Fig. 2: Infection dynamics and population-genetic diversity.

A The diversity of M.TB within a patient is reduced relative to Wright–Fisher expectations owing to stochastic progeny skew, as shown in the inset in which a single clone in generation t_i–1 leaves a large proportion of progeny in the following generation t_i. Each colored star represents a unique variant. B The transmission bottleneck associated with a new patient infection additionally acts to reduce diversity to a subset of that present in the infecting individual. Further, the cycle of clonality will continue to reduce variation and alter allele frequencies.