The effect of ascertainment bias on admixture graph fits illustrated on a population combination "Altai Neanderthal, Ju|’hoan North, Biaka, Yoruba, Agaw".

Five thousand best-fitting graphs (according to log-likelihood scores on all sites) of 32,745 possible graphs were selected, and correlation of worst f4-statistic residuals (WR) of admixture graphs was explored for models fitted on all sites and on ascertained sites. Results for ascertainment on variants common in Africans (either those having no detectable West Eurasian ancestry or all Africans in the SGDP dataset) are circled in red. Thirty eight site subsampling schemes were analyzed (see panel a): 1) AT/GC; 2) random thinning of the AT/GC dataset to the 1240K SNP count for a given combination of groups (no missing data allowed at the group level), results for 100 thinned replicates are shown; 3) random thinning of all sites to the 1240K SNP count, results for 100 thinned replicates are shown; 4) the 1240K enrichment panel; 5) major components of the 1240K panel: sites included in the Illumina 650Y and/or Human Origins (HO) SNP arrays, sites included exclusively in one of them, and remaining sites; 6) the 1000K and 2200K SNP panels; 7) archaic ascertainment (either all such sites or transversions only); 8) the largest HO panels (4, 5, 13) or their union (4+5); 9) MAF ascertainment in one of nine continental-scale groups; 10) the same procedure repeated on AT/GC sites. The size of the resulting SNP panels is coded by point size, and the ten broad ascertainment types are coded by color according to the legend. Squared Pearson correlation coefficients (R2) for admixture graph WR on unascertained vs. ascertained data are plotted. The 2.5th WR percentile of all the thinned replicates combined, including those on all sites and AT/GC sites, is marked with the brown line. The area of the plot where ascertainments are considered biased according to this classifier is highlighted in red on the left. Scatterplots illustrating effects of selected ascertainment schemes on WR are shown in panels b–i. Dots on these scatterplots correspond to distinct admixture graph topologies. The corresponding ascertainment schemes are marked with letters b–i in panel a.