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

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

Updated Europe analysis

New updated Europe regional analysis. I have removed the Orcadians as they give odd clusterings in the PCA because of relatedness, but one British group who have in earlier analysis clustered with them work fine as stand-ins. In the regional analysis more substructure is revealed. Caucasus not included.

As we can see for the Fennoscandians much is as before, but the addition of more continental Europeans have revealed more structure. We see that the 2 new Germans have clustered the dispora individuals Ux who have at least partly German and English ancestry into one group close to one group of the British, also containing a few French and one British.

The 1 new Austrian appears to cluster closest with the Romanians. We see 3 of the 4 new Polish cluster with the Ukrainians and Belorussian cluster while the last cluster with the Lithuanians. Most of the new Russians appears to cluster together with the 2 Estonians already in the project. However note the Estonians appears to pull away from the Russian cluster on the main PCA D1-D2 plot.

CC Europe Aggregated

CC Euro Populations

CC Euro Raw

(PCA plots in order D1-Dx+)

Updated World Analysis

This time I reduced the samplesize for Basque, Sardinians, Italians, Bulargians and Spanish to one each because of capacity problems as I would like to limited the analysis process to two threads to reduce the work with adding and formatting input filer, however they didnt cluster to their own as I expected like with the more distant populations. At the same time I increased the number of individuals to geographic closer population to make sure sample size is large enough to give good phasing.

The new thing this time is that we have have new samples from Germany, Austria, Poland and Russia. In the world analysis as said before its more difficult to differentiate similar European populations but also small sample sizes play a role her as Spanish, Iberian, Italians and French Basque didnt seperate into seperate clusters as in the previous analysis. This analysis will be presented in the next post.

Note that Romanian7 and Romanian3 appears to be Rom people as they cluster partly with different tribes in Pakistan.

CC World Aggregated

 CC World Raw

CL World Aggregated

CL World Raw

Updated local Fennoscandian analysis

New individuals added. We see much the same structure as seen before. However we see two Finns who share recent Saami ancesty groups together. We can as before differentiate between different influences between the different groups. The main sources is from Scandinavians, Finns and what appear to be two different kind of Saamis, North-Saami group and a South-Saami group. The South-Saami seems to diivide Swedes with ancestry from Dalarna and northwards out of the main Scandinavian cluster in different grades. Also Swedes with partly Finnish ancestry pull towards Finns. Finns again have different grades of sharing with Scandinavians.

ChunkCounts Aggregated Populations

 ChunkCounts Aggregated PCA 

 ChunkCounts Aggregated Individuals 

 ChunkCounts Raw Individuals  

ChunkCounts PCA Individuls

 ChunkLenght Aggregated Populations 

  ChunkLenght Aggregated PCA  

  ChunkLenght Aggregated Individuals 

Oceania influence in East-Asians

This is offtopic regarding the project goals but its so interesting I have to make a post about it. It appeared already in my first analysis including East-Asians, Siberians and Native Americans that these had increased sharing with my Sub-Sahara African individuals than many Europeans and therefore shared branch. I suspected then it may have something to do with Oceania like Papuans and Melanasians. In the most recent Chromopainter/Finestructure run it appears to confirm this.

Here we see first of all that the closest relatives to the cluster of Pygmy, San and a Bantu from Kenya outside Africa are a Papuan and a Melanasian. Then secondly to a Cambodian and a Panyian. This influence is also to a weaker extent seen in a clustered groups from Pakistan through i India to Malaysia.

However we can also see that among that the East-Asians in particular the populations from or close to China all have the highest level of sharing with the Africans, then to a weaker extent Siberian groups and at weakest with the Native Americans. This pattern is also seen vs the Papuan and Melanasian but to much stronger extent.

This pattern probably show that this Oceanic must be the influence of ancient migration as its even shows among all the Native Americans and is also shared between San, Pygmys and Papuan and Melanasian.

Updated Chromopainter/Finestructure World analysis

Same settings as before but added more populations (or basically almost the rest of populations I have in my reference database) from Middle-East, Caucasus and all the way to Pacific/Oceania. To properly view the images open them and copy them to a image program like MS Paint or something similar or just download them directly from the source webpage where you will get them in full size.

All members should have received the image through email, this time I have put them into Excel windows that make it easier to view individual result. I have only added 1 individual from each of the more distant populations, but it seems even with only 1 individual the analysis software manage to cluster and tree them quite well. Notice also that in worldview some individuals and populations that is close to each other will merge into the most similar cluster.

So what new information can be seen by adding more populations?

We now got a range of main European clusters seen in ChunkLenght (most of these can be further divided):

1. Common Scandinavian-Orcadian-PartBritish cluster
2. Common Lithuanian-Belorus-Ukrainian-Mordovian-Russian cluster
3. Common Saami-Finnish cluster
4. Common Sardininan-PartIberian-Basque cluster
5. Common Hungarian-Romanian-French-PartBritish-PartIberian-Spanish-Italian cluster
6. Common Caucasus-Middle-East cluster

From the heatmaps its possible to infer the following:

1. Scandinavians appears to have more similarity vs Middle East and Caucasus cluster than Saamis and Finns. Saamis and Finns share more with the Chuvash.

2. Saamis appears to show considerable sharing vs a group of northern Siberians however this appears to be mostly attributable to only 1 Saami individual. The single Aleut in the panel is partly mixed with Europeans and therefore shows more genetic sharing vs Europeans.

Whole analysis heatmaps:

ChunkCounts Aggregated World 



ChunkCounts Aggregated Raw World

ChunkLenght Aggregated World