To represent the genetic diversity of Europe in the POPRES sample we selected a stratified random sample from the database, including 50 British, 50 French, 100 Italian, 100 Portuguese or Spanish, 50 Swiss, 50 East-Central Europeans, and 45 South-Eastern Europeans. These 495 individuals, combined with the 156 Europeans in HGDP, were split into a base set (n = 330) for construction of the eigenmap and a projection set (n =321). The latter samples were projected into the eigenmap via the Nystrom approximation (Supplementary Figure 3). The projected individuals mimic the distribution of the base sample over the space. This shows that the eigenvectors separate the observations based on underlying features in the data and these same features are present in the projected data.
