Figure 5

Classification diagram for homogeneous infection. The diversity and the variance of the sampled sequences from animals with homogeneous infection (i.e. infections with a single founder strain without any selection pressure or recombination) are expected to be located within the conical region. Here, the red (blue) conical region represents the 95% CIs from 5 × 10³ runs where 20 (60) sequences were sampled at each time point. The black diagonal line denotes the average relationship between diversity and variance. The grey vertical line denotes the upper limit of the 95% CIs of simulated diversity at each time point. All of the sequence sets sampled from the two primates within 3 weeks since infection were successfully classified as homogeneous infections; measured diversity and variance are located within the red and blue conical regions and the diversity is less than the upper limit of the 95% CIs of diversity at week 1 from the homogeneous infection simulations.