Phylogeographic reconstruction
To perform phylogeny on our SNP dataset, a VCF file containing 218,266
SNPs was converted to phylip format using vcf2phylip (Ortiz., 2019) and
used as input for IQ-TREE (Nguyen et al., 2015) to generate a maximum
likelihood phylogeny with the ultrafast bootstrap option and ascertain
bias correction (-st DNA -o CBS707 -m GTR+ASC -nt 8 -bb 1000) (Hoang et
al., 2018). The number of parsimony informative sites was 10,680 SNPs.
Trees were visualized on the iTOL website (http://itol.embl.de).