Correlating haplogroups with ancient admixture

I don't think this is significant. R1b for instance also spread quite evenly across large parts of Europe and still it happened recently.



Well, Sardinia has no ANE but it has WHG instead. Loschbour in Luxembourg had no ANE and was fully WHG. For me this is enough evidence to assume a rather late ANE dispersal to west and south. The higher ANE/WHG > 1 ratio elsewhere in southern europe can be explained by bronze age invaders, because these places 'coincidentally' are accompanied by late haplogroups like R1b and R1a for instance and speak indo-european languages. I'm correlating haplogroups here because ANE is rare in these places and R1b is recent, which makes it more significant.

Also your map shows the absolute ANE levels only, not the ANE/WHG ratio. I agree that WHG would show almost the same east-west gradient as ANE, but that's why I think the ANE/WHG ratio is so important and because of the overlap of both in NE europe.

I just looked at Shtudgard low Asian admixtures and I have to agree that most ANE had to be introduced much later than I thought.
WHG case is easy forward. They were just pushed up north by EEF and it is easily viasable in gradual decline towards south. It corresponds exactly with history of agriculture. WHG doesn't exist in appriciable quantities outside Europe. It was only in Europe, didn't go anywhere much, only slowly declined, and was replaced by EEF and ANE. Not much mistery here. Same easy story with EEF.
However ANE doesn't have a simple story to tell. Maybe because ANE is 24 thousand years old, and EEF and WHG is 7-8k old. Today I suspect that EEF ancestors from Middle East brought about 5% of ANE with them, plus there have been a slight level of ANE in Europe already, although not very well mixed yet. The rest came in few waves with IE and Hunnic tribes. I think only multiple source can explain distribution of ANE in Europe.


I would love to see ancient Latin DNA to check who they correspond to. Anyone have Kurdish WHG reading, or rather WHG in Kurdish DNA?
 
if I am reading the map correctly, the ANE light areas in Italy include part of the Etruscan speaking areas, and perhaps the Raetian speaking areas? .
You are right Angela. This map was quick (too quick) based on table from post 1, completed with my guesses and research from other sites with people posting their results and locations. It is more about ANE major trends than percentile precision. I'm sure with more data and time Maciamo will make a beautiful new map.

Overall many intriguing thoughts in your posts. And I agree that it is so hard to find IE using autosomal admixtures. If not lots of Y hg R1 and IE language it would be hard to know that they existed, lol.
 
Scotlands relative high ANE admixture combined with a relative high WHG admixture makes it an interesting place. The British isles were in contact with the mainland as recent as 10.000 years ago. Recently a map has been produced of so called Doggerland, the name of the middle North Sea area that was above sea level then.

http://www.nature.com/news/2008/080709/full/454151a.html?s=news_rss

In the North Sea mesolithic finds are found by fisherman, as that article states. North Scotland could have been a refuge of these people, like the Baltic.

Epoch, I think I read somewhere that the samples come from Argyle. Did that area experience a higher level of gene flow from Vikings/Norwegians, and could that explain part of the ANE in them. Of course, it's also only four people, so I don't know how representative they are for all of Scotland.
 
Anyone have Kurdish WHG reading, or rather WHG in Kurdish DNA?
This test was made for the Europeans or for the 'New World' people with the European ancestry.


My GEDmatch Eurogenes K13 Admixture Proportions:
North_Atlantic
2.30%
Baltic
3.21%
West_Med
7.71%
West_Asian
39.60%
East_Med
31.77%
Red_Sea
5.03%
South_Asian
8.50%
East_Asian
-
Siberian
1.01%
Amerindian
0.38%
Oceanian
-
Northeast_African
0.06%
Sub-Saharan
0.42%


My results of EEF/WHG/ANE:
EEF
91,55903
WHG
-0,66906
ANE
9,110035


Anatolian Kurdish average (n=10) : http://www.anthrogenica.com/showthread.php?1781-Post-Your-EEF-WHG-and-ANE-Admixture-Proportions :

EEF: 89.891057
WHG: 0.6981958
ANE: 9.4272976
 
Epoch, I think I read somewhere that the samples come from Argyle. Did that area experience a higher level of gene flow from Vikings/Norwegians, and could that explain part of the ANE in them. Of course, it's also only four people, so I don't know how representative they are for all of Scotland.

