1. Phylogenetic and convergence analyses of rpoB mutations.
Phylogenetic and convergence analyses of rpoB mutations. (a) Reduced core genome phylogeny of the most prevalent RpoB substitutions. The tree represents the phylogenetic relationships of a subset of the 7,099 isolates. Only isolates carrying the most common RpoB substitutions (occurrence > 10) were kept. For each monophyletic clade sharing an identical RpoB substitution, the closest related isolates showing an absence of this mutation were also kept in the phylogeny in order to show cases of independent acquisition of the same RpoB mutation (convergence). The red outer heatmap shows RpoB substitutions associated with multiple acquisition/convergence events indicative of positive selection. The blue inner heatmap shows RpoB substitutions associated with single acquisition/convergence events indicative of genetic drift. The numbers circled in red indicate the positions of the monophyletic clades sharing the same RpoB substitution that are represented in Fig. 4. (b) Inferred number of independent acquisitions and prevalence of most common RpoB mutations. The dark gray bars represent the inferred number of independent acquisitions of most common RpoB mutations. The light gray bars represent the number of isolates identified with these mutations. Previously identified Rifr mutations are indicated by orange circles below the mutations on the x axis. (c) Sizes of monophyletic clades with identical RpoB mutations. Each circle represents a monophyletic clade sharing an identical RpoB mutation. The number of identified isolates per monophyletic clade (size of clades) is plotted on the x axis. The different types of RpoB mutations are plotted on the y axis and are represented by different shades of red.
Romain Guérillot et al. mSphere 2018; doi: /mSphere