Principal component (PC) analysis was performed and Fst determined between samples using EIGENSOFT [6] on three sets of samples: 1) HapMap+Europe, 2) Europe, and 3) Estonia alone with individual counties. All analyses were performed with the default parameters. Multidimensional scaling (MDS) analyses were performed with the PLINK software. The marker set was filtered according to pair-wise LD (r2 cut-off = 0.2) in order to remove correlated markers. The number of remaining markers was 68,201. All PC values and MDS dimensions were multiplied by −1 to render scatter plots more similar to the geographic distribution of individual origin.
