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Analysis reveals that in the high mutation regime, stochasticity in recurrence timing is driven by the random survival of small resistant populations rather than variability in production of resistance from the sensitive population, whereas the opposite is true in the low mutation rate setting.
The mutation rate setting was the same as in the above *BEAST analyses.
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With the mutation rate set to to zero no new phenotypes are generated, and existing phenotypes begin to outcompete each other.
In each simulation, a sample of haplotypes representing a single chromosome of 1 Morgan (100,000,000 base pairs) with the per-site mutation rate set to 10-8 was created using MaCS [ 8], which invokes a neutral coalescent model.
Null distributions of all test statistics were generated using coalescent simulations conditioned on the number of haplotypes in the sample with the mutation rate set to the population parameter θ (4Ne μ) estimated from the data using Watterson's estimator (Watterson 1975), as described in Zeng et al. (2007b).
For all these algorithms, the population size N is fixed at 256, the subpopulation size for the parallel model is fixed at N/ I n where I n denotes the number of islands, the crossover rate is set equal to 0.9, the mutation rate is set equal to 0.08, and the number of generations ℓ is set equal to 10,000.
Marker allele frequencies in the first historical generation were set equal to 0.5 and the mutation rate was set to 2.5e-5.
A background mutation rate is set for each chromosome and an additional mutation rate can be set during the simulation.
The recombination rate was set to be 10−8 per site per generation and the mutation rate was set to be 10−8 per site per generation.
The mutation rate was set to 2 × 10−8.
The mutation rate is set to 0.05.
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