0 500 1000 1500 2000 0 50 100 Complete Tagging 0 10 20 30 40 50 Region number Number of SNPs Threshold Total 99 98 97 96 95 90 85 80 70 60 50 Supplementary Figure 9: The number of principal components required to capture a predefined proportion of the variance. The 49 regions used for simulation are displayed, unlabelled and ordered by the total number of SNPs. The majority of variation can be captured by a relatively modest number of components even for regions containing large numbers of SNPs. Threshold specifies the minimum proportion of variance captured, or “Total” for the total number of SNPs in a region. 37