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



Looking again at Fennoscandia

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

Overview

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.

Finns

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.)

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.

Heatmaps:

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.

 

 

 





New analysis of the ancient gotlanders vs modern European populations

EDIT 30/08-2013: I now consider this analysis outdated. Please check the more recent posts with reanalysis of Ajv52, Ajv70, Ire8, Gok4 and Ste7.

Its time for a new ancient gotlander analysis using 22k, this time using the same reference panel and individuals as in the 289k analysis. However as 22k SNP's is a rather small number of SNP's the resolutation is much smaller and we will see that populations blend more into each other. In addition the ancient gotlander also affect the analysis because of these individuals unique genetic variation.

We will first look at the individual chunkcount aggregated heatmap. Much is familiar from previous analysis. We see generally that the modern populations to less extent paint there chromosome with the ancient gotlanders than the ancient gotlander paint the chromosome with the modern populations. This is a sign that the ancient gotlanders and modern populations have very different haplotypes because of divergence in time and difference in genetics. If we included a single San individual from Africa in the analysis we would probably see the same.

In the PCA plots we see that the ancient gotlanders place themself in dimension 1-2 in between the Vologda Russians to the left, Lithuanians to the right, the Estonians to the upper right. This seems to indicate that the geographical close populations of Lithuanians and Vologda Russians.

However if we look at the ancient gotlanders position in dimension 1-3 we find the ancient gotlanders close to part of the Finns to the left and close below to one Saami SWE7 and a few Scandinavian-Saami mixed individuals. This make it difficult to explain the ancient gotlanders only in the context of Lithuanians and Vologda Russians. Also in lower dimensions the ancient gotlander is in its own space seperate from the modern populations suggesting it has variance not seen in any current populations.

As we can see the plots are much more fuzzy than in the analysis we have seen earlier using 289k SNP's so it is very possible that we see large variations at the individual level. If we average the number of chunkcounts we see a clearer picture of affiliation. We see here that the Saamis appear to show the largest affiliation on average as both donor and receiver to the ancient gotlanders.

If we try to see these distributions geographically we appear to see that the ancient gotlander appear to affiliate with the more remote parts of the continent while the more central continent with the exception of the French appear to be the most different from the ancient gotlanders.

We also see a strange and a very different affiliation between the Finnish groups. West-Finns appears to affilaite well while the East-Finns appears to affilaite very little even when close populations like Estonians, Vologda Russians and Saamis appear to show affiliation. At the time beeing I cant explain this difference.

As the map suggests below maybe there have been a later genetic expansion to the north from maybe more south-weas European contries that have changed the genetic landscape since the time of the ancient gotlanders especially to the south-south-east.

Other maps and plots

Distinctive haplotypes in Saamis and Finns

I want to return to the differences one sees between donors and receivers. The sharp observer would probably notice the difference between the donation and receivers between f.ex Finns and the Chuvash or even in general between Saamis and Finns and other populations. The Finns dont use much Chuvash chromosomes to paint there chromosomes but Chuvash use on the other hand more Finn chromosomes to paint their chromosomes.

In the "newick" format it could be written as C(F1,F2). It has nothing to do about ancestral to who but is a tree representing three current populations. Where C vs F1,F2 coalesce at a time t1 and F1,F2 coalesce at a time t2. As we know it is correct to assume that F1,F2 coalesce at an later time than vs the C and probably F1,F2 similar coalesce time to C.

If we then assume that F1,F2 have have very distinctive haplotypes the painting of F1,F2 will ignore copying chunkcounts from C as it can find closer haplotypes internally, but C on the other hand is equally distant to F1,F2 will copy smaller chunkcounts from both of these. This will result in a symmetrical chunkcount heatmap.

ID    C    F1    F2
C     0    0.5    0.5
F1   0     0      1
F2   0     1      0

This can be seen very clearly as an extreme case with the ancient gotlanders vs modern populations, where the modern populations copy very little chunks from the ancient gotlander but the ancient gotlander copy much chunks from the modern populations as there a no other to copy from. If we had than one ancient gotlanders the picture would of course change. It would probably also be similar if we included a single San individual from Africa.

So asymmetrical donation-receiving for a population can be explained by distinct haplotypes for that population vs other populations.

(Thanks to the authors of Finestructure for their explanations and patience!)