Figure 4.

Core genome ML phylogeny. An ML phylogeny generated from the core genome alignment of 92 archival isolates, 5 contemporary isolates, and 21 BCG type strains. Three colored rings combine the genomic data with epidemiological data of each Bacillus isolate (n = 118). The tree is rooted with the B. paramycoides type strain (n = 345,224 total sites). The scale bar indicates substitutions per site. Bootstrap values were removed for ease of visualization. A tree with bootstrap values can be found in the Supplementary Information (Supplementary Figure S2).