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 

Europeans and Native Americans

Updated 14/02/2014 with individual results PCA plots

This is a furter investigation of the previous posts about East-Asian influences in Europe. This time I have extended the earlier studies by adding Native Americans. The results appears as expected but also contain unexpected results.

The first dimension in this new Finestructure run we have seen before several times in the previous run and peak on one side among Northern Europeans and the other among South-East Asians and especially Papuans/Melanasians. It will not be discussed more here.

The second dimension (X-asis below) on the other hand clearly separate Europeans from Native Americans, Siberians and East-Asians. The third dimension separate on the other hand Native Americans from East-Asians with the Siberians between.

Dimension 2 (X-axis/horizontal) and 3 (Y-axis/vertical)

If we zoom on the European panel we see as expected that especially Saamis, Mordovians and Vologda Russians pulls left toward the common East-Asian, Siberian and Native American dimension 2. Note that Finns doesn't show the same level of pull towards left as the Saamis, Mordovians and Vologda Russians.

 Dimension 2 (X-axis/horizontal) and 3 (Y-axis/vertical) zoomed Europe

Individual results D2-D3 as above

However if looking at dimension 3 /(vertical) we clearly see Saamis and Finns pulling towards the Native Americans dimension at about same level of intensity. It appears to be lacking among Vologda Russians and Mordovians who pull toward the common East-Asian, Siberian and Native American dimension 2 (horizontal). This seem to suggest (also noted by commentators of this blog from ealier posts) that there is different influences from the East in Europe.

If we move on to dimension 4 (vertical, keeping dimension 2 at horizontal). This is the same dimension as seen in the usual European PCA plot regularly seen on this blog with the charactaristic "V" shape. This is the branch (top) with Finns and Saamis and with Sardinians and Basque at the root (bottom). As we can see Siberians, East-Asians and Native Americans appear to cluster consistent separately vertical along the "European" dimension. I would guess the informed reader would agree without much thought what we see on the top with Siberians being placed at the same level with Saamis and Finns at the upper part of vertical dimension in the plot.

  Dimension 2 (X-axis/horizontal) and 4 (Y-axis/vertical) zoomed Europe

Individual results D2-D4as above zommed into Europe

However if we move down to the middle we see the cluster of East-Asian group. If we from this vertical level move horizontally toward right we see that this "East-Asian" level actually end up with the Mordovians, Vologda Russians, Russians and many Lithuanians with other Eastern Europeans in close proximity. This clustering is also difficult to explain but its striking that the East-Asians appear to fix among at least certain Eastern Europeans given known history of the area.

If we move even further down we reach the Native Americans and if we move right from the vertical level of the Native Americans we will meet Southern European populations like Italians, Basque and Sardinians. This appears to me to a big surprise I find difficult to explain. I have been thinking the thought of post-1492 admixture among Native Americans but these samples have been screened for outside admixture before included in the analysis.

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Europeans, East-Asians and Africans

This is a continuation of the previous post where I investigated haplotype variation between Europeans, East-Asians and Siberians. This time investigate further by including Africans as it shed some more light on the haplotype variation seen between Europeans, East Asians and Siberians.

The first dimension is surprising as I would expect there to be greatest haplotype variation in the dataset The first dimension is not to my suprise between Africans and non-Africans but strangely enough Europeans cluster by themself peaking among northern Europeans while Africans appear to show similarity with the East-Asians. Notice here that the PCA distance between Africans and East-Asians appear rather small.

Dimension 1 - brown Finns/Saami - blue Africans

This gradient map appear strikingly similar to dimension 1 in the previous Euroasian analysis. My interpretation of this connection between Africans and East-Asians I believe is remnants of a Papuan or/and Melanasian like population among todays East-Asians. I have earlier suggested that Africans and Papuans/Melanasians still shows a genetic connection especially to San and Pygmyes from a earlier post suggesting that it was a San/Pygmy like population that first migrated along the southern coast in Asia..

The second dimension dimension is also surprising as it instead of showing African vs non-African variation instead shows a common African-European variation vs East Asians and Siberians.

Dimension 2 - brown - Africans/Europeans - blue - East Asians/Siberians

This gradient map also shows a very striking similarity to dimension 2 in the previous Euroasian analysis. As we can see here this dimension does not only seperate Europeans and East-Asians/Siberians but seperate Europeans-Africans from East-Asians-Siberians. I am very unsure about the interpretation but as dimension 1 it appear to be ancient.

These two dimensions can be summed up into two dimensions and as we can see this plot is identical to the PCA plot dimension 1 and 2 in a previous analysis investigating relationship between Europeans, East Asians and Siberians. This may sugggest that the previous indication of East-Asian ancestry among Southern Europeans may be due to shared Papuan-Melanasian ancestry among East-Asians.and Southern Europeans.

PCA Dimension 1 (horizontal) and 2 (vertical) Overview

 PCA Dimension 1 (horizontal) and 2 (vertical) Overview Europe

   PCA Dimension 1 (horizontal) and 2 (vertical) Overview Europe individual results 

The third dimension finally appear to be a true African vs non-African dimension. The PCA coordinate distance between Africans and non-Africans is very large and outside Africa the haplotype variation appears rather uniform in comparison suggesting a bottleneck or/and foundereffect after leaving Africa. The fact that this dimension first appear as number tree suggesting this variation to be less than the previous dimensions make the previous dimensions intriguing. Maybe its just the effect of oversampling from the European region or maybe its traces of ancient migrations or mixing from earlier than out of Africa events. 

 Dimension 3 - blue - Africans, brown - Non-Africans.

This maybe make dimension 2 and 3 best for investigation of African and East-Asian/Siberian minority ancestry among Europeans. As we can see Spanish and Sardinians appear to have the most African like minority admixture while Saamis, Mordovians and Vologda Russians shows the most East-Asian or Siberian admixture.

PCA Dimension 2 (horizontal) and 3 (vertical)

 PCA Dimension 2 (horizontal) and 3 (vertical) Europe Overview

European zoomed gradient maps:

Dimension 1 - Europe

 Dimension 2 - Europe (Note Saamis should be blue)

  Dimension 3 - Europe