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.
Humphreys et al. (2011) observed it in Sweden:
This is a detailed survey of 5174 Swedes from many parts of Sweden. Genome-wide single nucleotide polymorphisms (SNPs) from them were studied. The researchers concluded that the Swedes aren't a homogeneous people. Those in the south of Sweden are closely related to people in northern Germany who descend to a large extent from Neolithic-era farmers who arrived in Europe from the Middle East after some tribes already had settled in Europe, while those in central Sweden have a higher quantity of indigenous Scandinavian ancestry stemming from hunter-gatherers, and many of those in northern Sweden are closely related to Finnish or Saami people.
And 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. Simulation analyses indicate that this genomic gradient could similarly be caused by ancient as well as by the more recent events in Dutch history.