Another view of "steppe" ancestry-Pagani et al

Angela

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The long knives are out and the paper isn't even available yet. These aren't light weights we're talking about here. How can you "deconstruct" an analysis when you haven't even read their "proofs" yet?

Oh well, fun and games.

"A Pre-Existing Isolation by Distance Gradient in West Eurasia May Partly Account for the Observed “Steppe” Component in Europe

Luca Pagani, Lehti Saag, Anto Aasa, Flora Jay, Mait Metspalu

Estonian Biocentre, Riia 23b, 51010 Tartu,
Department of
Geography, University of Tartu, 51010 Tartu, Estonia;
LRI, Paris-Sud University, CNRS UMR 8623, Orsay, France

It has been proposed that modern European populations can be modelled, by and large, as a three-way mixture of Hunter-Gatherer, Anatolian Neolithic and Steppe components that took place after 6kya (Haak et al. 2015, Allentoft et al. 2015). Particularly the pre-existing Hunter-Gatherer are thought to have admixed with incoming Early Neolithic people from Anatolian and, subsequently, with people carrying a “Steppe” component from the East.
These people were likely bearing the so called Yamnaya and/or Corded-Ware cultures, and their initial impact of the European gene pool was estimated to be as high as 75% (Haak et al. 2015).

However ancient DNA samples from East European and Caucasian Hunter-Gatherers as well as from Early Iranian Neolithic, dating from before the Yamnaya expansion, already show signs of this so called “Steppe” component (Lazaridis et al. 2016). Such an observation is compatible with the presence of a pre-existing genetic gradient ranging from Caucasus/Iran all the way to Europe, which likely formed through isolation by distance over thousands of years.

Here we show that such a gradient, defined as decrease of “steppe” component with distance from Iran, can be inferred from ancient samples pre-dating the Yamnaya expansion (r^2 = 0.93).

When analysed in the light of this gradient, later ancient and modern samples from Europe still display an excess of Steppe component, however this excess is less pronounced than previously estimated. Additionally we found that, of the analysed samples, modern South Asians show the highest excess of “steppe” component, pointing to the documented, recent links between the Caucasus/Iran populations and the South Asian peninsula."


I don't know if what they're labeling as the "steppe" component is CHG. If it is, couldn't some of this excess CHG have been pre-existing in South Asia? Or perhaps they know something about South Asian ancient dna which hasn't been published.

I also wonder if they have some new "steppe" samples which have been analyzed.

They seem to also be linking this "steppe" component with Iran, which may be part of the reason that it has aroused such ire already.
 
Perhaps a new interpretation of old numbers.
 
they seem to be formulating in a very strange way :
modern European populations can be modelled, by and large, as a three-way mixture of Hunter-Gatherer, Anatolian Neolithic and Steppe components that took place after 6kya
this means 'steppe' = WHG or ANE, no ?
but in the next part 'steppe' seems to mean something slightly different
it's best to just await the paper to be published
 
To analyze Steppe impact on Middle East one has to find how much WHG and EHG is in Middle East today, or better at the end of Bronze Age. There was no WHG and EHG there beforehand. Then increase it by half to compensate for CHG/Iranian Neolithic which Steppe ancestry carried in about 1/3rd of their DNA.

By my estimation, impact of Steppe on Iran was at 13% of new population, but genetically (due to local DNA coming back) was about 10%, of new DNA.
 
There was a J "Caucasian" HG in Karelia about 6000 BC, and there are some slight signals of CHG component in some EHG, so that I suspected that there was a mesolithic migration northwards, but if this paper exposes that there is a simple geographic gradient it must be read.

I figure out that radical Yamnayists are angry with this possibility as the steppe exclusivity would fade out even more...
 
There was a J "Caucasian" HG in Karelia about 6000 BC, and there are some slight signals of CHG component in some EHG, so that I suspected that there was a mesolithic migration northwards, but if this paper exposes that there is a simple geographic gradient it must be read.

