Figure 4

Predicted divergence, diversity, variance, and sequence identity from a simulation performed by starting with 41 sampled nef sequences obtained at day 7 from animal r00065. 50 sequences at day 11 and 31 sequences at day 18 were sampled by starting a simulation with the 41 sampled nef genes that were obtained at day 7 from animal r00065. The sampling time points were chosen to reflect those used in our initial simulation (i.e., day 11 corresponds to day 4 following the "initial" infection in this simulation, and day 18 corresponds to day 11 following the "initial" infection. The measured divergence at day 18, 0.0081%, from animal r00065 is located outside of the 95% confidence intervals of the predicted divergence at day 18, [0.00815%, 0.057%].