Is there a "East-Asian" influence in Continental Europeans? Part II

This post goes further in the the previous post "Is there a "East-Asian" influence in Continental Europeans?". It further elaborate on the separate run Finestructure using European, Siberian and East-Asian samples shown at the down part of the previous blogpost. In that part we only looked at the first dimension 1 and 2 and here we move further to the higher dimensions.

The third dimension is actually the same dimension we have seen many times when doing the PCA plot for the European panel in this project giving the characteristic "V" shape where South Europeans cluster at the root while Finns, Saamis cluster on one branch while Eastern Europeans branch on the other. This dimension is the Saami-Finnish branch variation vs South Europe. This variations peaks on one side among Saamis and Finns and as we can see from the gradient map it also exists consistently among the Siberians but not among the East-Asians. On the other side it peaks among Sardinians, Basque and Italians and the East-Asians cluster here with the South-Europeans. I am very unsure about the interpretation here but as both Siberians and East-Asians is not at the extreme on either side of the variation I tend to believe it may represent a gene flow from Europe towards Siberia and East-Asia. Maybe the northern spread represent a geneflow of Saami/Finnish like hunter gatherers eastward into Siberia and the lower part a geneflow from Europe towards East-Asia through todays India.

Dimension 3 - peaks among Saami, Finns vs Sardinians and Basque

Dimension 4 is the equivalent to the other branch of the "V" in Europe. On one extreme we found the Lithuanians, Mordovians and other Eastern European populations (actually here there is a Chukchi individual that a very little higher value than the top Lithuanian). The other extreme is Basque, Western Europeans, Saamis, Scandinavians and also the East-Asians. Also here I am unsure about the interpretation but it appear to show consistency as in dimension 3 but this time with a different spread. It may be a geneflow spread from Eastern Europe eastward through Siberia.

 Dimension 4 - peaks among Lithuanians vs Basque 

Dimension 5 appear to be a dimension that peaks among East-Asians on one side and Siberians on the other with the Europeans between. As we can see there is tendency to Siberian like influence in western part of Europe.

  Dimension 5 - peaks among Siberians vs East-Asians

This dimension appear interesting with regard to the question if there is any East-Asian influence among continental Europeans. So if we zoom to Europe and remove the PCA elements from outside Europe leaving only the European PCA elements we cen a more detailed view.

Dimension 5 - peaks among Siberians vs East-Asians

What is very striking here is that it appear to peak among Eastern Europeans and to some degree also Finns but appear least among the Basque, Western and South-West Europeans and among Norwegians and Saamis. It may suggest a gene flow from East-Asia that have divided in half an earlier haplotype distribution that may have gone from Western Europe to Siberia but now only remains among Western Europeans Scandinavians and Siberians. This dimension has a striking resemble to another dimension in Europe I have earlier believed to be internal European variation.

The PCA coordinates for all individuals and all dimensions can be downloaded here.
.

Is there a "East-Asian" influence in Continental Europeans?

Updated 27/01/14

This question have been following me since the last previous blogpost where I found this geographical distribution of chunkcounts PCA dimension 4 between Euroasian populations.

Everybody would probably agree about the northern distribution shown in blue and green apparently showing a genetic connection between North-East European populations like Saamis and Finns and Northern Siberian populations all the way from Fennoscandia to Beringia in Eastern Siberia as shown many times in this blog, from university research and from other bloggers. However if we look closer at the color distribution for the map:

We should of course not take this color distribution to literally as PCA plots distirbutions can be affected by many things but as we can see the red grade is close to the brown. This probably means the whole area from western continental Europe to East- and South-East Asia appear to show haplotype similarity. So it appears not only to have been a northern East-West influence but also a southern East-West influence as well.

To investigate this further I did a seperate run Chromopainter using 23k linked SNP at Chromosome 1 with a selection of individuals that had been phased together with over 2000 individuals using a high number of iterations in BEAGLE minimizing the error rate to a minimum. I used Chromopainters admixture functionality to design a admixture test using the relevant East-Asian, African and Siberian populations. As far I know from previous screening using ADMIXTURE all these individuals appear unmixed without any European admixture.

As we can see North-East Europeans appears to score low on East-Asian influence while continental Europeans from western and central Europe appear to score rather high vs the East-Asians. As expected we see the largest African like influence among the more southern populations and the North-Siberian influence in the more North-East European populations. Please note as this result is based on only 1 chromosome it doesn't always correlate 100% with the result of a whole genome analysis. There is a strong negative correlation between the East-Asian and Siberian component at -0.56 and there is even a stronger negative correlation between the Siberian and African component. The correlation between the East-Asian and Siberian component is weak at -0.17.

We can further see this using a area plot for the same data. The continental European populations from western and central Europe appear quite consistent to be closer to the East-Asian populations.

In Finestructure (from the previous run with the whole genome using superindividuals) the clustering appear to confirm what was observed above. The East-Asian influence appear rather consistent for all European populations included. In the North-East European populations this East-Asian influence appear to be lacking or less but the North-Siberian influence appear as expected from earlier analysis.

