Fig 3. Standard out-of-Africa model underestimates LD among low frequency variants.

(A) We fit the 13-parameter Gutenkunst et al. model to statistics in the two-locus, multi-population Hill-Robertson system. The remaining 35 statistics from the Hill-Robertson basis used in the fit are shown in Fig A7 in S1 Appendix, and residuals are shown in Fig A8 in S1 Appendix. Best fit values for labeled parameters are given in Table 1. Most statistics were accurately predicted by this model, including (B) the decays of $\mathbb{E}\left[D^2\right]$ in each population, (C) the decay of the covariance of D between populations, and (E) the joint heterozygosity $\mathbb{E}\left[{\pi }_2\left(i\right)\right]$. (D) However, $\mathbb{E}\left[D_i(1-2p_i)(1-2q_i)\right]$ was fit poorly by this model, and we were unable to find a three-population model that recovered these observed statistics, including with additional periods of growth, recent admixture between modern human populations, or substructure within modern populations. Error bars represent bootstrapped 95% confidence intervals on the statistic estimate.