ddRADseq of juniper hybrid zone
DNA was extracted from juniper leaves using the Qiagen DNeasy Plant Mini Kits. Genomic DNA from each individual was digested with EcoRI and MseI restriction enzymes. Custom oligos containing barcodes and Illumina adaptors were annealed to the EcoRI cut sites, and oligos containing the alternative Illumina adaptor were annealed to the MseI cut sites. Digests were PCR amplified with a high-fidelity proofreading polymerase and pooled for sequencing. Libraries were size-selected for fragments between 350 and 450 bp in length with the Pippin Prep System at the University of Texas Genome Sequencing and Analysis Facility. Four lanes of single-end 100-base sequencing were executed with an Illumina HiSeq 2500 at the University of Wisconsin Madison Biotechnology Center.