Radseq data for Brodiaea filifolia and Brodiaea santarosae

We used the 3RAD DNA sequencing approach (Bayona-Vsquez et al. 2019) to isolate single nucleotide polymorphism (SNP) markers for genomic analysis. We digested genomic DNA with EcoRI, MseI, and CviQl (New England Biolabs) in a single reaction and used Solid Phase Reversible Immobilization (SPRI) beads (Beckman Coulter) to purify the digestions prior to ligating uniquely bar-coded adapters with T4 ligase (New England Biolabs). Libraries were size-selected between 415 and 515 base pairs (bp) using a Pippin Prep 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 Bioanalyzer and qPCR was performed to determine library concentrations.