Digging deeper in Fennoscandian ancestry II

This is a continuation of the previous analysis (not a new analysis run!) and this time we look at the analysis possibilities of differentiating Scandinavians (Swedes, Norwegians, Danes). This time all individuals who shows considerable Saami (both North-Saami like or South-Saami like) or Finnish admixture in the previous analysis was removed from further analysis to keep any outside influence reduced to a minimum and lumped into the "other" group containing the rest of the world.

The data was run through Finestructures clustering processing but it was unable to differentiate the remaining Scandinavians meaning it appeared by the software to be one population. However in the PCA plot it was possible to infer structure. As we so in the previous analysis the first two dimensions of the PCA plot appears to reflect level of external influences in Scandinavians. In both dimensions the Norwegians clustered in the upper left corner closest to the "others" while Swedes clustered in much of the lower right corner but with a huge spread over large part of the plot. The single Danish individual appear to cluster with the Norwegians.

PCA dimension 1(horizontal) and 2 (vertical)

Dimension 3 on the other hand appears to be internal between Norwegians and Swedes, below together with dimension 2 and seem to give a better clustering. The Danish individual still in the Norwegian cluster but closer to the Swedes.

PCA dimension 2(H) and 3 (V)

So the Chromopainter-Finestructure pipeline appears to be able to differentiate Norwegian and Swedish ancestry even only using 289k SNP's. The division isnt entirely clear cut but there have been populations movement between these countries for many centuries so the classification labels may not be entirely correct and some individuals also have mixed backgrounds.

Digging deeper in Fennoscandian ancestry I

I have been the last few months become more aware by the authors of Chromopainter-Finestructure that I have not been doing the analysis completely "according to book" even the software manuals have not being saying it explicitly.

I have from the start had this practice of running the Chromopainter-Finestructure analysis with the whole world panel and then later extracted from the output file the subdata from each run into a European panel and into a Fennoscandian panel for more detailed local analysis. However actually you should use the "superindividual" and "continent" functionality in Finestructure to get the analysis right and no file editing necessary and you also need to do a new ChromoCombine run with the forcefiles with these superindividuals.

I have been testing the difference using my earlier practice in the last standard run (this is NOT a new run!) data with these new settings to compare the results. It appears that after the advice from the authors its possible to extract even more information from the run with the current resolution than I was aware of even at Fennoscandiia level. I have in this reanalysis grouped all others than Fennoscandia into the superindividual "Others".

First the heatmaps. As we can see as before the heatmap identify a range of main clusters as before, some may notice that the numbers of identified clusters seem to be lower than from previous runs.

CC Fennoscandia 289k Aggregated

CC Fennoscandia 289k Raw

We then turn the attention to the PCA plots to see if we can infer more resolution than the standard heatmaps. As the superindividual "Others" contain much of the rest of the world it appears quite distant in both heatmap tree and the PCA. The "Other" group dominate the first 3 PCA dimensions as it appears far away from the Fennoscandia group in sum. The direction of "Others" are indicated on the plot.

PCA D1-D2 Fenno vs Others

PCA D1-D3 Fenno vs Others 

As I understand it these PCA D1-D3 reflect level of external influences on Fennoscandinans possibly from continental Europe as DK1 is closest "Others" in both dimensions. Scandinavians are closest to "others" on both dimension 1 and 2 while Finns and Saamis are closest "others" in dimension 3 especially FI18. In any way all these 3 dimensions can be used to differentiate Scandinavians vs Finns and Saamis. We had a similar dimension in the earlier local Fennoscandia analysis.

In dimension 4 we get a dimension that is able to differentiate Saamis from Finns and Scandinavians. We see North-Saami individuals at the extreme. If we combine this dimension with any other two dimensions we would get a plot differentiating Scandinavians, Finns and Saamis. Notice that we now also get a better grouping of the Finns.

PCA D1-D4 Fenno vs Others

At this point from previous analysis we would not get any more information using my earlier method, however using these new setting we can dig even deeper in the PCA plot. This can be shown below as we move to dimension 5.

As we can see below SWE7 a South-Saami individual clearly stand out in a own dimension separately from dimension 4 peaking in North-Saami. What this mean that using this new method the project can explicit differentiate South-Saami ancestry from North-Saami ancestry.

In earlier analysis the South-Saami ancestry appear to blend in somewhere between North-Saami and Scandinavians but as this show they are in a dimension of their own even they do share ancestry with North-Saami in dimension 4. However the North-Saami share very little of this South-Saami specific component but it appears far more common among other Fennoscandians both Scandinavians and even some Finns than the North-Saami specific component.

