Figure 7.
Unobserved intermediates and compensatory mutations. (A) shows a scenario where the genotype with only 2 escape mutations (blue) was not observed even though this genotype was transiently at high frequencies. We fit this scenario by assuming both mutations have the same escape rate but occur sequentially (N = 107, r = 0, μ = 10−5). (B) shows a scenario where escape mutations 3 and 4 only occur together and any genotype containing only one of the two mutations is not viable. Hence the effective mutation rate into the genotype is μ2 = 10−10 and the waiting time for this genotype is longer. Note that the population size is N = 109 in this example (r = 0, μ = 10−5). The last escape only appears once the previous escape mutations have reached frequency one, and the seeding time is quite variable.