The supplementary material is also interesting. In Supp. Fig. 2 you can see the occurrence of 4 distinct clusters corresponding to the four corners of Europe, and also a barely perceptible tilting of Scotland toward Sweden relative to Ireland, within the NW cluster. As always, we should not interpret this as a lack of distinctiveness of the two populations, as such distinctiveness may hide in either higher-order dimensions, or a combination of more markers/individuals to be able to discern it. We could, however, say, as common sense would also dictate that these two populations are very close to each other in the European context.
Human Heredity Vol. 70, No. 2, 2010
Genetic Differences between Five European Populations
Valentina Moskvina et al.
Aims: We sought to examine the magnitude of the differences in SNP allele frequencies between five European populations (Scotland, Ireland, Sweden, Bulgaria and Portugal) and to identify the loci with the greatest differences. Methods: We performed a population-based genome-wide association analysis with Affymetrix 6.0 and 5.0 arrays. We used a 4 degrees of freedom χ2 test to determine the magnitude of stratification for each SNP. We then examined the genes within the most stratified regions, using a highly conservative cutoff of p less than 10–45. Results: We found 40,593 SNPs which are genome-wide significantly (p ≤ 10–8) stratified between these populations. The largest differences clustered in gene ontology categories for immunity and pigmentation. Some of the top loci span genes that have already been reported as highly stratified: genes for hair color and pigmentation (HERC2, EXOC2, IRF4), the LCT gene, genes involved in NAD metabolism, and in immunity (HLA and the Toll-like receptor genes TLR10, TLR1, TLR6). However, several genes have not previously been reported as stratified within European populations, indicating that they might also have provided selective advantages: several zinc finger genes, two genes involved in glutathione synthesis or function, and most intriguingly, FOXP2, implicated in speech development. Conclusion: Our analysis demonstrates that many SNPs show genome-wide significant differences within European populations and the magnitude of the differences correlate with the geographical distance. At least some of these differences are due to the selective advantage of polymorphisms within these loci.