I have from the start had this practice of running the Chromopainter-Finestructure analysis with the whole world panel and then later extracted from the output file the subdata from each run into a European panel and into a Fennoscandian panel for more detailed local analysis. However actually you should use the "superindividual" and "continent" functionality in Finestructure to get the analysis right and no file editing necessary and you also need to do a new ChromoCombine run with the forcefiles with these superindividuals.
I have been testing the difference using my earlier practice in the last standard run (this is NOT a new run!) data with these new settings to compare the results. It appears that after the advice from the authors its possible to extract even more information from the run with the current resolution than I was aware of even at Fennoscandiia level. I have in this reanalysis grouped all others than Fennoscandia into the superindividual "Others".
First the heatmaps. As we can see as before the heatmap identify a range of main clusters as before, some may notice that the numbers of identified clusters seem to be lower than from previous runs.
We then turn the attention to the PCA plots to see if we can infer more resolution than the standard heatmaps. As the superindividual "Others" contain much of the rest of the world it appears quite distant in both heatmap tree and the PCA. The "Other" group dominate the first 3 PCA dimensions as it appears far away from the Fennoscandia group in sum. The direction of "Others" are indicated on the plot.
As we can see below SWE7 a South-Saami individual clearly stand out in a own dimension separately from dimension 4 peaking in North-Saami. What this mean that using this new method the project can explicit differentiate South-Saami ancestry from North-Saami ancestry.
In earlier analysis the South-Saami ancestry appear to blend in somewhere between North-Saami and Scandinavians but as this show they are in a dimension of their own even they do share ancestry with North-Saami in dimension 4. However the North-Saami share very little of this South-Saami specific component but it appears far more common among other Fennoscandians both Scandinavians and even some Finns than the North-Saami specific component.