Argyll is West-Scotland. Parts of it have been part of the Norse kingdom once. The Orkney islands - inhabitants are Orcadians - has been known to be Norwegian settling grounds, and were also part of Norway once. They even spoke a Norse language called Norn.

http://en.wikipedia.org/wiki/Norn_language
http://en.wikipedia.org/wiki/Scandinavian_Scotland


Yet they have far less.


EEF WHG ANE
0.457 0.385 0.158 -- Orcadian

I have no idea how relevant this is, mind you. I would love to see more tested against this.
 
I just looked at Shtudgard low Asian admixtures and I have to agree that most ANE had to be introduced much later than I thought.
WHG case is easy forward. They were just pushed up north by EEF and it is easily viasable in gradual decline towards south. It corresponds exactly with history of agriculture. WHG doesn't exist in appriciable quantities outside Europe. It was only in Europe, didn't go anywhere much, only slowly declined, and was replaced by EEF and ANE. Not much mistery here. Same easy story with EEF.
However ANE doesn't have a simple story to tell. Maybe because ANE is 24 thousand years old, and EEF and WHG is 7-8k old. Today I suspect that EEF ancestors from Middle East brought about 5% of ANE with them, plus there have been a slight level of ANE in Europe already, although not very well mixed yet. The rest came in few waves with IE and Hunnic tribes. I think only multiple source can explain distribution of ANE in Europe.


I would love to see ancient Latin DNA to check who they correspond to. Anyone have Kurdish WHG reading, or rather WHG in Kurdish DNA?

I've thought that as well...that most of the WHG was pushed north and perhaps north east, despite the study that showed Mesolithic fishers inhabiting the same area as LBK people for about seventy years. That might have been an anomaly, or a late re-introduction. It just doesn't make sense to me that they would have done much more than replace their very small numbers until they adopted agriculture.

Somewhere on the net I saw a speculation that these HG's only started to expand in terms of population with Corded Ware, when they finally adopted agriculture. Might that be true, and would it explain why prior studies found that admixture between HG's and "farmers" didn't happen on a large scale for at least a thousand years? The WHG element could then have moved back into central and western Europe?

Believe me, no one wants to see ancient dna studies on "Etruscans" and "Romans" more than I do...I've been studying the ethnogenesis of Italians for years, and while some information has come out...there's still so much I don't understand. Actually, drawing conclusions from a totally sequenced Etruscan male might be easier to interpret than a "Roman" one, because depending on the area and era, the results might be quite different. Some early Empire landowner from the area of Lazio where the Flavians were born might be quite different from a landowner from the area and time of Livy...born in Cisalpine Gaul in approximately 60 B.C. although he was probably born in a Roman colony.

All I know for certain is that the phenotype snps must be extremely dominant, because there are tons of people walking around who look just like those old statues, lol.
 
Can you address this, sparky? If the results for I resembled those for R1a with respect to ANE, I think that would require different conclusions than one where the results for I seem fairly flat in all three graphs.

You guys aren't just seeing things. Without Sardinians, ANE has a much stronger correlation with Haplogroup I among the provided sample populations:

qqrx.png


That could indicate that the largest Haplogroup I expansions either expanded significantly into ANE carrying populations, or coincided with expansions of ANE. Germanic ANE/I1 and Slavic ANE/I2a-Din expansions perhaps? However, I don't think that it's entirely honest to simply drop Sardinians as insignificant outliers, as they show importantly that Haplogroup I expansions haven't necessarily coincided with ANE.

One difference I notice between (R1a, ANE) and (I, ANE) is that there is more of a sign in the (I, ANE) graph that the trend isn't increasing ever upward, but rather tailing off at the end. The Uralic speakers (Hungarians, Estonians) in particular form the right side of what looks like a Christmas tree pattern in the (I, ANE) graph. I suspect that continuing eastward into eastern Uralic populations would flatten the regression some more by completing the Christmas tree. I don't know if it would do the same for (R1a, ANE)... what are the R1a rates in eastern Uralic populations?
 
