Ajv52 and European variation II

This is a updated analysis of the previous Ajv52 analysis. In the previous analysis it was difficult to find any proper affiliation of the Ajv52 individual. The reason for seems now to be that I only did the mapping- and base quality filtering but not the additional filtering needed to remove what could be contamination. This would as suggested to me by the author of Skoglund 2012 make the ancient genomes appear more African like than they really were. So this time I followed the remaining contamination procedure except for gap filtering as this wasn't described in detail in the supplementary and I removed all positions with multiple reads (author randomly chosed one random if multiple). I also this time didn't do any LD prunning in PLINK as the authors of Chromopainter-Finestructure commented LD would be taken into consideration in the Chromopainter unlinked mode. I also grouped all individuals not of interest into superindividuals ("others") in Finestructure also as recommened by the Chromopainter-Finestructure authors. This analysis is therefore based on 261k SNP after contamination filtering.

As we can see below the Ajv52 have made an interesting clustering at large together with other groups of mixed Scandinavian and Saami or Finnish ancestry and in particular to the group of mixed Scandinavian-Saami ancestry (NOR-SAM). This is interesting if one sees this in light of my earlier Ire8 analysis (Ire8 will be reanalyzed using similar approach later) where Ire8 very clearly clustered with the Saami-Finnish group. If looking at the heatmap we can see that Ajv52 shows an increased affiliation to the Baltic populations compared to others in the larger group at the same time as Ajv52 shows increased affiliation to Saamis and Finns the Baltics continental Europeans and even Scandinavians doesn't have.

CC Europe Overview 261k SNP 

This suggest that Ire8 may have represented the receiving population of ancient Gotland who had similarity to modern day Saamis and Finns while Ajv52 may represent a mix with this population and a population migrating across from the Baltic region.

EDIT 9 Nov 13: have added individual results. I have added heatmap results both in haploid and diploid mode as the Ajv52 analysis is Chromopainter have been done in haploid mode (Ajv52 have only "homologus" data). Diploid mode have been made by using superindividuals.

In diploid mode we see that Ajv52 cluster with NO6, NO7 and SWE40. In haploid mode we see Ajv52 cluster with SWE40_A, SWE40_B, NO7_A, NO7_B, NO6_A, NO6_B, SWE7_A and SWE11_A. All these individuals are of mixed Scandinavian-Saami ancestry.

CC Europe Haploid 261k SNP

 CC Europe Diploid 261k SNP 

Edit 11 Nov 13: The PCA plot for dimension 4 and 5 clearly shows that Ajv52 have a shift toward Eastern Europe compared to Ajv70 who is in the Scandinavian cluster. See discussion about Ajv70 position on PCA vs heatmap in the Ajv70 post as it relates to Ajv52 as well.

CC Europe diploid D4-D5 261k SNP

Edit 19 Nov 13: Extended Overview of Ajv52's clustering with European populations. We still see that Ajv52 cluster with Scandinavian-Saami mixed ancestry individuals.

 CC Europe extended Overview 261k SNP