Genome-wide phylogenetic relationships
SAGUARO (Zamani et al. , 2013) analysis resulted in a total of 11 possible phylogenetic relationships across the genome (Fig. S6). None of the phylogenetic relationship matrixes could separate eastern and western monarchs, consistent with the lack of differentiation based on PCA and ADMIXTURE analysis. The Z-chromosome showed a different pattern of phylogenetic relationships compared to the autosomes (Fig. S7, Table S5), with an over-representation of certain cacti (Cactus 0,1,7,8, and 10). As with our ADMIXTURE results, while eastern and western monarchs could not be separated, three monarchs from Big Sur, California, did appear to cluster (Fig. S6).