TABLE 2

The effect of a selective sweep on the mean nHaps/(S + 1)

t00.010.050.100.250.501.00No sweep
N = 106, s = 0.005(0.44)(0.60)(0.82)0.890.980.990.930.89
N = 104, s = 0.010.760.790.830.850.830.760.700.67
N = 104, s = 0.05(0.58)0.690.810.840.840.770.700.67
N = 106, s = 0.005a(0.53)(0.57)(0.81)(0.93)(1.10)(1.19)(1.23)1.25
N = 104, s = 0.01a(0.70)(0.76)(0.84)(0.88)(0.90)(0.90)0.930.93
• The time since the fixation of the favored allele, t, is scaled in units of 4N generations, where N is the effective population size. nHaps is the number of distinct haplotypes and S is the number of segregating sites. The sample size is 50, the population mutation rate for the neutral locus, θ, is 5, and the genetic distance to the selected locus, c, is chosen such that c/s = 0.01 (where s is the selection coefficient of the favored allele). In simulations where N = 106, the population recombination rate for the neutral locus, ρ, is 20 (corresponding to 1 kb if the recombination rate is 5 × 10−9/bp/generation); where N = 104, ρ is 5 (corresponding to ~25 kb if the recombination rate is 0.5 cM/Mb/generation). In parentheses are those entries for which E(nHaps/(S + 1)) is less than the neutral expectation.

• a nHaps/(S + 1) is calculated excluding singleton mutations.