WHG case is easy forward. They were just pushed up north by EEF and it is easily viasable in gradual decline towards south. It corresponds exactly with history of agriculture. WHG doesn't exist in appriciable quantities outside Europe. It was only in Europe, didn't go anywhere much, only slowly declined, and was replaced by EEF and ANE. Not much mistery here. Same easy story with EEF.

I understand what you mean, LeBrok. But in large parts of Europe WHG survived in somewhat of one third of the gene pool; that is no small admixture. There is archeological evidence that hunter-gatherers lived alongside the farmers for two thousand years. They started to emulate agriculture - kept pigs - and were absorbed in the newer neolithic culture that emerged. Possibly these even had characteristics derived from the hunter-gatherers turned farmers.

If we assume that farmers had a slightly larger survival rate for children they grew faster in population size. That would mean that the later farmers arrived in a spot the larger the WHG admixture, only because the farmer population did not outgrow the WHG long enough. So possibly no need for a scenario where farmers kept pushing hunter-gatherers north. The latter simply kept doing what they did as long as the farmers stuck to the very fertile bits of Europe.


http://dienekes.blogspot.nl/2013/10/ancient-central-european-mtdna-across.html
 
Here is a map of WHG cline, straight South/North direction, in agreement with history of farming in Europe. Nothing much, EEF had outbred the WHG. Only Basque shows as anomaly. There will be few more but the resolution of this map is very low.

WHG map.jpg
 
Here is a map of WHG cline, straight South/North direction, in agreement with history of farming in Europe. Nothing much, EEF had outbred the WHG. Only Basque shows as anomaly. There will be few more but the resolution of this map is very low.

View attachment 6167

Thank you, LeBrok.
 
You guys aren't just seeing things. Without Sardinians, ANE has a much stronger correlation with Haplogroup I among the provided sample populations:

qqrx.png

So Sardinia skews the relation between I and ANE. That is odd. Y-DNA I starts to look mesolithic hunter-gatherer if we consider recent published samples. Y-DNA I2 is about of a third of Sardnia's Y-DNA, yet WHG admixture in Sardinia is absent. This does look like reversed Basques, who have large hunter-gatherer admixture yet seem to have an nonhunter-gatherer Y-DNA prevalence (R1b).
 
You guys aren't just seeing things. Without Sardinians, ANE has a much stronger correlation with Haplogroup I among the provided sample populations:

qqrx.png


That could indicate that the largest Haplogroup I expansions either expanded significantly into ANE carrying populations, or coincided with expansions of ANE. Germanic ANE/I1 and Slavic ANE/I2a-Din expansions perhaps? However, I don't think that it's entirely honest to simply drop Sardinians as insignificant outliers, as they show importantly that Haplogroup I expansions haven't necessarily coincided with ANE.

One difference I notice between (R1a, ANE) and (I, ANE) is that there is more of a sign in the (I, ANE) graph that the trend isn't increasing ever upward, but rather tailing off at the end. The Uralic speakers (Hungarians, Estonians) in particular form the right side of what looks like a Christmas tree pattern in the (I, ANE) graph. I suspect that continuing eastward into eastern Uralic populations would flatten the regression some more by completing the Christmas tree. I don't know if it would do the same for (R1a, ANE)... what are the R1a rates in eastern Uralic populations?

The fact that Sardinia is an outlier may just mean that ANE expanded into I territory without reaching one island. The flattening as you move east may mean that there was already ANE in the east but it later expanded into the west. Would that work? I also notice that Sardinia is the only place in Europe, other than Cyprus, that's all I2 but I don't think that means anything in terms of ANE, I think it just means that I1 expanded later than I2, which the contrasting ages of I1 and I2 already indicates - probably I1 came from the late I* found in mesolithic Scandinavia.
 
Ashkenazi case:
Ashkenazi_Jew EEF-0.931 WHG-0 ANE-0.069
2,000 years in Europe and they didn't pick any WHG?! Possibly they've isolated themselves very well as a community. From Old Testament we know that they were population isolates for a long time even before coming to Europe. In this case they might actually carry admixture proportions of First Neolithic Farmers from Fertile Crescent. At least how I see it, that first farmers brought first few percent ANE to Europe.

