Friday, December 19, 2014

EEFs like Stuttgart had some WHG admixture

I'm surprised that I let this perhaps go over my head but upon browsing through the Eurogenes thread at Forumbiodiversity; it began to occur to me that that the Neolithic Near Eastern Farmers (NNEF) or what Lazaridis et al. calls "Early European Farmers" (EEF) likely have a certain amount of European Forgaer (EF) / WHG (Wester European Hunter-Gatherer) ancestry. 


I began to notice this for example in a Intra-West Eurasia PCA (Principal Component Analysis)/ cluster the author of Eurogenes (Polako/ Davidski) recently released:


Link to plot





Go to the plot and observe the general pull towards the principal components in this analysis; ENF ("Near Eastern" in a sense), ANE (Ancient North Eurasian) & WHG. 

Now, this plot is actually more aimed toward demonstrating what Polako discovers to be "ANE is the primary cause of west to east genetic differentiation across West Eurasia" [1]

Now, I've stated in the past (and I'm sure some of you if you know your way around European genetics) that Sardinians are the richest in the EEF/ NNEF component. So much so that in both Lazaridis & Gamba et al.'s PCAs for West Eurasia at large, Sardinians consistently overlap with/ cluster close to the Neolithic Near Eastern Farmers:


[2]


.


[3]

Now, I always wandered why the EEFs/ NNEFs never completely just clustered in the Middle East/ "Near Eastern" zone of the West Eurasian plot. If they were full-true-blue Middle Easterners-> especially ones with little to 0% ANE admixture; they actually shouldn't look so different from the Peninsula Arabian (Saudi, BedouinB) samples to their right. 

Nevertheless, they do and this is what I finally noticed and ever so slightly suspected the first time I observed the EEFs Lazaridis et al.'s plot a while back-> they have an undeniable pull toward the WHGs/ EFs. As a matter of fact; they straddle in-between the Peninsula Arabian samples and "unmixed" Hunter-Gatherers/ Foragers like Loschbour who is also a little bit more North of the other WHGs.

Some of the Bedouin samples likely only go more "Southward" because they have "African" admixture (East African + Niger-Congo) at a rate of about 10-15%~ (10 to 20%~ for Muslim Yemenites) [4] which pulls them away from Eurasians who tend to lack such admixture, their lack of ANE (or near lack) which seems to be present in Levantines, Turks, Iranians/ Persians and the like also pulls them more "Southward" away from where ANE stands at the top in that plot from Lazaridis, they also likely have more "Basal Eurasian" than WHG admixed Near Easterners like EEFs.

Loschbour & NNEFs like Stuttgart are also essentially 0% ANE, hence their southward pull away from MA-1 and the like.

 Side note: Though Saudis do show "African" admixture as well as would those BedouinB samples who overlap with the Saudi samples to right of the EEFs so I suppose it should be food for though that they have "African" admixture and still go about as North 0% (to practically/ almost 0%) ANE Sardinians & EEFs .

The thing is; Lazaridis et al. makes mention of there being WHG-like gene flow into farmers like Stuttgart:

"In SI10, we estimate that the proportion of Near Eastern ancestry in Stuttgart is definitely less than 100% and possibly as little as 61%. Further analyses of f4-statistics, however, show patterns that cannot all be explained by a history of Loschbour-related mixture."

I'd read the study but apparently let that part slip my attention. However they do note some clear non-Loschbour/ EF-like "West Eurasian" admixture.

I remember them mentioning that a component related to the ancestry in WHGs like Loschbour makes up a good amount of the ancestry in Stuttgart however I believed that to merely be "Middle Eastern West Eurasian" (MEWE) (and the end of that quote does imply this), as when you look at them at a basal level MEs seem to be "West Eurasian" + "Basal Eurasian" (whatever it might be) + "ANE" with some such as Peninsula Arabians lack ANE to only having perhaps small trace amounts of 1 to 2%~.


Lazaridis et al. claimed it couldn't test Peninsula Arabians for ANE due to their African admixture. They however spoke of releasing a new algorithm this holiday season for better identifying ANE in populations and I'll go into in more detail that in another blog post but the author of Eurogenes/ Polako/ Davidski essentially shares the results for Stuttgart using the best test we have for ANE & WHG admixture and the like:


Stuttgart (Neolithic)

ANE 0
Near_Eastern 72.19
East_Eurasian 0
WHG 27.8
Oceanian 0


It would seem to me that this is the best result we have so far and farmers like Stuttgart were relatively about 70%~ Near Eastern/ Middle Eastern in origin. They had to some extent by the time Stuttgart was alive; mixed with European Foragers. The result is also very similar to some of the most sensible estimates Lazaridis et al. comes up with for their Near Eastern admixture; as the author of Eurogenes makes note of.

I'm ashamed to say that I just recently noticed this but eh; life's a learning experience.



Reference List:

1. ANE is the primary cause of west to east genetic differentiation across West Eurasia, Eurogenes blog, Davidski/ Polako.  

2.  Genome flux and stasis in a five millennium transect of European prehistory, Gamba et al.

3. Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al.


Note:

The last paper is not focused at all on the subject at hand; it merely proves a decent enough reference for the "African" admixture in Peninsula Arabians (Yemenites of non"Jewish" origins, Qatari Arabs, Saudis etc.) which it disseminates into "Nilo-Saharan" & "Niger-Congo" for example K=13 or K=7 in its ADMIXTURE run (Light Blue & Dark blue components) or you can simply observe "West Asia" and then those Peninsula Arabian populations at K=2 where everyone's ancestry is looked at a Basal level for being either "Eurasian" or "African" ("European" & "Niger-Congo" being stand ins for those two usual K=2 "ancestral components").



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