Figure 4.

Maximum likelihood phylogeny constructed using core genes detected among 326 genomes assigned to the Genome Taxonomy Database (GTDB) B. anthracis species, plus GTDB B. paranthracis outgroup genome B. cereus s.l. strain AH187 (NCBI RefSeq Assembly Accession GCF_000021225.1; omitted for readability). Predicted anthrax toxin gene gain events among PubMLST Sequence Type 365 Clonal Complex (ST365 CC) genomes are denoted by black arrows. Branch colors and clade labels differentiate genomes that are members of the clonal, historical B. anthracis lineage (darker pink) from genomes that are not (lighter pink). The heatmap to the right of the phylogeny denotes the following (from left to right): (i) whether a genome was sequenced in this study or publicly available (“Origin”); (ii) selected PubMLST lineages assigned using seven-gene multi-locus sequence typing, to which the genomes sequenced in this study were assigned (“MLST”); (iii) whether a genome possessed two or more anthrax toxin-encoding genes (cya, lef, pagA) or not (“Anthrax”); (iv) whether a genome possessed four or more polyglutamate capsule-encoding genes (capBCADE) or not (“Cap”); (v) whether a genome possessed two or more hyaluronic acid capsule-encoding genes (hasABC) or not (“Has”); (vi) the panC Group to which each genome was assigned (using BTyper3 and an eight-group scheme; “panC”). The phylogeny was rooted along the outgroup genome (omitted for readability), with branch lengths reported in substitutions per site. For complete ancestral state reconstruction results, see Supplementary Figure S4.