Figure 2.

The Smaller Effective Population Size in East Asians Than in Europeans Has Two Competing Effects on Patterns of Neandertal Ancestry

(Left) The average Neandertal allele frequency at the end of the simulation given that the site segregates for the Neandertal and human allele (p_seg). Note that here, the average allele frequency in East Asia is higher than that seen in Europe as a result of the greater effects of genetic drift in East Asia than in Europe.

(Center) The percentage of sites (out of a total of 1,000,000 sites) where a Neandertal allele and a human allele are both still segregating at the end of the simulation (p_var). Note that fewer sites are segregating in the East Asian population because more were lost by genetic drift in this population.

(Right) The mean Neandertal ancestry per individual (p_all) is the product of both the mean frequency of alleles given that they are segregating and the percentage of sites that are segregating. Note that these two effects cancel each other out. These results suggest that East Asian and European individuals will have similar amounts of Neandertal ancestry under this model of demography and selection.