Interestingly, PC analysis was also capable of highlighting intra-population differences, such as between the two Finnish and the two Italian samples, respectively. A low level of intra-population differentiation in Germany has been reported previously [18], and was confirmed here. In addition, we detected intra-population differences within the Czech and Estonian samples (Figure S3). In the case of the Czech, two samples were available: Prague and Moravia. Although their pair-wise Fst was virtually zero, the median values of PCs for the two samples sets are different. This is explicable by the fact that Moravia has a long shared history with the remainder of the Czech Republic, but is nevertheless separated from the rest of the country by the Czech-Moravian highlands, which in the past hindered stronger intermixing.
