Figure 3

Classical multidimensional scaling plots using identical-by-state and identical-by-descendent matrices of the Dutch samples. A) Plot of the first two dimensions of a classical multidimensional scaling (MDS) analysis performed with the identical-by-state (IBS) distance matrix between pairs of 952 individuals using the linkage disequilibrium (LD) pruned set of genome-wide autosomal single nucleotide polymorphisms (SNPs). This set of individuals did not include 17 individuals identified by Mclust (see Methods and [see Additional file 1: Figure S2(B)]). B) Plot of the first two dimensions of an MDS performed using an identical-by-descendent (IBD) distance matrix between pairs of individuals. For explanation of the subpopulation abbreviations see Table 1 and Figure 2.