Variance in <i>f</i>_<i>4</i>-statistic Z-scores resulting from ascertainment and random site subsampling expressed as residual standard deviation of a linear trend fitted to a scatterplot of Z-scores on unascertained vs. ascertained data (abbreviated as “residual SE” and expressed in the same units as <i>f</i>_<i>4</i>-statistic Z-scores).

Results for ascertainment on variants common in Africans (either those having no detectable West Eurasian ancestry according to Fan et al. [67] or on all Africans in the SGDP dataset) are circled in red. Results are shown for 27 classes of f4-statistics indicated in plot titles in panels a-e. The following abbreviations are used for naming the f4-statistics classes: AFR, African populations; AMRSIB, Native American and Siberian populations; ARCH, archaic human individuals (Neanderthals and Denisovans); chimp, chimpanzee; EAS, East Asian populations; EUR, European populations; ME, Mediterranean and Middle Eastern populations; PAP, Papuan and Australian populations. Residual SE values for f4-statistic Z-scores lying not far from 0 (absolute Z-scores on all sites a, b, c, and d. Size of the resulting SNP panels is coded by point size, and ten broad ascertainment types are coded by color according to the legends. Thirty eight site subsampling schemes were explored (see a list in the legend for Fig 2). (PDF)