Still can't explain what happened in Sardinia to ANE. Maybe a small sample size?

Edit:
From Sparkey's table Sardinia shows ANE at 0.041, almost as much as I could expect early farmers to bring with them.
Extended Data Table 3 (from here http://arxiv.org/ftp/arxiv/papers/1312/1312.6639.pdf) shows ANE at 0.008, five times less.
 
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What I get out of this analysis is that ANE(R1a) and EEF have mixed relatively recently, as opposed to WHG who mixed with the farmers in the Neolithic. So in the late Neolithic WHG became farmers, and the only hunter-gatherers were the ANE. Obviously the lifestyles of hunter-gatherer and farmer do not co-exist well (if you're a farmer, the hunter-gatherer will come to gather your crops and be all surprised when you come to fight him). It might be that R1b+EEF pushed R1a further North-East in Eurasia, as farming expanded, then R1a made a comeback in the Metal-Ages and later with the Huns.
 
Somewhere on the net I saw a speculation that these HG's only started to expand in terms of population with Corded Ware, when they finally adopted agriculture. Might that be true, and would it explain why prior studies found that admixture between HG's and "farmers" didn't happen on a large scale for at least a thousand years? The WHG element could then have moved back into central and western Europe?
I would say so too. Only in Bronze age with development of bronze axe, the farmers were able to chop/de-wood heavy northern forests on industrial scale, clearing the land for white fields. Till then copper axe was too soft for the job. Also breeding new varieties of wheat, like rye, for northern climate was paramount for farmers to spread north successfully. The process was long enough to allow natives of I and R1a varieties to slowly adapt to farming, hence bigger proportions of WHG when going north.
The WHG element could then have moved back into central and western Europe?
Most population movements, that we know of, happened from North to South and West to East. We should conclude that these movements elevated WHG and ANE level somewhat. Deep South of Europe is at around 10% level of WHG, so how much was there before many invasions, 5%?

Fan with math:
Let's say population of Italy is 5 million at the end of Roman Empire (at 5% of WHG). Germanic tribes of 500 thousand people (WHG at 40%), invaded Italy. I think math goes like this: (5*10+0.5*40)/10.5=8.19% of WHG for all mixed population of Italy, giving enough time for mixing.
It is not an accurate example by no means, but it illustrates how numbers of WHG can go up every time there was an invasion from North or North East, and how much effort it would take to make a dent.

Believe me, no one wants to see ancient dna studies on "Etruscans" and "Romans" more than I do...I've been studying the ethnogenesis of Italians for years, and while some information has come out...there's still so much I don't understand. Actually, drawing conclusions from a totally sequenced Etruscan male might be easier to interpret than a "Roman" one, because depending on the area and era, the results might be quite different. Some early Empire landowner from the area of Lazio where the Flavians were born might be quite different from a landowner from the area and time of Livy...born in Cisalpine Gaul in approximately 60 B.C. although he was probably born in a Roman colony.
All I know for certain is that the phenotype snps must be extremely dominant, because there are tons of people walking around who look just like those old statues, lol.
I would look for ancient "Roman" village with any DNA to sequence, before the rise of the Rome. As long as the village could be identified as Latin, and older the better. Later people started mixing a lot to be sure of results.
 
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I would say so too. Only in Bronze age with development of bronze axe, the farmers were able to chop/de-wood heavy northern forests on industrial scale, clearing the land for white fields. Till then copper axe was too soft for the job. Also breeding new varieties of wheat, like rye, for northern climate was paramount for farmers to spread north successfully. The process was long enough to allow natives of I and R1a varieties to slowly adapt to farming, hence bigger proportions of WHG when going north.
Most population movements, that we know of, happened from North to South and West to East. We should conclude that these movements elevated WHG and ANE level somewhat. Deep South of Europe is at around 10% level of WHG, so how much was there before many invasions, 5%?

