Genome-wide phylogenetic relationships
We used SAGUARO (Zamani et al. , 2013) to investigate genome-wide phylogenetic relationships between samples, and to identify differentiated genomic regions and regions that may have introgressed between populations. We used the program VCF2HMM, implemented in SAGUARO, to convert VCF file to HMM format, and implemented this file to analyze phylogenetic patterns across autosomes and the Z chromosome.