Ajv70 and modern European variation II

Updated: 20 Nov 2013. This is a updated analysis of the previous Ajv70 analysis. See previous blogpost about the improvements. This analysis is based on 444k SNPs after all filtering (mostly imputed for all the modern populations, for Ajv70 all SNP are actuals).

Ajv70 appears different from Ajv52 who in the previous analysis appeared to be of mixed ancestry between what appeared to be a Saami like and a Baltic like or Eastern European like population. Ajv70 on the other hand in large cluster with Saamis, Vologda Russians and Mordovians and in particular with Saamis.

CC Euro Overview 444k SNP

As we can see the heatmap ancestry profile for Ajv70 and for the other close clustering groups seem resemble each other. Note that Mordovians and Vologda Russians doesnt cluster with Saamis and Finns in Chromopainter-Finestructure linked mode on the heatmaps but with Eastern Europeans. This is likely due to the linked mode reflect more recent ancestry and that the unlinked mode shows more ancient ancestry and Vologda Russians and Mordovians do seem to have more recent Eastern European admixture and in the past being part of the Finnic and Volga Finnic language area. This is seen both in linked and unlinked mode but probably weights more in linked mode than in the unlinked mode making them cluster with Eastern Europeans in the linked mode. The unlinked mode also give a lower resolution as its based only on allele frequencies adding to uncertainty.

The low affiliation for Ajv70 vs the Mediterranean populations on the heatmaps is only matched by Saamis and Finns among the modern populations. Finns appears more influenced by Eastern European populations and Scandinavians than the Ajv70 while Vologda Russians and Mordovians appears more influenced by Eastern European populations. Saamis show less affiliation to Scandinavians and Eastern Europeans than both Finns and Ajv70, but Ajv70 heatmap profile do seem to resemble the Saami most. 

The PCA dimensions dimension 4-5 showing internal European variation does not at first glance support the common heatmap clustering of Ajv70 vs Saamis, Vologda Russians and Mordovians as the Ajv70 appears among Scandinavians on the PCA and the Saami/Finns and Vologda Russians/Mordovians appear on very different locations on the PCA,  However the heatmaps neither indicate any Scandinavian like ancestry for Ajv70 even the individual's variation is plotted in this cluster. What could explain this seemingly contradictory result that Ajv70 resemble Saamis on the heatmap but not on the PCA is the fact that Ajv70 is not close in geneology to the populations it cluster closest with on the heatmap and that the Saamis, Finns, Mordovians and Vologda Russians are more dissimilar to "Others" and similar to "Others" than the others, however what this dissimilarity and similarity could be can be different..

CC Euro PCA 444k D4-D5

First about "not close in geneology". It can be best observed if we on a Europe PCA included related Orcadians and unrelated British. The Orcadians would form a clear outgroup on the PCA from the British even their ancestry profile on the heatmaps for the Orcadians wouldnt look much different from the British except for their internal sharing due to close relatedness and would else branch close to the unrelated British.

For the same reason Ajv70 would not cluster with Saamis and Finns on the PCA plot even they do cluster on the heatmap and else shows very similar profile with Finns and especially Saami. The explanation would therefore be that Ajv70 was not part in the founder effect that made the modern day Saamis and Finnish cluster due to closer relatedness to each other and therefore Ajv70 appears among the next best they could cluster with, the Scandinavians on the PCA plot (In earlier linked analysis Scandinavians shows both Saami and Finnish admixture) compared to continental Europeans so it would make sense.

Second about "dissimilarity" and "similarity" vs external influences or "Others". In dimension 1 and 2 vs the "Others" (the rest of the world panel) we seem to catch variation that could also explain why the Ajv70 heatmap clustering also include Mordovians and Vologda Russians even the European PCA dimension 4-5 do not support this clustering.

CC Euro PCA 444k D1-D2

This PCA plot describe the degree of similarity and dissimilarity vs the "Others". As we can see here Lithuanians, Scandinavians and many more form the upper left extreme and middle of the plot showing variation closest to the "Others" while the Saamis showing variation most distant to the "Others" in the lower right. The Ajv70 is within the range of the Saamis in this plot. There is also one Vologda Russian within this range too else the Vologda Russians and Mordovians is the next to follow up to the left after the Saamis and Ajv70. In PCA dimension 3 we also have a dimension where the Saamis, Vologda Russians, Mordovians and to some extent Finns is closest to the "Others" (not shown). The position on these dimensions can have have multiple explanations whatever each individual have been or been not influenced in various degree by the category "Others" and the very diverse panel included in this. So this means the dissimilarity for Saamis, Mordovians and Vologda Russians not necessarily is the same dissimilarity just more dissimilar than "Others" category, for example the Saamis probably pull high towards "Others" dimension 3 due to what appears as Siberian like minority ancestry while the Ajv70 who shows no such similar pull probably pull towards the "Others" because of what may be minority Afircan like ancestry (may also be erroneous affiliation due to contamination). This could affect the Finestructure tree clustering in unlinked mode giving adding Vologda Russians and Mordovians to the Saami, Finns and Ajv70 cluster.

Conclusion: Ajv70 appear to have the most similar heatmap profile to the Saamis but this individual do not seem to have been part of the same founder effect that made the higher genetic sharing between modern Saamis and Finns and therefore do not cluster together with the Finns and the Saamis on the PCA instead making Ajv70 cluster "incorrect" with their closest neighbors Scandinavians. Ajv70 neither show any significant degree of influence from the Baltic or Eastern European populations like Ajv52 who made Ajv52 appear to shift away into open space from Ajv70 position among Scandinavians closer to the Eastern European populations. The Ajv52's clustering with Scandinavian-Saami mixed individuals when adding some Baltic like admixture seem to further support that Ajv70 mostly resemble a Saami like population. Next it would make sense to check if Ire8 may have been part of the common modern Saami-Finns foundereffect. Earlier analysis may suggest it to certain degree.

Edit 19/11-13 broader overview with more European and Middle-Eastern populations. It is again very clear that Ajv70 cluster with Uralic or earlier Uralic populations and especially the Saami.

 CC Euro Overview extended 444k SNP 

Individual results:

CC Euro haploid 444k

CC Euro diploid 444k

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