Fan with math:
Let's say population of Italy is 5 million at the end of Roman Empire (at 5% of WHG). Germanic tribes of 500 thousand people (WHG at 40%), invaded Italy. I think math goes like this: (5*10+0.5*40)/10.5=8.19% of WHG for all mixed population of Italy, giving enough time for mixing.
It is not an accurate example by no means, but it illustrates how numbers of WHG can go up every time there was an invasion from North or North East, and how much effort it would take to make a dent.


I would look for ancient "Roman" village with any DNA to sequence, before the rise of the Rome. As long as the village could be identified as Latin, and older the better. Later people started mixing a lot to be sure of results.


Those figures for the Ashkenazim don't seem to support very much admixture in central or eastern Europe with "European" women. I would have a hard time believing that the WHG component wasn't present in the Rhineland at the time of the Crusades at figures close to what they are today. If, and to what extent admixture occurred, it looks as if the majority of it would have had to have been admixture with Greek and/or southernItalian/Sicilian and and/or Balkan type populations of the Iron Age.

I'm getting confused with all of the data floating around...and accepting other people's statements without checking for myself, for which I apologize. Although the numbers for ANE are all close, Sicilians don't have the highest ANE of the Italian populations. It's actually the Tuscans, which means this is one of those situations where the components are not on the predicted cline. (I'll also correct the record on the original post.)

Here are the actual proportions for the ten tested populations:
EEF/WHG/ANE:

Bergamo: .715, .177, .108
Tuscan: .746, .136, .118
Sicilian: .903, 0, .097
Sardinians: .817, .175, .008

The virtual lack of ANE in Sardinians is striking, but in keeping with all the ADMIXTURE analyses run in the past on them which show no "West Asian". At the same time, the WHG is as high as Bergamo, or about 18%. The question for me is, were there WHG's on the island who were absorbed by incoming EEF (who, of course, like all EEF people, also carry another hidden 20% or so WHG?) or did it arrive later. Jean Manco is on record as saying that there were no actual H/G settlements on the island, and the few traces found were transitory camp sites. She then proposes that the yDNA I2a and E1b1b on the island comes from young clades that arrived from the Balkans in the Copper Age. You guys would know more about the yDNA than I do, but if it did come from the Balkans from the period after the collapse of "Old Europe" and the movement into the area of Indo-European speaking steppe people, shouldn't they also have carried some ANE into Sardinia? Not even mentioning they'd bring some sort of PIE. I'm going to have to research the dates for these movements. Another possibility is that it came by way of Spain and then the southern French coast. There is another very old yDNA 12a strain in western Europe, and E1b1b was also found, of course. Also, from the northern Mediterranean into Sardinia is far easier than approaching it from the east.

As for when I2a became involved with agriculture and admixed with the EEF people, I think one good bet would be the Balkans. There was a paper that found evidence that there was admixture between the female EEF and the male HG/s within a couple of generations. Perhaps some of the I2a H/G's returned the complement and became part of the farming community. This wouldn't have impacted any H/G YDNA I further north for a long time.

I can't wait until we get the results from the Bean project. They're studying not only the Mesolithic but also the Neolithic peoples of both the Balkans and Anatolia. I'm very interested to see how different the people in Thessaly, for example, could have been from the people in NW Anatolia. I do hope they're also testing people from further east in Anatolia, near the Zagros mountains, and also down the coast a bit to northern Syria.

Perhaps we'll be surprised and there is another HG group which has to be taken into consideration. A study by a Greek academic, which was posted by Dienekes, shows no mtdna U whatsoever, not even in the Mesolithic samples. And the mtDNA she found is what we have become accustomed to call "European" or at least "Neolithic" dna: J1b, H, lots of K, and even X. What will that do to all of our calculations?

And, will we find that the EEF population didn't mostly come from the Near East or the very southern Levant, as we all have been postulating, but came from southern and south eastern European Mesolithic populations with only a small input from further south or east. Or, as another possibility, as Hunter Gatherers from Siberia to the gates of Europe weren't that different from one another, as the AF finds may show, perhaps the HGs, soon to be farmers of the European southeast, were not very different from the people in Anatolia. Who knows...I'm sure it will be a surprise.

