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søndag 28. april 2013

Updated Europe Analysis

The updated Europe analysis shows much the same as before. The addition of Germans, Danes and Poles appears to fill out more of the gaps in the PCA plots. The addition of  Greek and Albanian have also made a small group in the PCA that seem to place the Balkans on the PCA map in the vicinity of the Romanians and Bulgarians.

In this run the Scandinavians do not switch between east and west branch when comparing the CC and CL runs as in the World Analysis. They do however branch out at the highest level of the Western European tree likely due to Saami or/and Finnish like influence as seen on the heatmaps, on the other hand we can see that of the European populations the Germans including diaspora individuals of part German ancestry are the Scandinavians closest relative in continental Europe.

Its also interesting to see that according to the color scale that the Scandinavians cluster and the German cluster appears to have very little asymmetry between them suggesting that there is a close geneology between them. The asymmetry vs the Saami and Finns however appears to be less obvious (meaning greater) except for individuals of mixed Scandinavian and Saami/Finn background. Here

The asymmetry occurs because Scandinavians find their closest haplotype neighbours among Saamis and Finns, but Saami and Finns finds to less extent their closest haplotype neighbor among Scandinavians but between themself. This do not appear to be the case Scandinavisn vs Germans where both find their closest haplotypes to the same extent between each other.

Saamis and Finns form on both CC and CL their own branch separating them from both the western and eastern european branches. On the CL heatmap Finns and Saamis closest relatives appears to be the Vologda Russians.  The asymmetry do not seem to be great and what makes the Vologda Russians branch out earliest of the East-European branch.

CL Euro Aggregated

CL Euro Raw

CL Euro PCA D1-D2

CC Euro Aggregated

CC Euro Raw

CC Euro PCA D1-D2

onsdag 24. april 2013

Updated World Analysis

The updated world analysis shows much the same as before. The tree structure is different for the number of chunk counts shared (CC) and an total chunk length shared (CL). In the latter Scandinavians CL clusters with the western European populations but in the former Scandinavians CC cluster with eastern populations.

The heatmaps for both these measures appears to show somewhat equal relationship to western and eastern populations suggesting that Scandinavians are intermediate between these two major branches in addition to have more Caucasus and Middle-East ancestry than Finns and Saami. In addition Saami and Finns appears to show relationship to Vologda Russians and Russians that Scandinavians have less of. The relationship to Lithuanians appears to be closer to Scandinavians than Finns and Saamis in general.

CL Aggregated

CL Raw

CC Aggregated

CC Raw

tirsdag 23. april 2013

Updated local Fennoscandian analysis

New individuals added included a Danish who appears to cluster with Scandinavians. This time BEAGLE was not run with default settings but with settings to increase phasing accuracy and this seem to have changed clustering for some individuals like FI2 who now appears to cluster with Finns who appears to have part Saami minority ancestry. We can as before differentiate between the different groups. The images below is in full size at the source and may be seen by right clicking your mouse and then select "open image" (works in Windows 7 and 8) or downloaded by saving link.

CL Aggregated

CL Raw

CL Individual PCA

CC Aggregated

CC Raw

CC PCA Individual

mandag 1. april 2013

Possible application of asymmetries in Chromopainter

I have for some time tried to understand more about the reasons why asymmetries occurs between received and donated chunks in Chromopainter. I have in an earlier post got the understanding that when there are large asymmetries between these it also means they are mutational more distant also meaning more distantly related and opposite if the asymmetries are smaller.

In essence I understand it the way that if the segments are more closely related to each other the more symmetric the segments would be. In a world with no mutations the segments would be identical like in a IBD (identical by descent) analysis and only divided by recombination there would be no asymmetry.

Motivated by a post on another blog called "No Mongolian admixture in Poland" I tried to see if this asymmetries could provide anything of information not only about Poles but to other European populations as well.

First let us look at the CL asymmetries in Europe. The central position of Poles shows that the asymmetrical distances are small only showing some minor deviations to Finns ad Saamis on one side and to French and Romanians on the other.

We can then look at a number of European populations vs Siberian, East-Asian and Native American populations (please note color scales are identical to all):

The tables shows in general that Native Americans and Siberians appears to have smaller asymmetries to Europeans than East-Asians as they appear green while East-Asians who have larges asymmetries appears more in red.

However internally among European populations there is different asymmetries towards these eastern populations. It appears like continental European populations like Poles, French, Hungarians and Chuvash have similar and less asymmetric profiles while northern populations Finns, Saami, Scandinavians and Vologda Russians have similar more asymmetrical profiles. The Romanians also have a similar profiles to the continental Europeans but with even less asymmetries than these towards the eastern populations.

This must be said to be surprising as f.ex Saamis and Vologda Russians especially among the northern European populations appears in absolutte CL terms to have the largest CL shared with these eastern populations.

This may mean that even the sharing are large vs these eastern popuilations it may not mean that the sharing are closer in geneology than with those who share less CL.

As a side note when looking back at earlier posts, the above may explain the positions of some Siberians vs Europeans on MDS plots not close to Saamis or Finns but on the same Y-axis as French and Romanians suggesting similar genetic variations on that dimension.

Little Study of the Saami, Finns and Scandinavians