Individual results for project participants for PCA dimension 4 shown in the first image above. The first column show the actual PCA plot value and the second the ranking seen from top as in East-Asian and bottom as in Siberian.

This is a seperate PCA run using Europeans, East Asians and Siberians as reference. The X axis (horizontal) shows dimension 1 and the Y-axis (vetical) shows dimension 2. The X axis shows the European vs East-Asian influence, the Y-axis shows the European vs Siberian influence.

Europe vs East Asia and Siberians overview

 Europe vs East Asia and Siberians zoomed at Europeans

  Europe vs East Asia and Siberians zoomed at Europeans detailed 

Gradient map of PCA dimension 1 - blue most East-Asian, brown least East-Asian like.

 Gradient map of PCA dimension 2 - blue least Siberian like, brown most Siberian like 

Euroasian variation gradiation maps

This is a graphic presentation of the 7 Euroasian haplotype based (chunkcount) PCA plots from the latest project run using 289k linked SNP's. The average number of SNP in each segment chunk in the world panel is 13 (with a heavy overweight of Europeans and Northern Europeans in particular). This analysis is at this stage experimental. Please ignore coloring in Africa, Australia and Greenland as no populations are included from these continents.

The first dimension peaks on one side among Finns and Saamis (brown), and on the other side among Panya, Chukchi and Cambodians (light blue or blue). It appears all Fennoscandians in general belongs to this brown component.. This component appear identical to dimension 1 in the previous analysis. As this is the first dimension it also explain the largest variation in haplotypes between the populations. As the "blue side" here appear mostly at the coast peaking among populations that show affiliation to Papuans and Melanasians I suspect it seperate this ancient population from old European hunter gatherers.

Euroasian dimension 1

The second dimension peaks on one side among Lithuanians and Scandinavians and on the other side among the "The Others" containing the remaing individuals, but in the remaining panel it is peaks among Miao and some other East-Asian population. It seem to show a clear division of West and East Euroasian populations. All Fennoscandians belong in general to this western cluster.

Euroasian dimension 2

The third dimension peaks on one side among the "Others" and secondary at Bedouins and other Middle East populations and on the other side among North Siberian populations. It seem to represent influence from the African continent. This influence have reached as far north as South-Scandinavia but to less extent among Saamis and Finns. This dimension may be related to dimension 3 in the previous analysis.

 Euroasian dimension 3 

The fourth dimension peaks among Dai, Cambodian and Han in South-East Asian on one side and among Koryak, Yugagir and Nganassans in North-Siberia. Saamis, Finns and to a degree Scandinavians seems most similar in variance to the North-Siberian group while Continental-Europeans appears more similar to the South-East Asian group.

 Euroasian dimension 4

The fifth component peaks among Saamis, Finns and some South-East Asian populations on one side and among Northern Siberians on the other. Scandinavians appear less related to this dimension. This dimension may be related to dimension 3 in the previous analysis.

This component appears more difficult to explain as other analysis have shown no connection between Saamis, Finns and South-East Asians but to North-Siberians as in dimension 4. It may be an effect of having large sample of Europeans and small sample of other populations however its striking that the clustering appears consistent among the various non-European populations and not spread out randomly as if there was no structure. As far as I know and can remember there has not been done such wide scale analysis before using linked haplotypes so it may be something not seen before.

  Euroasian dimension 5 

The sixth dimension peaks among East-Asians on one side and the Indian subcontinent on the other. Saamis  Finns appear a little closer to the Indian subcontinent than Scandinavians.

 Euroasian dimension 6  

The seventh dimension peaks among the Lithuanians and Koryak on one side and among the Chukchi, South-Indians and among some North-Siberians. In more general terms as the heatmap shows similarity between Eastern Europe and South-East Asians. This dimension as dimension 5 appears difficult to explain and the same stated about this there apply here as well.

 Euroasian dimension 7

The remaining higher dimensions appear to show local variation between Siberian groups. 

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)

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)

Ajv70 and modern European variation II

Updated: 20 Nov 2013. This is a updated analysis of the previous Ajv70 analysis. See previous blogpost about the improvements. This analysis is based on 444k SNPs after all filtering (mostly imputed for all the modern populations, for Ajv70 all SNP are actuals).

Ajv70 appears different from Ajv52 who in the previous analysis appeared to be of mixed ancestry between what appeared to be a Saami like and a Baltic like or Eastern European like population. Ajv70 on the other hand in large cluster with Saamis, Vologda Russians and Mordovians and in particular with Saamis.

CC Euro Overview 444k SNP

As we can see the heatmap ancestry profile for Ajv70 and for the other close clustering groups seem resemble each other. Note that Mordovians and Vologda Russians doesnt cluster with Saamis and Finns in Chromopainter-Finestructure linked mode on the heatmaps but with Eastern Europeans. This is likely due to the linked mode reflect more recent ancestry and that the unlinked mode shows more ancient ancestry and Vologda Russians and Mordovians do seem to have more recent Eastern European admixture and in the past being part of the Finnic and Volga Finnic language area. This is seen both in linked and unlinked mode but probably weights more in linked mode than in the unlinked mode making them cluster with Eastern Europeans in the linked mode. The unlinked mode also give a lower resolution as its based only on allele frequencies adding to uncertainty.

