Population structure analysis
SNPs that were covered in all the individuals were used to estimate the genetic structure of North American monarchs. Principal component analysis (PCA) of the SNPs was performed using SNPRelate (Zheng et al. , 2012) in the R/Bioconductor package. Cross validation error rates were checked using ADMIXTURE (Alexander, Novembre & Lange, 2009) for ‘K’ values ranging from 1 to 5 to determine the total number of populations in the dataset.