Fig. 3

Structure of MTBC populations in TB patients. a Folded site frequency spectrum: a histogram of estimated variable allele frequencies within MTBC populations in TB patients. Cumulative distributions of allele frequencies for all variable SNPs (v-SNPs) are shown in black—80% of all the v-SNPs are present at an estimated frequency of less than 20% (dotted line). The corresponding distributions for v-SNPs that were detected in sputa from a single time point (unstable, yellow) or from multiple time points (recurrent, blue) are also shown. The observed distribution of alleles could arise from b a dominant clone of MTBC colonizing the lung and minor genetic variants continuously emerging from it which are selected against by purifying selection. Alternatively, c a large number of physically separated populations each produce minor variants. In this setting selection would be less efficient and population dynamics would be driven by genetic drift