Figure 9. Estimation of N_e using the linkage disequilibrium test.

The frequency of the least abundant haplotype in a two-locus/two-allele model determined from our simulations (solid symbols) and by Rouzine and Coffin [15] (open symbols) as functions of the population size, C, assuming neutral evolution (purple), evolution with selection (cyan), and evolution with selection and recombination where the number of infections per cell is constant at 3 (blue), or follows a distribution determined from a viral dynamics model (see text) with k_i = k ₀ (green) or k_i = 0.7k_{i -1} (orange). Error bars represent standard deviations. Values of C at which predictions from simulations match experimental estimates [15] of the least abundant haplotype frequency (black line) yield N_e. 95% confidence limits on the experimental data are also shown (dotted line).