Performance of ascertainment schemes explored across 12 population quintuplets assessed as squared Pearson correlation coefficient (<i>R</i>^<i>2</i>) for log-likelihood scores (LL) of admixture graphs fitted to unascertained vs. ascertained data, based on 5,000 graphs that are best-fitting according to log-likelihood (LL) scores on all sites, or based on all graphs.

We also applied the binary classifier to determine if an ascertainment produces unbiased or biased results (the latter cases are highlighted in bold and underlined text). Median R2 values across all population quintuplets or ascertainment schemes are shown in the second rightmost column and in the bottom row, respectively, and the numbers of population quintuplets affected by bias (according to this classifier) are shown in the rightmost column. The composition of the population sets is shown above the table in an abbreviated way: arch, archaic humans, followed by the number of archaic groups; afr, Africans, followed by the number of African groups; nafr, non-Africans or Africans with substantial non-African admixture [67], followed by the number of such groups. The SNP counts correspond to sites polymorphic in larger collections of groups from which the analyzed population quintuplets were taken, see S2 Table. The same results based on WR of admixture graphs are shown S4 Table. SNP counts vary across the population sets, and minimal and maximal values are shown in separate columns. (XLSX)