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tirsdag 18. februar 2014

La Braña 1 diploid genome vs Europeans first look

I finally got my hand on the latest La Brána 1 diploig genotype from the Iñigo Olalde et al.2014 paper. In previous analysis of the La Braña 1 and other ancient genomes they have only been the available in a "haploid" state meaning that it has not been possible to phase it and analyze using high resolution linked haplotype based models but instead using only unlinked single SNP models. I also had to "haploidize" all the other indnviduals I compared him with both in Chromopainter-Finestructure, ADMIXTURE or in Plink runs. It could possibly have affected the analysis as this seem to show at least for the La Braña 1 part.

I initially used a 1.1 mill SNP diploid La Braña 1 genotype and of these to 54k SNP matched by current 289k standard panel used in most of the project standard runs. I further LD pruned in PLINK down to 25k and run in PLINK's own MDS plotting function. It gave the following very familiar "V" shape with Saamis and Finns at one branch and Vologda Russians, Mordovians and Lithuanians on the other branch.

Please note this is a preliminary analysis and not the state of the art analysis but as we can see from the positioning the La Braña 1 without much doubt cluster with Saamis and Finns in dimension 1 (horizontal) and 2 (vertical) but not in dimension 3 where Scandinavians and Lithuanians cluster closest.

My first impression is that it is North Saamis and Eastern or Northern Finns who cluster closest in these two first dimensions but not in dimension 3 where they cluster closest with Scandinavians and Lithuanians but the distance appears huge. It may suggest that the La Braña 1 have a variation in this dimension that very much dissappeared but still exists to some extent among Scandinavians and Lithuanians.

The haplotype based analysis that will for certain come later will be able to give a better image of clustering.. The La Braña 1 individual will be included in all future Chromopainter-Finestructure haplotype based analysis and very probably the 24 000 year old individual from Siberia as well.

La Braña 1 diploid genome 25k Plink MDS D1-D2

 La Braña 1 diploid genome 25k Plink MDS D1-D3

If assuming that this position also will be at this location in the future Chromopainter-Finestructure haplotype analysis (as seen in the last run)we may get an idea of what have happening genetically speaking in Europe since 7000 year before present. Please note that the below is not made from the above MDS run but from a earlier Chromopainter-Finestructure run.

Dimension 1 - Agricultural expansion

Dimension 2 - Expansion from the East

 Dimension 3 - Expansion from Northern and Southern edges

Individual results D1-D2
 Individual results D1-D3 

5 kommentarer:

  1. Now that is something.

    Dimension 2 does seem to correspond to the theories of kurgan-style expansions from Eastern Europe.

  2. Dimension 3 is also pretty strong in Vologda Russians who should be very affected by population movements from north.

    Maybe it shows some small variation in La Brana that was reduced in Finland because of founder effect, and doesn't exist in South Europeans like Italians and Sardinians?

    1. It could be that there have been movements later that in time have somehow "diluted" the Vologda Russians in this dimension.

      Anonym wrote:

      "Maybe it shows some small variation in La Brana that was reduced in Finland because of founder effect, and doesn't exist in South Europeans like Italians and Sardinians?

    2. Perhaps.

      Just wondering about the founder effect/bottleneck factor being a possibility in dimension 3, because Olalde et al. also had a PCA where especially late settlement finns looked as distant as Sardinians from La Brana over one dimension.

  3. If Dimension 2 is showing some kind of expansion from Pontic (IE or take your pick of theory), then that makes me wonder if Saami/Finns once lived further south and were pushed out to the margins over time.

    What is the thinking on prior Saami range? Were they living in more temperate areas of the North/Central Europe in the past but were gradually marginalized - in the same way !San were pushed out into the less habitable Kalahari Desert?