Sequencing data analysis and SNP callingĀ 
Raw sequence data were processed using the Universal Network-Enabled Analysis Kit (UNEAK) pipeline implemented in the Iplant collaborative platform. This pipeline produced a hapmap file for downstream analysis. This file was used as input for SNP identification using the GBS pipeline implemented in TASSEL (Version: 3.0.166). Raw SNPs were filtered following the dDocent guidelines (Puritz, Hollenbeck and Gold 2014). In short, using vcftools (Danecek et al. 2011) variants were filtered for depth > 5, quality >Q30, and initially 50% missingness. This file was used to screen samples for high levels of missingness (all were <30%). The final SNP set was filtered for a maximum of 5% missing values and a minor allele frequency < 0.05.