Fig. 1.

—Phylogenetic tree inferred from the concatenated amino acid alignments of the 2,650 complete single-copy protein families. The total alignment length is 786,198 amino acids, 4,305 (0.55%) of the sites are variable and 1,714 (0.22%) are parsimony informative. The number of strains grouped in the collapsed clade is shown in brackets. See supplementary figure S2, Supplementary Material online for the complete phylogeny. The root position is estimated using midpoint rooting, the MAD method (Tria et al. 2017), and the outgroup method with Mycobacterium canetti based on 2,557 complete single-copy protein families. All approaches infer the root position on the branch splitting lineage 1 from the others; this result is in agreement with previous analyses (Comas et al. 2013).