Distribution of correlation coefficients between neutral polymorphism and the polymorphism-recombination rate ratio (Rp-p:r). The observed correlation (Spearman rank correlation = 0.930; vertical line) falls within the distribution simulated for background selection (A), but not for the genetic hitchhiking model (B,C). The hitchhiking model in B uses scaled output of neutral coalescent simulations, whereas C uses direct simulation of a recurrent sweep process (Jensen et al. 2008). Simulations for A assume π0 = 0.0138 and for B assume π0 = 0.0486 (similar distributions result when π0 are identical), as well as c = 0.000158, a = 7.67 × 10−9, 800-bp loci, μ = 1.7 × 10−9 (see Supplemental Fig. 2), and the observed fine-scale crossover rates for 22 loci. Parameters from both A and B are based on least-squares fitting of analytical selection models. Explicit recurrent hitchhiking simulations for C are based on π0 = 0.035, c = 0.000158, s = 0.001, λ = 1 × 10−6, and fine-scale crossover rates for 22 loci.
