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EDIT: This analysis is outdated and have been reanalyzed here.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

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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

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Ire8 and modern European variation

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

The Ire8 genome had in common 51k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for 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 22k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panal was extracted from a world Chromopainter run output files resulting in about 19k SNP's for Finestructure analysis.

As the results shows from Finestructure heatmap Ire8 appears to give an clear clustering to a commom Saami-Finnish box, and at the group level appears to be closest to SA1-SA2, Swe-Sam (equal) and Finns3. However we do not see a clear clustering as with the La Braña's vs the Saamis in the tree structure.

It seems from the heatmap coloring like Ire8 appears to have more southern  ancestry than both the Saamis and the Finns suggesting contact with early farmers.

CC Euro Ire8 unlinked 19k

CC Euro Ire8 unlinked detailed 19k

CC Euro PCA unlinked 19k

EDIT 23/9-13

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Gok4 and modern European variation

The Gok4 individual is as the earlier analysed Ste7 individual in the previous posts belonging to the Funnelbeaker culture finding in Gökhem, Sweden and the first farmers in Fennoscandia. Gok4 belonged to mtDNA haplogroup H. However the autosomal DNA coverage is for this ancient individual far better than for Ste7. I managed this time to match 294k SNPs vs the 1000 genome autosomal panel that I used to impute the missing markers for a standard selection of project participants and reference populations using phasing and imputation software Beagle. These was further LD pruned down to 76k in Plink to get a set of unlinked SNPs. The data was then run in Chromopainter-Finestructure pipeline unlinked mode using a world panel and then the European panel was extracted from the outpul files giving around 63k remainng SNPs for analysis.

As the results belows shows Gok4 appears to resemble quite much the earlier Ste7 individual. The strongest affiliation is with the Sardinians, then to Italians, Iberians, Albanians, Croat and Spanish. We also see an increased affiliation with populations in Central and Northern Europe like British, Scandinavians and Austrians. The most distant populations appears to be Saamis, Mordovians and Finns.

This appear to suggest some continuity between the first farmers of Fennoscandia and the modern Scandinavians. This was not seen in the earlier Ste7 analysis but may be due to the low number of markers (6k SNPs) giving high margin of error and possible partly different ancestry in Ste7 (possible Saami like or La Braña like ancestry). This analysis however has 63k SNP's used in the analysis comparable to the earlier La Braña of Northern Spain using 68k.

CC Euro Unlinked 63k

CC Euro Unlinked 63k detailed

CC Euro PCA Unlinked 63k (haploid individuals)

EDIT 23/9-13

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Ste7 and modern European variation

I have this time followed the same procedure as for the La Braña analysis and extracted in total 13k SNP's that matched the 1000 genome reference SNP's. I further imputed these markers to a panel of project participants and reference populations, and then linkage pruned these down in Plink to 7k SNP's. I then run the data through the unlinked Chromopainter-Finestructure pipeline editing out the European populations from the output file resulting in 6k of European panel SNPs.

Again because of the very small number of SNP's the inferred structure can be both noisy and inaccurate especially for the defined groups that consists of only one individual. I also again used the "superindividuals" functionality in Finestructure for all individuals except Ste7 based on earlier 289k SNP haplotype linked clustering.

The Ste7 individual was found in Funnelbeaker culture context in Gökheim, South Sweden and appears to represent the first farmers in Fennoscandia.

The result shows not unexpected that Ste7 shows strongest affiliations to Europe's more southern populations like especially Sardinians and Iberians, then Bulgarians, Albanians. Also some other close by populations shows stronger affiliations like Romanians, Hungarians, French, Austrian, Polish and Croat. Strangely neither the single Greek individual, Basque, Italians and Spanish shows any larger affiliation but this could be an artefact of the low resolution and large variation at individual level for the Greek individual but not for the Basque, Italians and Spanish overall.

CC Europe Unlinked 6k



Also Ste7 shows a surprising strong sharing to the two mixed Norwegian individuals with party Saami ancestry "NOR-SAM" and two of the North-Saami individuals "SA1-2" as the more Central-European populations. This link is not seen between the Saamis and the Central-European populations so it could reflect part ancestry with a more Saami or La Braña like populations. This finding could also be the result of large individual variation (error margin) due to the low resolution (only 6k SNPs).

Other populations that show less affiliation than the above of the more southern populations are Basque, Spanish and Italians. Further north the British, Germans, Danish, Finns and Scandinavians. Further east also Ukraine, Russians, Lithuanians, Mordovians and Vologda Russians shows less affiliation.

CC Europe Ste7 detailed

CC Europe Ste7 PCA D1-D2

Conclusion: It appears like Ste7 are mainly of southern European ancestry but may also have "local" or ancient ancestry (se La Braña posts) as there appears to be affiliation with part of the Saami samples as well.

EDIT 20/9-13

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La Braña and modern World variation II

I have done a new analysis of the La Braña, now using ADMIXTURE with only 4k SNP's (both LD pruned and MAF 0.05 filtered in PLINK) and over 2200 samples worldwide from different reference sets and because of the large sample size it was possible to increase the numbers of K up to 8. As a caution please remember that compared to earlier analysis the number of SNP's are very low and so the resolution is low and the individual variation large especially for the minority components compared to earlier analysis linked and unlinked, but by pooling individuals into populations this is to some extent made more even.

As we can see from the enclosed admixture bars the La Braña appears (given the considerations above) to have a very high level of North European like affiliation similar to the ones we see from the northernmost populations in Europe and is consistent with earlier analysis but ADMIXTURE is here not able to differentiate between them as Chromopainter-Finestructure did. The Middle-Eastern like admixture is close to 0 very different from the modern Iberian peninsula populations who reach levels up to 34%.

We further see that the Central Asian like admixture is close to zero similar to todays Iberian populations and Saamis (please note that the CA admixture in the Saami is due to only 1 individual, the rest shows close to 0 admixture), so is the affiliation to Siberians and Native Americans.

The implication of this result may be that large part of Europe was populated by hunter gatherers who mostly resembled todays North-Europeans and especially the Saamis. Later Middle-Eastern farmers moved westward and northwards. Their genetic impact was minimal in the fringe populations in the far north. Later Central-Asian like populations moved west from the east but their genetic impact was minimal in the Iberian populations and among Saamis in Fennoscandia. The Finns, Mordovians and especially the Saami on the other appears to have received considerable Siberian like admixture from the arctic.

First in alphabetical order:

Then in order of North-European (NE) admixture:

Then in order of Middle-East (ME) admixture:

Then in order of Central-Asian (CA) admixture:

Then in order of Siberian (SIB) admixture:

This ADMIXTURE study appears to show similartity to the study of Hughe 2011.