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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.

2 kommentarer:

  1. You forgot to include me (NO5) it seems :(

  2. No, you replced yourself with some other individuals.