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torsdag 20. juni 2013

La Braña and the Saamis II

EDIT 23/9-03. I now consider this analysis outdated. Please see the new individual analysis for La Braña 1 and La Braña 2.

In a earlier post I showed that the La Braña have variation that fit the common Saami-Finn Plink MDS based cluster. I have now again done the same analysis with the exact same populations and markers using a different method unlinked Chromopainter-Finestructure pipeline.

Finestructure PCA 68k
As we can see in the Finestructure PCA D1-D2 above the La Braña individuals also here do cluster with the Saami-Finns as in the Plink MDS analysis. If we further define superindividuals representing different population clusterings found in earlier 289k analysis we can see the La Braña also correctly located in the tree in the heatmap below.

Finestructure tree and heatmap 68k
However we do not still see a clear clustering of the La Braña to either Finns or Saamis. We see in the above that Finns actually split into two branches seperate from each other. This is probably due to the effect of different external influences included in this analysis as the La Braña have shown African minority admixture and Saamis and Finns have shown Siberian like minority admixture. If we take the 68k dataset from the earlier world analysis and extract from the output file the same European populations we used here we end up with ca 55k SNP and get a much better clusterings of both the Finns, Saamis and the La Braña.

Finestructure tree and heatmap 55k
By removing these it appears like the common component for Finns and for Saamis have been revealed and so the La Brãna now cluster with the population its closest to after removing external influences, the Saamis.

Other related posts in chronologial order, most recent first:

La Braña and modern World variation
La Braña and modern European variation
La Braña and the Saamis
La Braña individuals and the 1000G European populations

Edit 1: This is the same run as above but with all the Saamis (incl. SWE7) and Finns except "Finn-Sam" joined together in each group. NO6 and NO7 joined into "Nor-Sam".

Finestructure tree and heatmap 55k

Edit 2: This is the original run but the North-Saamis SA1-SA4 have been grouped and all Finns except Finn-Sami have been grouped. We now see that when taking into consideration external influences the La Braña move together with the South-Saamis (SWE7) and Scandinavians with Saami ancestry (both Scandinavians with North-Saami and South Saami ancestry). The North-Saamis (SA1-SA4) group with Finns and Finns with Saami ancestry when taking into account external influences. This make sense as North-Saamis and many Finns shows elevated Siberian like ancestry compared to SWE7 and other individuals of Scandinavian-Saami ancestry.

Finestructure tree and heatmap 68k
(Updated 22/6-2013)

torsdag 6. juni 2013

La Braña and modern World variation

The previous analysis of the La Brãna was based on a two dimensional MDS plot. In this analysis using a wider word-panel I will atempt to analyse them using the unlinked Chromopainter-Finestructure pipeline using what the Finestructure calls "superindividuals" and is similar to the "supervised" method used in ADMIXTURE. I used as before 68k unlinked SNPs in this analysis.

As we can see the substructures makes a lot of sense vs the previous analysis but more detailed. As we can see the La Braña is put into a larger branch containing Saamis, Finns, Vologda Russians and Mordovians. Further they are clustered into a subbranch shared only with Vologda Russians and Mordovians. I am not entirely sure why it has this branching as there is not doubt from the heatmap that there is huge sharing with the Finnish-Saami cluster.

What is different between the La Braña individuals vs the Saami-Finns is first of all the obvious larger African like minority admixture. Second we see smaller East-Asian, Siberian minority like admixture. Third we also seem to see smaller West-Asian influence.

In the more subtle it seems the La Braña shows affiliation to the Vologda Russians that the Saami-Finn group dont have possibly explaining some of the clustering. There is also appears to be affiliation to Basque and a Croat.

There also finally appears to be a larger asymmetry in the chromopaints received vs donated suggesting the affiliation between the groups is differentiated in time.

This also rise the question about where this common component seen in La Braña and the Saamis and Finns really come and what time the different infleunces from Africa and Asia arrived.