One final thought before I fall asleep over the computer...the Bollingino study that was cited above made some pretty broad claims based on one incidence of HG's and EEF sharing time and space in central Europe. I don't know if that finding can be extrapolated to the situation over all of Europe, i.e. that there were a lot of HG's who remained basically in place, tending to their fishing and ignoring the farmers tilling the good loess soils. Actually, they were'nt totally ignoring each other. The mtDNA data doesn't show any EEF females being absorbed into the HG community, but a good number of the WHG mtDNA lines did show up among the members of the Neolithic farming community. So, it's those U mtDNA signatures that show that admixture was indeed taking place.

The big question is, what was the Y signature of these EEF men...G2a, and some I2a, doubtless, and if they were happily outbreeding all the HG males, you would have a big increase in G2a for example. So what happened? Are R1b and R1a, ANE carriers for the sake of the argument, responsible for the decrease in the EEF males lineages? They certainly didn't replace the autosomal make-up of these people however. I read somewhere that the median in Europe is over 56 for EEF.

And here I was thinking that some good ancient DNA would clear everything up? LOL
 
Here are the actual proportions for the ten tested populations:
EEF/WHG/ANE:

Bergamo: .715, .177, .108
Tuscan: .746, .136, .118
Sicilian: .903, 0, .097
Sardinians: .817, .175, .008

Sicilian 0 of WHG doesn't make sense. Please give me at least 0.001 lol. What happened to WHG from Greeks, Romans, Vandal, or even some tourists from North who settled there. Are you sure sampling wasn't from one village only? (My comical rant and a question are towards scientists of the paper not to you personally)
Sardinian ANE is also suspicious, it should be at least 0.04, and Ashkenazi WHG is ridiculous, at least 0.002 should be more appropriate. We should wait for more samples.

As for when I2a became involved with agriculture and admixed with the EEF people, I think one good bet would be the Balkans. There was a paper that found evidence that there was admixture between the female EEF and the male HG/s within a couple of generations. Perhaps some of the I2a H/G's returned the complement and became part of the farming community. This wouldn't have impacted any H/G YDNA I further north for a long time.

I can't wait until we get the results from the Bean project. They're studying not only the Mesolithic but also the Neolithic peoples of both the Balkans and Anatolia. I'm very interested to see how different the people in Thessaly, for example, could have been from the people in NW Anatolia. I do hope they're also testing people from further east in Anatolia, near the Zagros mountains, and also down the coast a bit to northern Syria.

Perhaps we'll be surprised and there is another HG group which has to be taken into consideration. A study by a Greek academic, which was posted by Dienekes, shows no mtdna U whatsoever, not even in the Mesolithic samples. And the mtDNA she found is what we have become accustomed to call "European" or at least "Neolithic" dna: J1b, H, lots of K, and even X. What will that do to all of our calculations?

And, will we find that the EEF population didn't mostly come from the Near East or the very southern Levant, as we all have been postulating, but came from southern and south eastern European Mesolithic populations with only a small input from further south or east. Or, as another possibility, as Hunter Gatherers from Siberia to the gates of Europe weren't that different from one another, as the AF finds may show, perhaps the HGs, soon to be farmers of the European southeast, were not very different from the people in Anatolia. Who knows...I'm sure it will be a surprise.

One final thought before I fall asleep over the computer...the Bollingino study that was cited above made some pretty broad claims based on one incidence of HG's and EEF sharing time and space in central Europe. I don't know if that finding can be extrapolated to the situation over all of Europe, i.e. that there were a lot of HG's who remained basically in place, tending to their fishing and ignoring the farmers tilling the good loess soils. Actually, they were'nt totally ignoring each other. The mtDNA data doesn't show any EEF females being absorbed into the HG community, but a good number of the WHG mtDNA lines did show up among the members of the Neolithic farming community. So, it's those U mtDNA signatures that show that admixture was indeed taking place.

The big question is, what was the Y signature of these EEF men...G2a, and some I2a, doubtless, and if they were happily outbreeding all the HG males, you would have a big increase in G2a for example. So what happened? Are R1b and R1a, ANE carriers for the sake of the argument, responsible for the decrease in the EEF males lineages? They certainly didn't replace the autosomal make-up of these people however. I read somewhere that the median in Europe is over 56 for EEF.