PCA D1-D5 Fenno vs Others 

This means that we can combine dimension 4 and 5 to map further explicit for Saami ancestry both North and South in Finns and Scandinavians.

PCA D4-D5 Fenno vs Others

There are more dimensions after dimension 5 but they appear to become more unclear and increasingly reflect individual variation. However dimension 6 (vertical axis) may be something worth looking at in the future as it appears populated with what seem to be western Finns, central Swedes and two Saamis depending on where you set the borderline.

 PCA D1-D6 Fenno vs Others 

CONCLUSION: This study shows that using superindividuals one can extract even more detailed ancestry information from autosomal genetic data within Fennoscandia. This new knowledge will be used in future project updates.

Saami ancestry and the MDLP Oracle-x Population Fitting

Update 08.10.2014: The MDLP calculators have been updated and now do not give the results as shown below. This post is then considered outdated and should not be used as guide vs the MDLP calculators.

This is a short test of MDLP Oracle-x Population Fitting at Gedmatch ability to catch Saami ancestry. Only MDLP calculators have been tested as these are the only one with Saami population reference.

As the test shows finding Saami ancestry using these calculators may give very different and even erroneous results (no Saami ancestry or minor Saami ancestry when there is actually major Saami ancestry) but one stand clearly out as the preferred choice. The "test subject" (with consent) is a North-Saami individual participating in the project with mostly Saami ancestry.


Absent = Saami ancestry not detected.
Minor = Saami ancestry detected but as minority ancestry.
Top but minor = Saami ancestry detected as top population but with less than 50%.
Top majority = Saami ancestry detected as top population with more than 50%.

As the result shows using MDLP K=5 Oracle X "Pct. Calc. Option 1" appears to be the preferred choice to detect Saami ancestry.

EDIT 20/9-13

Please note that all the other functionalities of the different versions of the MDLP calculators like Oracle and Oracle-4 was neither able to find that the Saami individual had majority Saami ancestry. Some where able to infer Saami minority ancestry and some didnt detect anything at all. The exception again is the MDLP K=5 that managed in Oracle to get a Saami population as number two and 3 of 4 in Oracle-4. Thie MDLP 27 calculator (not in Gedmatch) managed using Gaussian method 1 population mode to infer the correct population but failed in the 2,3 and 4 approximations.

La Braña 2 and modern European variation

This is a reanalysis of the La Braña's but this time separately. The La Braña 2 matched the 1000 genome reference panel with 56k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 56k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 26k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 21k SNP's.

The heatmap, tree structure and PCA plot below shows somewhat different result than for the La Braña 1 as La Braña 2 appears to have a position that cluster around with the Scandinavian-Saamis (individuals with both Scandinavian and Saami background).

This means that the original analysis of the composite La Braña need to be adjusted after the findings here. La Braña 2 appears most similar to individuals of mixed Scandinavian and Saami ancestry..

CC Euro unlinked 21k

 CC Euro unlinked 21k detailed 

 CC Euro unlinked 21k D1-D2

  CC Euro unlinked 21k D1-D3

EDIT: 20/9-13

Download BRA2 individual results

La Braña 1 and modern European variation.

This is a reanalysis of the La Braña's but this time separately. The La Braña 1 matched the 1000 genome reference panel with 129k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 129k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 47k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 38k SNP's.

The heatmap and tree structure below shows somewhat different result than for the composite La Braña individual consisting of both La Braña 1 and La Braña 2. As we can see the La Braña 1 do not completely cluster witht the Finns and Saamis anymore but appears to have a more intermediate position between the Saami-Finnish cluster and the Eastern European cluster.

CC Euro 47k unlinked La Braña 1

This is also reflected in the PCA D1-D2 (horisontal and vertical) where La Braña 1 appears to appear in the middle between the Finnish-Saami cluster and Eastern Europeans.

 CC Euro 47k unlinked La Braña 1 detailed 

CC Euro 47k PCA unlinked D1-D2

CC Euro 47k PCA unlinked D1-D3

The analysis of La Braña 2 will follow later

EDIT 23/9-13

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Ajv52 and European variation

EDIT: This analysis is outdated and have been reanalyzed here.

The Ajv52 like Ajv70 and Ire8 individual belonged to a 2800-2000 BC Pitted Ware Culture complex found in Ajvide, Gotland, Sweden. Ajv52 belonged to mtDNA hg V. The PWC was a hunter gatherer culture.