I figure out that radical Yamnayists are angry with this possibility as the steppe exclusivity would fade out even more...

That gradient however must be the result of migrations post-dating the glacial maximum. The Eastern European Epigravettian of the plains seems to have been completely terminated by adverse climate or something akin. During the Epigravettian the plains seem to have been seasonal hunting grounds. I'd think everything we find there in the Mesolithic must have arrived rather recently from Cetral & Western Asia and Europe.

The point that Mesolithic Eastern European material cultures generally have Iranian & Anatolian associations (when they aren't derived from Western Europe as is the case in Kunda and others) was already made by Sulimirski and more recently Semenov & Bulat (2016).
 
There was a J "Caucasian" HG in Karelia about 6000 BC, and there are some slight signals of CHG component in some EHG, so that I suspected that there was a mesolithic migration northwards, but if this paper exposes that there is a simple geographic gradient it must be read.

I figure out that radical Yamnayists are angry with this possibility as the steppe exclusivity would fade out even more...

The J wasn't Caucasian, it was autosomally EHG.

Radical Yamnayism. I like that. That's a punk band.
 
If I had to guess, they must be taking Baloch or some permutation of Iranian Neolithic to be "steppe".

Perhaps they already know what the Indus River genomes look like and they're Iranian Neolithic as well with the same "steppe" admixure.

This is really the only way they could fit such a model.
 
However ancient DNA samples from East European and Caucasian Hunter-Gatherers as well as from Early Iranian Neolithic, dating from before the Yamnaya expansion, already show signs of this so called “Steppe” component (Lazaridis et al. 2016).

Because the Yamnaya people were descended from East European and Caucasian Hunter-Gatherers.

Also what is located between North-East Europe and Caucasus? How is this region called? Ste... ???

What they basically say is that the "Steppe" component was in the Steppe already before Yamnaya.

=======================

Davidski's comments: http://eurogenes.blogspot.co.uk/2017/04/population-geneticists-often-not-very.html

(...) In any case, whether the authors relied on ADMIXTURE or not is immaterial to the fact that all of their main points are clearly wrong. Before I go through these points, and explain why they're wrong, I need to explain exactly what the Steppe component really is and isn't.

The Steppe component is the genetic structure of Early and Middle Bronze Age (EMBA) steppe pastoralist groups Afanasievo, Poltavka and Yamnaya. And it's a very specific thing. It isn't a component inferred from a random run of ADMIXTURE that peaks in Afanasievo, Poltavka and/or Yamnaya, or any other ancient populations.

So, Steppe component = Afanasievo, Poltavka and Yamnaya, or Steppe_EMBA. Nothing more, nothing less. Certainly nothing from outside of the steppe predating Afanasievo and Yamnaya.

Keep in mind also that Steppe_EMBA is a very specific mixture of older and contemporaneous populations. Using the formal-statistics-based qpAdm method, which models ancestry directly based on f4-statistics, Steppe_EMBA is probably best modeled as a mixture of Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), and Anatolia Chalcolithic (Anatolia_ChL), with ancestry proportions of around 0.453, 0.453 and 0.094, respectively. See here.

I believe that in this model Anatolia_ChL represents some type of minor western admixture amongst the close relatives of CHG still living in the Caucasus during the Eneolithic/Early Bronze Age, and/or minor gene flow from the Balkans onto the steppe. But that's a topic for another day, perhaps after the release of the Bell Beaker behemoth?

Below is a visual representation of the model, using a typical Principal Component Analysis (PCA) of Western Eurasian population structure. Note the tight cluster formed by the Steppe_EMBA groups and individuals, which is easily differentiated from all ancient populations outside of the steppe, except, importantly, Corded Ware.

https://4.bp.blogspot.com/--_ATkEG-...zy8AcQCLcB/s1600/Steppe_EMBA_visual_model.png

Steppe_EMBA_visual_model.png


Thus, considering that I know what the Steppe component is and isn't exactly, then I can try to test for admixture from it and its ancestral components as best I can using qpAdm. Below are results for a few pertinent ancient populations (no idea how to model the farmers from Early Neolithic Iran at this stage, but I've already underlined their unique genetic character here and have no reason to believe that they're responsible for any part of the Steppe_EMBA signal in Europe or South Asia). If you're wondering why I chose Hungary_HG as the potential Western Hunter-Gatherer source, it's because it provided the best statistical fits overall. Also note that Ukraine_HG/N is based on samples from the Pontic Steppe. (...)

