Fig. 1

MTBC phylogeny. ML phylogeny based on 42,760 SNPs from 405 genomes using a general time-reversible substitution model and 1000 resamples. Seven major MTBC lineages and animal-adapted species are highlighted. Where warranted, these were differentiated further into subgroups (as shown on the circumference of the figure). Red dots indicate branches (n = 334) with a resampling support of > 0.9 and which were investigated for branch-specific mutations in 92 genes implicated in antibiotic resistance