The most interesting new fact from this study:
Estonia is a small country with no geographic barriers and its Estonian population is merely one million. In order to study the genetic structure of Estonia in more detail, all Estonian individuals were grouped here by their county of birth. Then, PCA was performed and the mean values of the two first PC of the counties were plotted onto the Estonian regional map (Figure 2). Surprisingly, the resulting genetic map correlates almost perfectly with the geographic map, although Estonia is only 43,400 km2 in size, and the mean area of a county only 2,900 km2. Thus, fine-scale genetic difference can be revealed by PC analysis, and the results can be useful for identification of the distant relatives.Figure 2 is reproduced here; the Estonian map is on the bottom right.
What seems very interesting is how Swedes and Estonians both deviate towards Finns but from different "starting points", a North German-Central European one and Baltic-West Russian one respectively. This is quite reasonable, as Swedes are Germanics who absorbed some Finnish elements, while Estonians are Finno-Ugrians surrounded by Balto-Slavs.
As the authors note, the multi-dimensional scaling plot is quite similar to the results of the PCA analysis:
Also of interest is the result of PCA within individual countries for which more than one geographical sample were available.
as the authors note:
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 , and was confirmed here. In addition, we detected intra-population differences within the Czech and Estonian samples (Figure S3).The two Finnish samples were from Helsinki and Kuusamo. The German ones from Schleswig-Holstein and Augsburg. The Italian ones from Borbera valley in the Piedmont and Apulia.
PLoS ONE doi:10.1371/journal.pone.0005472
Genetic Structure of Europeans: A View from the North–East
Mari Nelis et al.
Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).Link