The low affiliation for Ajv70 vs the Mediterranean populations on the heatmaps is only matched by Saamis and Finns among the modern populations. Finns appears more influenced by Eastern European populations and Scandinavians than the Ajv70 while Vologda Russians and Mordovians appears more influenced by Eastern European populations. Saamis show less affiliation to Scandinavians and Eastern Europeans than both Finns and Ajv70, but Ajv70 heatmap profile do seem to resemble the Saami most. 

The PCA dimensions dimension 4-5 showing internal European variation does not at first glance support the common heatmap clustering of Ajv70 vs Saamis, Vologda Russians and Mordovians as the Ajv70 appears among Scandinavians on the PCA and the Saami/Finns and Vologda Russians/Mordovians appear on very different locations on the PCA,  However the heatmaps neither indicate any Scandinavian like ancestry for Ajv70 even the individual's variation is plotted in this cluster. What could explain this seemingly contradictory result that Ajv70 resemble Saamis on the heatmap but not on the PCA is the fact that Ajv70 is not close in geneology to the populations it cluster closest with on the heatmap and that the Saamis, Finns, Mordovians and Vologda Russians are more dissimilar to "Others" and similar to "Others" than the others, however what this dissimilarity and similarity could be can be different..

CC Euro PCA 444k D4-D5

First about "not close in geneology". It can be best observed if we on a Europe PCA included related Orcadians and unrelated British. The Orcadians would form a clear outgroup on the PCA from the British even their ancestry profile on the heatmaps for the Orcadians wouldnt look much different from the British except for their internal sharing due to close relatedness and would else branch close to the unrelated British.

For the same reason Ajv70 would not cluster with Saamis and Finns on the PCA plot even they do cluster on the heatmap and else shows very similar profile with Finns and especially Saami. The explanation would therefore be that Ajv70 was not part in the founder effect that made the modern day Saamis and Finnish cluster due to closer relatedness to each other and therefore Ajv70 appears among the next best they could cluster with, the Scandinavians on the PCA plot (In earlier linked analysis Scandinavians shows both Saami and Finnish admixture) compared to continental Europeans so it would make sense.

Second about "dissimilarity" and "similarity" vs external influences or "Others". In dimension 1 and 2 vs the "Others" (the rest of the world panel) we seem to catch variation that could also explain why the Ajv70 heatmap clustering also include Mordovians and Vologda Russians even the European PCA dimension 4-5 do not support this clustering.

CC Euro PCA 444k D1-D2

This PCA plot describe the degree of similarity and dissimilarity vs the "Others". As we can see here Lithuanians, Scandinavians and many more form the upper left extreme and middle of the plot showing variation closest to the "Others" while the Saamis showing variation most distant to the "Others" in the lower right. The Ajv70 is within the range of the Saamis in this plot. There is also one Vologda Russian within this range too else the Vologda Russians and Mordovians is the next to follow up to the left after the Saamis and Ajv70. In PCA dimension 3 we also have a dimension where the Saamis, Vologda Russians, Mordovians and to some extent Finns is closest to the "Others" (not shown). The position on these dimensions can have have multiple explanations whatever each individual have been or been not influenced in various degree by the category "Others" and the very diverse panel included in this. So this means the dissimilarity for Saamis, Mordovians and Vologda Russians not necessarily is the same dissimilarity just more dissimilar than "Others" category, for example the Saamis probably pull high towards "Others" dimension 3 due to what appears as Siberian like minority ancestry while the Ajv70 who shows no such similar pull probably pull towards the "Others" because of what may be minority Afircan like ancestry (may also be erroneous affiliation due to contamination). This could affect the Finestructure tree clustering in unlinked mode giving adding Vologda Russians and Mordovians to the Saami, Finns and Ajv70 cluster.

Conclusion: Ajv70 appear to have the most similar heatmap profile to the Saamis but this individual do not seem to have been part of the same founder effect that made the higher genetic sharing between modern Saamis and Finns and therefore do not cluster together with the Finns and the Saamis on the PCA instead making Ajv70 cluster "incorrect" with their closest neighbors Scandinavians. Ajv70 neither show any significant degree of influence from the Baltic or Eastern European populations like Ajv52 who made Ajv52 appear to shift away into open space from Ajv70 position among Scandinavians closer to the Eastern European populations. The Ajv52's clustering with Scandinavian-Saami mixed individuals when adding some Baltic like admixture seem to further support that Ajv70 mostly resemble a Saami like population. Next it would make sense to check if Ire8 may have been part of the common modern Saami-Finns foundereffect. Earlier analysis may suggest it to certain degree.

Edit 19/11-13 broader overview with more European and Middle-Eastern populations. It is again very clear that Ajv70 cluster with Uralic or earlier Uralic populations and especially the Saami.

 CC Euro Overview extended 444k SNP 

Individual results:

CC Euro haploid 444k

CC Euro diploid 444k