Fig. 2.

Subtree of a core genome SNP maximum-parsimony phylogeny of global B. anthracis isolates. Core genome SNPs were identified using Harvest suite (Treangen et al., 2014) from the strains listed in Table S1. Phylogeny reconstructed in mega6 (Tamura et al., 2013) using the spr algorithm, with 11 392 SNPs identified across 124 isolates Consistency Index (CI = 0.975). The full tree is included as Fig. S1. Bootstrap values (1000 replicates) are shown, but likely underestimate confidence in clonal populations with little homoplasy (Pearson et al., 2009). Groups A and B refer to the groups defined in Fig. 1. Sequence accession numbers are shown in Table S3.