Figure 3 .

The within-patient viral census and effective population sizes. The initial population size (bottleneck) is one genome. The effective population size used in the model, N_model, is the harmonic mean of the census population size, N. The variance effective population size, N_e(V), estimated from simulations, overlaps N_model. The coalescent effective population size, N_e(θ), also estimated from simulations, underestimates N_model because the population is not at mutation-drift equilibrium. Both effective population sizes were estimated from 10,000 replicate simulations with an initial population size of one genome and no selection.