 The Ajv52 genome had in common 281k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for Ajv70, Ire8, Gok4, Ste7 and La Brañas (se earlier posts) imputed using BEAGLE with the same reference panel as before using both project individuals and public reference populations. The populations was further LD pruned in PLINK down to 77k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panel was extracted from a world Chromopainter run output files resulting in about 61k SNP's for Finestructure analysis. The high number of SNPs should give good resolution for further analysis.

The result seems mostly similar for Ajv52 as for Ajv70. In the above heatmap appears not to give a clear clustering to any modern European populations as Ajv52 doesnt fit into any heatbox clusters and branch out very early from the rest of the European tree, in other words no more systematic affiliation as we have seen in the analysis of the Ire8, Gok4, Ste7 and the La Brañas. There is however no doubt that Ajv52 belongs to the more northern populations in Europe if looking at the PCA plots below.

In the heatmap it seems like CR1, NO6 and NO7 appears to affliate strongest on the heatmap, this can however be the effect of these groups beeing of only one individual, but if looking at more systematic affiliation with larger samples one sees.some weaker affliation to northern and northeastern continental European populations and to south-west populations. So it might appear like Ajv52 may have some more southern ancestry than Ajv70 even they appear similar.On the PCA D1-D3 it seems Ajv52 cluster with Scandinavians but not in D1-D2.

CC Europe 61k unlinked

 CC Europe 61k unlinked detailed

CC Europe PCA 61k unlinked D1-D2

 CC Europe PCA 61k unlinked D1-D3

EDIT 20/9-13

Download individual results

Ajv70 and modern European variation

Edit: I now consider this analysis outdated please look at the updated analysis of Ajv70.

The Ajv70 like Ire8 individual belonged to a 2800-2000 BC Pitted Ware Culture complex found in Ajvide, Gotland, Sweden. Ajv70 belonged as Ire8 to mtDNA hg U4. The PWC was a hunter gatherer culture.

The Ajv70 genome had in common 421k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for Ire8, Gok4, Ste7 and La Brañas (se earlier posts) imputed using BEAGLE with the same reference panel as before using both project individuals and public reference populations. The populations was further LD pruned in PLINK down to 105k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panel was extracted from a world Chromopainter run output files resulting in about 85k SNP's for Finestructure analysis. The high number of SNPs should give good resolution for further analysis.

Ajv70 CC unlinked Europe 85k

Ajv70 CC unlinked Europe 85k

Ajv70 CC unlinked Europe 85k (changed color scale to emphasise more subtle differences)

The result for Ajv70 above heatmap appears not to give a clear clustering to any modern European populations as Ajv70 doesnt fit into any heatbox clusters and branch out very early from the rest of the European tree, in other words no more systematic affiliation as we have seen in the analysis of the Ire8, Gok4, Ste7 and the La Brañas. There is however no doubt that Ajv70 belongs to the more northern populations in Europe if looking at the PCA plots below..

Ajv70 CC PCA D1-D2 unlinked Europe 85k

As we can see from the main variation in thie first dimension D1 (horizontal) Ajv70 appears to cluster in the same middle area of the plot as many populations from especially northeastern continental Europe and some of the Scandinavians. The secondary dimension D2 (vertical) appears more difficult to explain. Ajv70 and one of the Saami SA2 appear alone on the upper part of the plot.but when moving further down the plot looking at the upper part of the major cluster not only other Saamis shows up but also some of the Vologda Russians, Mordovians, Belorussians, Bulgarians and Sardinians..The reason for this could be that there are individuals in continental Europe that to larger extent have Ajv70 like ancestry in this dimension than many other individuals of their own population. Scandinavians and Brits appears to show the most distant to Ajv70 in this dimension D2.

 Ajv70 CC PCA D1-D3 unlinked Europe 85k 

If looking further to dimension D3 (vertical) on the PCA plot above we get a more familiar plot also seen in other analysis. Here we can see Ajv70 appears to locate between the Scandinavians in the middle of the plot and Vologda Russians, Russians and Mordovians.

Conclusion: 

Ajv70 appears not to fit very well any specific modern European population but appears for certain northern, but at group level (infered from 289k analysis) from the heatmap colours Ajv70 appears to be somewhere between SA4, SWE-SAM,  AUS1, NO6 and EST.

This analysis also oppose the following claim about Ajv70 made by other genome bloggers:

"Prehistoric Scandinavians genetically most similar to modern Poles"

EDIT 23/9-13

Download individual results