Fig. 5.

Selection model fits to observed CAPs. Site frequency spectra (SFS) for SNPs with AF > 5%. Site frequency spectra (SFS) were scaled to have the same number of sites for AF > 5%. Black bars represent all EP < 0.05 alleles observed in 1000G Phase 3 individuals. (a) Observed and fitted SFS for all candidate adaptive polymorphisms (CAPs). A neutral model (blue) does not explain the preponderance of alleles found at very high AF, and does not fit the observed data well (lnL= −4,124). (b) Observed and fitted SFS for all CAPs. A model with weakly deleterious (purple) and beneficial (green) showed the best fit (lnL = −3,080). It was significantly better than any other combination of models (LRT P ≪ 10⁻¹⁰). All CAP alleles shared with great apes (5%) were excluded from observed SFS.