FIGURE 1.

Global phylogeny of the Mycobacterium tuberculosis complex L4.4 sublineage and genomic structure and phylogenetic placement of the DS6^Quebec deletion. (A) Whole genome SNP maximum likelihood phylogeny of L4.4 comprised of 236 isolates from 19 different countries, including 23 isolates from the New Zealand Rangipo and Otara clusters. Scale bar indicates substitutions per polymorphic site. A black asterisk indicates the DS6^Quebec deletion and the CS clade is highlighted in gray. Branches and tip labels are colored by geographic region and lineages labeled according to the nomenclature of Coll et al. (2014). A black circle indicates the node position of the most recent common ancestor of L4.4 (rooted to H37Rv, not shown). (B) Schematic of the DS6^Quebec deletion. Genomic regions in H37Rv that are deleted by the DS6^Quebec deletion and the RD152 deletion in the Beijing/W lineage are shown.