Figure 4.

Predicted Neandertal Ancestry in East Asian and European Populations under the Gravel et al. Complex Demographic Model when f = 2%

Each column depicts results for a different dominance coefficient (h). Γ denotes a gamma distribution of fitness effects. Error bars denote approximate 95% confidence intervals on our simulations.

(A) The fraction of Neandertal ancestry in East Asian (ASN) and European (EUR) populations.

(B) Ratio of Neandertal ancestry in East Asians to Neandertal ancestry in Europeans (R). Horizontal lines indicate the ratios of mean Neandertal ancestry observed in empirical comparisons of an East Asian and a European population.⁹ Models where the final proportion of Neandertal ancestry is concordant with the empirical data (between 0.5% and 5% in A) are colored black. Otherwise, they are colored gray. Note that across these models, the maximum value of R is only slightly higher than 1.0. However, the lowest observed value of R in the empirical data⁹ (in a comparison of IBS and CHS) is 1.14. Thus, demography differences combined with purifying selection cannot generate an excess amount of Neandertal ancestry in East Asians relative to Europeans as large as that seen in the empirical data.