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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 I now consider this analysis outdated.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)

6 kommentarer:

  1. Anders how do you explain the fact that Latvians and Lithuanians who are supposed to have a lot of Mesolithic ancestry barely score much at all in the North-European-Mesolithic component that both La Brana and the Saami score so high in for the MDLP World-22 analysis that Vadim Verenich carried out? Latvians and Lithuanians only seem to score about 3% on average in this component while the La Brana samples are dominated completely by it and both the Saami and Finns core quite high for it. British people even seem to score more than Latvians and Lithuanians in the North-European-Mesolithic component. Maybe this is more of a West European type of Mesolithic ancestry while Latvians and Lithuanians have an Eastern type?

  2. Devoni: I suspect its because they are located on the European Mainland. Saamis and Finns have remained isolated on the Fennoscandian peninsula.

    It is also possible that the Lithuanians represent another Source, but I have seen that Vadim Verenich have done some comparisment and the ancient Iberians and the ancient Gotlanders appears very similar.

  3. How can you explain that British people score more than Lithuanians in the North-European-Mesolithic component for MDLP World-22 analysisÉ

  4. It may be the same reason. Brits live on an island, not on continental Europe.

  5. Ahhh okay thank you for the answers. This is my last question then about this. What do you think the North-European-Mesolithic component from the MDLP World-22 analysis represents then? Exactly what type of ancestry does it represent? Western European Mesolithic ancestry?

  6. If it is the same as for my La Braña analysis it obviously appear today to be most common among Saamis and Finns, and rather absent in the modern populations of Western Europe today. Its seen among the La Braña 7000 years ago so it seems it was there at that time. Of course nothing is 100% certain but it seems this may be one source. My recent Ajv70 and Ajv52 from PWC culture on Gotland doesnt appear to suggest similar ancestry as the La Braña and Ire8.