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).