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tirsdag 28. august 2012

New analysis of the ancient gotlanders vs modern European populations

EDIT 30/08-2013: I now consider this analysis outdated. Please check the more recent posts with reanalysis of Ajv52, Ajv70, Ire8, Gok4 and Ste7.

Its time for a new ancient gotlander analysis using 22k, this time using the same reference panel and individuals as in the 289k analysis. However as 22k SNP's is a rather small number of SNP's the resolutation is much smaller and we will see that populations blend more into each other. In addition the ancient gotlander also affect the analysis because of these individuals unique genetic variation.

We will first look at the individual chunkcount aggregated heatmap. Much is familiar from previous analysis. We see generally that the modern populations to less extent paint there chromosome with the ancient gotlanders than the ancient gotlander paint the chromosome with the modern populations. This is a sign that the ancient gotlanders and modern populations have very different haplotypes because of divergence in time and difference in genetics. If we included a single San individual from Africa in the analysis we would probably see the same.

In the PCA plots we see that the ancient gotlanders place themself in dimension 1-2 in between the Vologda Russians to the left, Lithuanians to the right, the Estonians to the upper right. This seems to indicate that the geographical close populations of Lithuanians and Vologda Russians.

However if we look at the ancient gotlanders position in dimension 1-3 we find the ancient gotlanders close to part of the Finns to the left and close below to one Saami SWE7 and a few Scandinavian-Saami mixed individuals. This make it difficult to explain the ancient gotlanders only in the context of Lithuanians and Vologda Russians. Also in lower dimensions the ancient gotlander is in its own space seperate from the modern populations suggesting it has variance not seen in any current populations.

As we can see the plots are much more fuzzy than in the analysis we have seen earlier using 289k SNP's so it is very possible that we see large variations at the individual level. If we average the number of chunkcounts we see a clearer picture of affiliation. We see here that the Saamis appear to show the largest affiliation on average as both donor and receiver to the ancient gotlanders.

If we try to see these distributions geographically we appear to see that the ancient gotlander appear to affiliate with the more remote parts of the continent while the more central continent with the exception of the French appear to be the most different from the ancient gotlanders.

We also see a strange and a very different affiliation between the Finnish groups. West-Finns appears to affilaite well while the East-Finns appears to affilaite very little even when close populations like Estonians, Vologda Russians and Saamis appear to show affiliation. At the time beeing I cant explain this difference.

As the map suggests below maybe there have been a later genetic expansion to the north from maybe more south-weas European contries that have changed the genetic landscape since the time of the ancient gotlanders especially to the south-south-east.

Other maps and plots

7 kommentarer:

  1. I think that the Pitted Ware peoples belonged to a migrant population from Eastern Europe but pre-Indoeuropean. They must have contributed to the genetic makeup of modern Swedes but are only one of the contributors and maybe the Megalithic Western Swedes were a more important pillar of modern Scandinavian makeup, of course later modified by Indoeuropean flows from Central Europe (ultimately originated in Eastern Europe but with many centuries of consolidation in Central Europe before the Corded Ware explosion).

    In this sense I'm not at all surprised by their Lithuanian/Vologda affinities but neither by the Finnic ones - after all the Finnic founder culture of Combed Ware is related to Pitted Ware even if not the same thing.

    I doubt that there has been any "recent" migration northwards from Italy (must be an artifact), however the Ukranian affinities make all sense because it was the Dniepr-Don culture which was at the origin of the Pitted Ware "forest neolithic" phenomenon. Later also Ukraine and the Don were a major intermediate region in the Westerly flows of Indoeuropeans.

    The Balcanic affinities may make sens in connection with the Balcano-Danubian Neolithic maybe. But these seem less obvious because there was no Danubian Neolithic as such in Scandinavia but at most tenuous influences.

  2. Maju: Wasnt the 5000 year old Scandinavian peasent analysed (Gok4) found to be similar to todays southern Europeans? In that context I suspect it may have *also* something to do with the agricultural migrations. Why French stand out like they do so close to the Italians I dont fully understand but maybe its trace of a western migration from Iberia to the north-east. Remember the image displays the ancient gotlanders view to the modern populations.

    1. Well, yes, Gok4 looks more southern than modern Scandinavians but modern Scandianvians look more Southern and therefore more Western than the Götland samples.

      French and other Europeans' position in the graphs (towards the center) is caused by oversampling of exotic NE Europeans like not just Finns and Saami but also Chuvash, who take over the dimensions. By contrast: mainstream Europeans make up the main cluster but lack the extremely marked "personality" of these groups.

  3. Maju: The heatmaps do not suffer from typical PCA problems like relatedness and samplesizes. The comparisment there is individual vs indivdual in a matrix. The problems you possibly could see there is proxying because of not enough diverse samples. Like f.ex if I only had French and Chinese, a Finn would cluster to the French even this individual is not French. So I recommend primary using heatmaps for any interference of ancestry.

    1. Hmmm... I have to say that the heatmaps usually leave me quite cold because populations always cluster with themselves and very close relatives (themselves again by another name) but the rest is almost invariably neutral and hence non-informative (or very very subtle).

      Also I'm not sure if heatmaps would render any connection with such a distant individual, considering that they only show up intense relatedness. If I read correctly the heatmap, this is the case here also.

      But not because the ancient Götlanders are not related in any way with the moderns but because the distance in time is superimposed to the distance in "space", so to say. Autosomal DNA is not preserved but it's recombined once and again and it's been more generations (roughly 300 generations) from those guys than from a random Italian (for example). In other words any modern day European has surely many common ancestors out of 300² with any other modern European and this is probably not so dense with the Götlanders of c. 6000 years ago (exact age? I forgot).

      But they still cluster in the PCA or Bayesian analysis, what is informative on its own merits.

      My opinion in any case.

    2. Erratum: "Autosomal DNA is not preserved"... should read "Autosomal DNA is not preserved in vivo"...

      Obviously it is sometimes preserved inside bone, hair, etc. but that's not what I meant; I meant in the "real life" sequence of generations, in which uniparental lineages are preserved much better instead.

    3. Actually I feel heatmaps are very informative. You can f.ex see that many of the Saami show strong affiliation both as donors and receivers, so do also some other groups. Also the large deviation in donor and receiver relationship tell that they are quite distant from modern populations but at the same time do show affiliation.