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torsdag 29. august 2013

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EDIT: This analysis is outdated and have been reanalyzed here.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