Totalt antall sidevisninger

mandag 19. november 2012

Looking again at Fennoscandia

This is a further local study of the Fennoscandian participants using the previous Chromopainter analysis data.


As we can see here the Finns and Saamis clearly deviate from each other in this "local" analysis. This is something we also have seen in earlier MDS analysis. In earlier analysis using wider population panels Saamis and Finns have shown a tendency to be close to each other as regional differences is emphasised more in such analysis. We also see the same in this analysis as the Saamis and Finns share the largest branch with each other opposite to Scandinavians. What appears to be East-Finns (Finn1) and North-Saamis appear to be most distant to Scandinavians.

South-Saamis and Scandinavians

The difference between this analysis and previous similar MDS analysis is that the software to larger degree is able to differentiate the different groups. The Saamis appears much the same as in previous analysis but what is interesting here is what appear to be South-Saami influence on Scandinavians especially Swedes and to some parts Finns too "from" SWE7 in particular.

SWE7 appears to have a special position. This indvidual appears to show strongest affiliation with the subgroup of Scandinavians in particular Swedes that appears to show South-Saami admixture and to much lesser degree to "normal" Scandinavians. The intermediate position of SWE7 between North-Saami and Scandianvians also seem to suggest SWE7 is some kind of North-Saami and Scandinavian admixture but this is not supported when comparing to NO6 and NO7 who appear to be straightforward Scandinavian-North-Saami admixted individuals. Actually SWE7 appears to be much less affiliated with the North-Saamis than NO6 and NO7. So SWE7's pull away from Scandinavians cant therefre be explained directly as direct North-Saami like admixture.

Software not able with current resolution to detect obvious Saami admixture in some Finns

However the software have not been able to detect obvious Saami influence on FI26 and FI5 among Finns that is very observable on the PCA plot as a strong pull toward the North-Saami individuals also seen in the CC raw heatmap. It may be due to the fact that Finns and Saamis are closer to each other than Scandinavians.


We also see that Finns splinter into 3 Finn only groups and 2 Finns joined into a mixed group. Finn1 group appears to be East-Finns, Finn2 appears to be West-Finns and Finn3 group appears to also be a West-Finn group. The third mixed group containing two Finns appears to be a group that appear to share branch with the Saamis and the South-Saamis influenced individuals in particular.

Heatmaps and PCA plots

ChunkCount Aggregated

ChunkCount Populations Aggregated
ChunkCount Raw Aggregated
ChunkCount PCA Populations Aggregated
ChunkCount PCA Populations Aggregated

(To view images, click and copy image to MS Paint or similar program.)

mandag 12. november 2012

Extending reference populations - looking beyond Europe

I am now in a first stage to extend the reference populations to the Chromopainter analysis. In this first run I have increased the number of individuals from different populations, but because of constraints in how many individuals my computer system can handle I have only included 1 or 2 reference individual from the more distant populations from Asia, America and Africa. However as one can see from the heatmap even with only 1-2 individual these distant populations do cluster nicely and as expected. I have also in this run modified the color scales to concentrate on the lowest scales to get a clearer picture of the dissimilarities among the populations especially for the more closely related populations.

Whats do the addition of more distant reference populations give?

In earlier analysis using ADMIXTURE we have seen that Saamis appear to have the highest level Siberian like admixture. In the ChunkLenght analysis we appear to see the strongest sharing for all the Saamis with the Nganassans (Nenets). Note that this affiliation also appears among East-Finns, Vologda-Russians, Moldavians and Chuvash. A faint influence also appears among Scandinavians.

There also appears to be sharing with a group of Kets and Selkup but these individuals have also in earlier ADMIXTURE analysis shown to be about 50% Siberian clustering with over 20% European ancestry and considerable Central-Asian ancestry so thats why we also see increased affiliation with populations that do not affiliate with the Nganassans individual. This increased sharing is also reflected among Finns, Vologda Russians, Mordovians and Chuvash.

Among the Saamis SA2 appears to have an additional affiliation that the other Saamis do not have. Its the only Saami individual that show increased affiliation with a cluster containing Daur, Xibo and Mongolian. The Chuvash and a group of Adigey is the only other groups that shows a similar profile. SA1 and SA2 also appears to have an increased affiliation with the Koryak and Yukagir than the remaining Saamis.

We also see that Finns and especially East-Finns appears in general to have a increased affiliation to Siberian populations but less than both the Saamis and Vologda Russians and Moldovians.

Also notice that the Saamis appears to have increased assymetric relationship between receiptant and donor to the Siberian populations compared to the Chuvash appears to be much more symmetrical. This indicate that the Siberian like ancestry among the Chuvash must be more recent or similar to these Siberians than the Saamis relationship to the same populations. Also the higher color intensity suggest closer relationship to the Siberians for the Chuvash.


ChunkLenght Aggregated
ChunkLenght Raw

ChunkCounts Aggregated
ChunkCount Raw
Average SegmentSize Aggregated (ChunkLength divided by ChunkCounts)
Note here that the Africans share very small segmentsize with each other compared to any other group, This is because of higher genetic diversity. Segmentsize include both identical and related or mutated segments.