A) Effective population size and B) population splits used for creating the simulated data. C) Coancestry heatmaps for linked and unlinked model with regions and 20 individuals per population, showing for (bottom left) the unlinked model, and (top right) the linked model; note that the linked heatmap is slightly asymmetric. D) PCA applied to the dataset using Eigenstrat on the raw SNP data. E) PCA on the coancestry matrix assuming markers are unlinked and F) linked (see text for details).