Fig. 2.

Phylogenetic position of B. anthracis isolated from the NCA within the global population. (a) Global phylogeny of B. anthracis , showing the major clades (A, B and C) and sub-lineages. This tree was estimated based on a core SNP phylogeny of 80 publicly available genomes (Table S1). (b) Maximum-likelihood phylogenetic tree of the ancient A lineage (cluster 3 based on work from Bruce et al. [7]). All isolates from the NCA form a monophyletic lineage within cluster 3.2, along with the publicly available isolate A2075 (accession no. SRR2968187) isolated in 1999 from a baboon in central Tanzania. This tree was inferred using the general time reversible (GTR) model of nucleotide substitution, using the Ames Ancestor reference genome (accession no. NC_007530) as an outgroup. Tree scales reflect the number of substitutions per site.