One possible explanation for the genetic differences observed between the 11 regions of Iceland is varying contributions from ancestral populations. To explore this possibility, we used genotypes from the 79,641 overlapping SNPs to project [17] the Norwegian and Scottish samples onto principal components computed using the subset of 877 Icelandic samples (Figure 3). This analysis is robust to the concern that projected samples may be affected by regression towards the mean (see Text S1, Figure S1, and Figure S2). The Norwegian and Scottish samples were tightly clustered near the origin, with each having a mean of 0.004 on PC1 and −0.005 on PC2. This indicates that the genetic differences between Icelandic subpopulations represented on the top two PCs are orthogonal to genetic differences between the Norwegian and Scottish ancestral populations. In other words, varying contributions from ancestral populations are not a major determinant of genetic differences between Icelandic regions. Rather, the most plausible source of these differences is genetic drift during the 1100 years that have passed since the settlement of Iceland.
