Figure 5
From: Inferring population size changes with sequence and SNP data: lessons from human bottlenecks
LD measures and analytic approximations. A sample of 100 chromosomes (of length 500 kb) was simulated for a constant population size model of 10 000 diploid individuals assuming a recombination rate of 1.5 × 10−8 per site and per generation, and a mutation rate of 1.2 × 10−8 per site and per generation. Only pairs of segregating sites with genetic distance <0.25 cM were considered. At least 10 million simulated pairs of segregating sites were grouped into 500 equally spaced bins according to their genetic distance between 0 and 0.25 cM. The product of allele frequencies, D2 values and r2 values were averaged across all pairs of segregating sites in each bin. The Ohta and Kimura (1971) expectation was computed following Equation (7). The McEvoy et al. (2011) approximation corresponds to 1/(2+ρ).
