(A) Constant population size: plot of the cumulative distribution functions of the test statistic *T*(*K*) for neutral evolution (lines with dark and light shading) and a selective sweep (solid line). Simulations are for a region of 600 kb with 15 microsatellite markers (with spacings as shown in ) and an average distance of 37.6 kb. Additional parameters: recombination rate *R* = 2 × 10^{−3}, mutation rate θ = 5, sample size *n* = 60, selection coefficient *s* = 10^{−3}, effective population size *N =* 5 × 10^{5}, time of completion of sweep τ = 0.001 (in units of 2*N*). Dashed vertical line: 5% quantile of the distribution of *T*(*K*) for the neutral data set **N** (constant population size, 10,000 samples). Dashed horizontal lines: power (99.8%) obtained on data set **S** (recent selective sweep, 500 samples) and false-positive rate (15.8%) on data set **N**_{L} (candidate region scenario, 500 samples; see materials and methods). (B) Bottlenecked population: plot of the cumulative distribution functions of the test statistic *T*(*K*) for a bottlenecked population (dashed lines with dark and light shading) and a selective sweep (solid line). For comparison also the distribution for a neutral constant size population is shown (solid line with light shading). Parameters are γ = 2 (bottleneck severity) and τ = 0.05 (end of bottleneck; in units of 2*N*); other parameters are as in A. The false-positive rates are 15.8% for data set **B** (10,000 samples) and 37.2% for data set **B**_{L} (candidate region scenario, 500 samples). Note that for this case the false-positive rates obtained by the analytical approach are only 7.9 and 24.0%, respectively (see supplemental Tables S4d and S4e at http://www.genetics.org/supplemental/).

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