads were then mapped to the S. lycopersicum genome, build SL2.50, using the default settings of the MEM algorithm of BWA.