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mandag 26. august 2013

Ajv70 and modern European variation

Edit: I now consider this analysis outdated please look at the updated analysis of Ajv70.

The Ajv70 like Ire8 individual belonged to a 2800-2000 BC Pitted Ware Culture complex found in Ajvide, Gotland, Sweden. Ajv70 belonged as Ire8 to mtDNA hg U4. The PWC was a hunter gatherer culture.

The Ajv70 genome had in common 421k SNPs vs the 1000 genome reference individuals. These was as with the earlier analysis for 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 105k SNPs and run through Chromopainter-Finestructure unlinked pipeline. The European panel was extracted from a world Chromopainter run output files resulting in about 85k SNP's for Finestructure analysis. The high number of SNPs should give good resolution for further analysis.

Ajv70 CC unlinked Europe 85k

Ajv70 CC unlinked Europe 85k

Ajv70 CC unlinked Europe 85k (changed color scale to emphasise more subtle differences)

The result for Ajv70 above heatmap appears not to give a clear clustering to any modern European populations as Ajv70 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 Ajv70 belongs to the more northern populations in Europe if looking at the PCA plots below..

Ajv70 CC PCA D1-D2 unlinked Europe 85k

As we can see from the main variation in thie first dimension D1 (horizontal) Ajv70 appears to cluster in the same middle area of the plot as many populations from especially northeastern continental Europe and some of the Scandinavians. The secondary dimension D2 (vertical) appears more difficult to explain. Ajv70 and one of the Saami SA2 appear alone on the upper part of the plot.but when moving further down the plot looking at the upper part of the major cluster not only other Saamis shows up but also some of the Vologda Russians, Mordovians, Belorussians, Bulgarians and Sardinians..The reason for this could be that there are individuals in continental Europe that to larger extent have Ajv70 like ancestry in this dimension than many other individuals of their own population. Scandinavians and Brits appears to show the most distant to Ajv70 in this dimension D2.

 Ajv70 CC PCA D1-D3 unlinked Europe 85k 

If looking further to dimension D3 (vertical) on the PCA plot above we get a more familiar plot also seen in other analysis. Here we can see Ajv70 appears to locate between the Scandinavians in the middle of the plot and Vologda Russians, Russians and Mordovians.


Ajv70 appears not to fit very well any specific modern European population but appears for certain northern, but at group level (infered from 289k analysis) from the heatmap colours Ajv70 appears to be somewhere between SA4, SWE-SAM,  AUS1, NO6 and EST.

This analysis also oppose the following claim about Ajv70 made by other genome bloggers:

"Prehistoric Scandinavians genetically most similar to modern Poles"

EDIT 23/9-13

Download individual results

5 kommentarer:

  1. In the first PC we see clearly where it sits, because it is near one of the positive extremes (PC2), which is defined by SA2, Bulg, Al1, Vrus... and is opposed by samples like NO1 and other Scandinavian and NW European.

    Instead it sits indifferent re. the PC1 ("Sardinianness", negative value: Finns) and PC3 ("Lithuanianness", negative values: Finns, Basques).

    So I think this sample clearly likes Eastern Europe: not in the Lithuanian way (PC3) but in a "deeper" Eastern way (Belarussians, Russian, Bulgarians, Finns): PC1. This corresponds well, I understand with the Dniepr-Don origin of Pitted Ware culture (via Belarus).

  2. Erratum: "in a "deeper" Eastern way (Belarussians, Russian, Bulgarians, Finns)" should read "(... Bulgarians, Saami)". Finns are clearly not like this individual.

  3. Maju: Your right but the affiliation is weak. The Ajv's genomes appears not to exist anymore in any complete form. The story is different for the La Brañas and Ire8, and also for farmers Gok4 and Ste7 who find quite much of their variation in existing populations.

    1. You know I do not trust ChromoPainter much. But, assuming it works, this Ajv70 guy shows up as relatively strong donor (purple) for a number of random individuals from the region. Also his (her?) own stronger donor is Aus1, whom I presume Austrian.

      I would expect relatively low intensities at such long time distance, rather than the strangely strong colors you got for some of the others (notably La Braña, who is not even from the region): it's hundreds of generations ago after all and at purely random dilution rates nothing at all would be detectable: it should be homeopathic dilution levels, unless it's being mixed it once and again with almost nothing but itself (endogamy).

    2. Maju: In the analysis of the other ancient genomes except the Ajv's they all fall quite natural into the cluster boxes and trees of the modern populations. This is not the case for the Ajv's. There is certain variation in the individual results vs individual results thats why I used the infered group-structure from the 289k linked analysis to get a better estimate and thats why somewhat question these groups consisting of single individuals affiliation.