From the Comments section:

If the gradient is from Iran (modern day?) then it sounds like they are relabeling steppe to be Iranian bronze age/CHG.

That makes no sense. The "Steppe" component is literally a designation for the people living on the steppe between the neolithic and bronze age. We have not found this component, (.5)EHG/(.5)CHG, anywhere prior to its existence on the steppe. This component has never been prominent in Iran so Iran cannot be a source for this "steppe" component. There is good indication that the "steppe" component developed locally since the steppe gradually went from EHG to (.75)EHG/(.25)EHG to (.5)EHG/(.5)CHG or "steppe" for shorthand. It makes sense that the "steppe" component would develop on the steppe since the steppe was at the border of EHG and CHG.

Now, it would not surprise me if the "steppe" component developed in other places like Romania or Belarus but it pretty much needs to be outside of the middle east and india since neither of these places have ever had sufficient EHG.

So the paper is misusing the term for the "steppe" component. I dont think laz' conclusion, which is that north europeans harber about 50% "steppe" which came directly from the steppe or near to it. What this paper might try to do is claim that there is a deeper source of population movements which started in Iran and that this population truly ties the indo europeans together. If that is what the authors are trying to prove then they should rewrite their abstract since it sounds like they are disputing laz' claim that north europeans have about half of their heritage come from bronze age steppe groups or close to them and south europeans have around a quarter of their ancestry from such groups.
 
Because the Yamnaya people were descended from East European and Caucasian Hunter-Gatherers.

Also what is located between North-East Europe and Caucasus? How is this region called? Ste... ???

What they basically say is that the "Steppe" component was in the Steppe already before Yamnaya.

It looks like what they call 'steppe' is Yamnaya purged of West Eurasian HG ancestry, hence the gradient with regard to proximity to Iran.

It's kind of confusing that terminology with clear geographic connotations comes to mean something else in every other paper, imho.
 
The J wasn't Caucasian, it was autosomally EHG.

Radical Yamnayism. I like that. That's a punk band.

J's originated in the Caucasus, so no matter if he was much or less CHG. Do you expect that J's apeared somewhere in the north?
 
And the R originated in India hence Indo-European language, the Rs brought the Indo to it.
Seems fairly logical
 
And the R originated in India hence Indo-European language, the Rs brought the Indo to it.
Seems fairly logical
You are ignorant beyond belief. Please go educate yourself in the subject before you open your mouth. And it goes equally for all the subjects you took part in. What you call logic is your crude assumption and beliefs.
 
Gypsies always believed they came from India even before the DNA research. Turns out they were actually right. Beliefs should not always get underestimated.
 
Gypsies always believed they came from India even before the DNA research. Turns out they were actually right. Beliefs should not always get underestimated.
What the heck migration of Gypsies in Middle Ages from India has to do with spread of IE over two continents during Bronze Age?!!!
 
Yeah this paper basically re-invented what "steppe" means, then published all these awesome conclusions about it.

This is actually pretty hilarious. I'm going to define Natufian as "European", then drop the bombshell paper. Watch out yo.
 
J's originated in the Caucasus, so no matter if he was much or less CHG. Do you expect that J's apeared somewhere in the north?

I think it's for the most part a CHG male line, but this line must have been in North Eurasia for a long time.
 
It would be a good study to see what CHG have different Js. By the way there was a north Eurasian refugium other than the Altai area?

Haplogroup_J_(Y-DNA)
 

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