To further explore the relationship among European population groups and examine population substructure, PCA was performed using the genotype results from a set of ~300,000 autosomal SNPs that was common to each of the populations examined. For most individuals with self-reported ethnic identities, there was a general correspondence with the geographical location of origin (Figure 1A). For example, the relationship of Italian groups and the subjects from the island country of Sardinia shows a striking resemblance to maps of Europe. In addition, genotypes from the same or related population groups typed in different laboratories showed similar PCA results (for example, north Italian and Tuscan groups genotyped as part of HGDP overlapped with Italian American subjects).
The same thing can be seen in other large countries, like Germany for example. Below is a detail of Figure S2 from Nelis et al. (2009). The Germans are spread out over an even greater area than the Italians, with Northern Germans (from Schleswig-Holstein) tending to the right and Southern Germans (from Bavaria) tending to the left, similar to the pattern observed with the Northern Italians (from Piedmont) and Southern Italians (from Puglia):
The distance between the Northern and Southern locations in each country is about 430 miles (690 km), and accordingly, the median values of PCs for the corresponding sample sets are about the same genetic distance:
In addition, Germany has East-West differences that seem to be even more prominent. The cities of Munich and Dresden are only 223 miles (359 km) apart, yet according to Heath et al. (2008), their populations form two distinct genetic clusters connecting Eastern and Western Europeans, just like on the map:
All of this is ultimately related to the clinal distribution of Mesolithic hunter-gatherer and Neolithic farmer ancestry, which shifts Northern and Eastern Europeans slightly toward Siberia, and Southern and Western Europeans slightly toward the Middle East, and can also have an effect within nations. Indeed, even smaller and less populous Germanic nations have noticeable population structure that follows the same pattern seen in Italy, Germany and Europe as a whole.
Lao et al. (2013) observed it in the Netherlands:
We detected a subtle but clearly noticeable genomic population substructure in the Dutch population, allowing differentiation of a north-eastern, central-western, central-northern and a southern group. Furthermore, we observed a statistically significant southeast to northwest cline in the distribution of genomic diversity across the Netherlands, similar to earlier findings from across Europe. [...] This genetic diversity cline is traditionally explained by several major prehistoric demographic events in Europe: the first colonization of Europe by anatomically modern humans together with a postglacial re-expansion from the southern European refugee areas in Palaeolithic times, and the introduction of the Neolithic agricultural lifestyle by people from the Near East.
And Humphreys et al. (2011) observed it in Sweden:
In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. [...] The first principal component showed the presence of a north-south genetic gradient that was mainly driven by each northern county being different from other counties. Systematic variation was present in the south of Sweden although to a markedly smaller degree than in the north of Sweden. [...] The overall North-South axis of variation is consistent with previous studies that have shown axes of variation on a European scale that closely line up with geographical axes.
