The imputation was done in BEAGLE and for the record I have attempted to see if a non-imputed dataset was different from a imputed dataset as most SNPs in this analysis are imputed and I have noticed a certain "drift" making the imputed individuals more similar to each other than to non-imputed individuals like 1000G individuals. I have therefore excluded all non-imputed individuals except the La Braña individuals assumming that if same minor error affect all individuals the analysis will not be so very wrong. All the genotypes used for the La Braña is actually observed genotypes (no imputation).
As we can see below in the Chromopainter-Finestructure using a selected "world" panel seem to have structuring that make sense both at the World and European level suggesting the imputation have worked well and can be used for further analysis.
We here see again that the La Braña individual seperates strongly from the rest of the modern Europeans as in the earlier post using non-imputed haplotypes. The reason for this appears in world view to be much stronger African ancestry than the rest of the Europeans. The East-Asian, Siberian and Native American affiliation appears to be similar to todays Finns.
The question then further of course what population is the closest to the present day populations. I first run a simple IBS (identical by state) clustering in PLINK and got these distances where in diploid mode sees Lithuanians and Finns on the top while in haploid mode see total domination of Lithuanians.
However from own experience these direct IBS comparisment cant be thrusted fully just by direct comparison as many factors may affect the similarity. I therefore made a new Chromopainter-Finestructure run using only European populations to see if its more information in the data.
However in the Principal Component analysis or PCA we can disect the different influences seen in the ChunkCount or CC data. We see here first in Dimension 1 or the X-asis that shows the largest variance the La Braña individual on the far left and the Lithuanians on the far right. On Dimension 1 there is no doubt that the Saamis appears closest to the La Brãna and on Dimension 2 that shows the second largest variance is to the Lithuanians. Note that here the Saamis and the Basques form opposites suggesting a North-East vs South-West Component.
In Dimension 1 and 3 (Y-axis) we see that the La Braña are closest to Finns and to some extent also the Vologda Russians. In dimension 3 we also see that the Basque and the Lithuanians shows opposite variation where the Saamis appears intermediate between the two.