Digging deeper in Fennoscandian ancestry II

This is a continuation of the previous analysis (not a new analysis run!) and this time we look at the analysis possibilities of differentiating Scandinavians (Swedes, Norwegians, Danes). This time all individuals who shows considerable Saami (both North-Saami like or South-Saami like) or Finnish admixture in the previous analysis was removed from further analysis to keep any outside influence reduced to a minimum and lumped into the "other" group containing the rest of the world.

The data was run through Finestructures clustering processing but it was unable to differentiate the remaining Scandinavians meaning it appeared by the software to be one population. However in the PCA plot it was possible to infer structure. As we so in the previous analysis the first two dimensions of the PCA plot appears to reflect level of external influences in Scandinavians. In both dimensions the Norwegians clustered in the upper left corner closest to the "others" while Swedes clustered in much of the lower right corner but with a huge spread over large part of the plot. The single Danish individual appear to cluster with the Norwegians.

PCA dimension 1(horizontal) and 2 (vertical)

Dimension 3 on the other hand appears to be internal between Norwegians and Swedes, below together with dimension 2 and seem to give a better clustering. The Danish individual still in the Norwegian cluster but closer to the Swedes.

PCA dimension 2(H) and 3 (V)

So the Chromopainter-Finestructure pipeline appears to be able to differentiate Norwegian and Swedish ancestry even only using 289k SNP's. The division isnt entirely clear cut but there have been populations movement between these countries for many centuries so the classification labels may not be entirely correct and some individuals also have mixed backgrounds.