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søndag 22. desember 2013

Updated Europe Analysis

(Updated 26/12-2013) This is the first updated Europe analysis using the "superindividual" approach where all individuals not of interest is group into the "other" group. Just as in the Fennoscanda analysis it appear to give added resolution to the results.

The chunkcount heatmap show much the same as in previous analysis but the new cluster seen in the Fennoscandia analysis also appear here. Chunkcounts is the total number of identical and related segments of DNA between any individual. The intensity of the colors on the heatmap and the closeness in the tree branch indicate relatedness to other individuals or groups.

CC Aggregated Europe linked 289k

 CC Raw Europe linked 289k 

The PCA overview of Europe appears to be better than previous analysis by using superindividual grouping for "others". We can now for example see a clear differentiation between Finns and Saamis in dimension 3 horizontal and dimension vertical 4. The differentiation in dimension 4 appears to be that Saamis pull to the same level as the Basque and Sardinians in this axis. 

CC Europe PCA Overview linked 289k

CC Europe PCA Individuals linked 289k

The PCA components presented in geographical heatmaps:

Dimension 1 - external peaks in Finns. Opposite Spanish, Sardinians and Romanians. What source "Others" is is not known but appears to be close.

Dimension 2 - external peaks in Albanians, Mordovians, Vologa Russians and Saamis. Opposite Scandinavians. May suggest a non-European influence that have arrived far north and far south into Europe or/and foundereffect among Scandinavians.

Dimension 3 - internal peaks in Finns and Saamis. Opposite Basque and Sardinians. May reflect expansion of agriculture to Europe.

Dimension 4 - internal peaks in Lithuanians, Mordovians, Belorussians, Ukranians. Opposite Basque Sardinians and Saamis. May reflect Eastern European expansion and/or foundereffect. The ancestry sharing along the Western European shores from Iberians to the Saamis may suggest old coastal migrations from the south to the north.

Dimension 5 - internal peaks among Scandinavians and Saamis. Opposite Basque, Sardinians, Spanish and Finns. This may show an agricultural expansion from South-East Europe to Finland.

Dimension 6 - internal peaks among Basque and secondary Saami. Opposite Sardinians. May suggest a common autosomal link between Saamis and Basque.

Dimension 7 - internal peaks among Saamis and secondary Sardinians. Opposite British and Vologda Russians. Appears specific to Saamis as rest of Europe appears quite uniform except for the Sardinians.

(Analysis in progress)

torsdag 19. desember 2013

Updated Fennoscandia Analysis

(Updated 26/12-13) Its finally time for updated Fennoscandia analysis. Its been over a half year since the last update. We have more than 53 new participants most of these are Swedes.

We do as usually look first at the heatmap that catches the main structure of the data. CC is ChunkCounts and is the total number of shared segments including identical and related segments. CL is ChunkLenght and is the total shared (both identical and related) segments in cM (centimorgans).

CC Linked Aggegated 289k 
 CC Linked Raw 289k  

CL Linked Aggregated 289k

CL Linked Raw 289k

The most different we see from previous Fennoscandia level analysis is the huge influx of Swedes creating a bigger cluster especially for the northern part (Norrländingar) of the country.  This cluster of Swedes at the middle of the heatmap appears to show affiliation to the Southern Saami cluster consisting of SWE7 and SA3. So it appears like there must have been some kind of founder effect and maybe drift in this process that have made them look more related to each other than other Swedes and other Scandinavians from further south. This foundereffect appear to have included a Saami population or Saami like population. 

There is also a secondary cluster consisting of mostly Swedes but also some Norwegians in the upper part of the heatmap below the Saami. These appears to show affiliation to the Northern Swedish cluster, Finns and individuals of mixed Scandinavian and Finnish ancestry.

External influenced varuation

The PCA plots can as seen before be divided into external influenced variation and internal variation. Dimension 1 and 2 appear to be very similar external variations that peaks in "Others" and with Danish and Scandinavians and lowest among Finns. That this variation peaks among Danish suggest a central-European origin of this external influence. These two dimension effectively divide Scandinavians and Finns.

 CC Linked PCA D1-D2 289k 

Dimension 3 on the other hand reflect an external variation from "Others" that peaks among Finns and to large extent Saami and the least among Scandinavians suggesting a Eastern European continental origin for this influence. As we can see also this dimension appear to be effective to differentiate Finns and Saamis from Scandinavians but it doesnt appear so clear cut as dimension 1 and 2 above.

 CC Linked PCA D1-D3 289k 

Internal influenced variation

As dimension 1 horizontal axis appears to differentiate so well the Scandinavians and Finns at each extreme we will continue to use this dimension. All the dimensions above 3 appear to show internal variation. The dimension 4 vertical axis appears to show the Scandinavian-Finn and Saami at each extreme.

CC Linked PCA D1-D4 289k

We clearly see from the new participants that NO25, SWE56, SWE62, SWE53 and SWE52 very clearly pull out of the Scandinavian cluster towards the Saamis and to some lesser degree also SWE59 and SWE55. Most of the appear to belong to the " Norrländingar" cluster.

Of individuals going away from the Finnish cluster towards the Scandinavians we can mention FI35, FI40. Of Scandinavians moving towards Finns we can mention NO21, SWE65, SWE54, NO26, SWE45, SWE55, SWE59, SWE50, SWE68.

As we can see from the heatmap the north-Swedish cluster appear to be much closer related to each than the normal Swede. This also shows in the PCA plot dimension 1-5 with dimension 1 at the horizontal and dimension 5 at the vertical.

 CC Linked PCA D1-D5 289k  

The "Norrländing" cluster appears to peek in Norrbotten area. As we can see the South-Saamis (SWE7+SA3) appears to attract the most of other groups to this cluster.

DImension D1-D6 appears diffcult to explain. It appears to be Finnish variation as its more dispersed among Finns than others.

CC Linked PCA D1-D6 289k

I will need some more research about this dimension. It doesnt seem to reflect the structure of Finnish subgroups in the heatmaps.

CC Linked PCA D1-D7 289k

In this plot the horizontal dimension 1 is the same as above while the dimension 7 appears to peak among the South-Saami individuals SWE7 and SA3. As we can see that both some Finns and Scandinavians climb towards these individuals. However the top other individuals closest to these South-Saamis appears to be from Västergotland and Skania area. On the Finnish side I am not sure but maybe coastal areas of Finland or from Karelia.

This clustering make me unsure and it maybe will not be cleared out properly with higher marker resolution, something I have been planning to do at least for the Fennoscandia analysis to higher power of differentiation.

I have also been looking at dimension 6 and it doesn't make sense to me currently so it add further uncertainty to the interpretation of dimension 7 a higher dimension than dimension 6 as higher dimensions means more uncertainty as individual variation become more visible in the data than in the lower dimension that capture more at the group level. 

(Work in progress)