And here I was thinking that some good ancient DNA would clear everything up? LOL
Denm ancestors kept moving around too much, lol.

All great inquiries Angela, I can't wait either. From now on I'm going to vote for politicians who promise more genetic tests of ancient DNA, lol.
 

This test was made for the Europeans or for the 'New World' people with the European ancestry.


My GEDmatch Eurogenes K13 Admixture Proportions:
North_Atlantic2.30%
Baltic3.21%
West_Med7.71%
West_Asian39.60%
East_Med31.77%
Red_Sea5.03%
South_Asian8.50%
East_Asian-
Siberian1.01%
Amerindian0.38%
Oceanian-
Northeast_African0.06%
Sub-Saharan0.42%


My results of EEF/WHG/ANE:
EEF91,55903
WHG-0,66906
ANE9,110035


Anatolian Kurdish average (n=10) : http://www.anthrogenica.com/showthread.php?1781-Post-Your-EEF-WHG-and-ANE-Admixture-Proportions :

EEF: 89.891057
WHG: 0.6981958
ANE: 9.4272976

Wow, that's much lower than I expected for WHG, and ANE not high either. I wonder if the calculator is doing the job right. If I understood correctly, in original paper, scientists used comparable statistics of whole (all they could sequence) genomes of Stuttgart, Loschbour and MA1 (mal'ta boy?). On other hand we amateurs use K13 for calculating admixtures, and from this 3 ancestral groups. It is a shortcut and contains inaccuracies, especially for some populations. Someone correct me if I'm wrong.
 
I don't see a problem of WHG being wholly transferable from hg I giving the long timescale from LGM or at least all neolithic. Same way that blond hair was transferred from original population to Baltic area across many haplogroups and cultures. At the time of Bronze Age Corded Ware, WHG admixture could have been spread very far into eastern Europe infiltrating R1a.
It is still plausible that transfer happened later from Bronze Age till current times. From native population to R1a/Corded Ware newcomers. 5k years it is not such short time to make it impossible. I just think it is less likely though, because newcomers were farmers and as such they outnumbered local H-Gs 10 to 1. The WHG signal would have dropped to 10%, same as it happened in south Europe in presence of EEF.
I think Corded Ware period was the time when finally H-Gs of North-East became successful farmers, both R1a and I at the same time. That's why WHG admixture survived in substantial level.
Other reason why R1a already contained WHG is that otherwise they would have to contain only EEF+ANE before Corded Ware. I'm not sure how EEF could have gotten to R1a area circumventing WHGs?

I looked at the table again and to my understanding ANE has to be very ancient all over the europe, so old that it transcends all the haplogroups. It is very evenly spread all over europe with slight gradient from east to west, and this denotes a very ancient event. It might be so ancient that EEF had ANE at 10% already before they arrived. Therefore EEF didn't change much of ANE level in south Europe. Eastern Europe is more elevated with ANE from later migrations of steppe tribes.

LeBrok
For a comprehensive analysis it can be very simplistic that hunter-gatherers in the Europe, Balkans and beyond could not learn and take knowledge from the early farmers. On another topic, you gave an example of contact of cultures of Europeans and Indians in America, but letting the opportunity to not always be such a scenario. In other words, the native populations of hunter-gatherers (most likely I carriers maybe plus R) could also learn agriculture. It is quite possible. Take for example the Vinca culture on the territory of Serbia. It was culture of farmers and hunter-gatherers (and they also had domestic animals). In any case such a scenario would be possible, then the percentages are quite different.
 
Are R1b and R1a, ANE carriers for the sake of the argument, responsible for the decrease in the EEF males lineages? They certainly didn't replace the autosomal make-up of these people however.

I see no reason to assume that ANE carriers did not carry EEF. I personally think that many IE-tribes were slightly more EEF than anything, similar to old-europe average, except they had more ANE than WHG. I also think like you that West Asian admixture is strongly related to ANE. This makeup fits well to the north Caucasus region before the Russian colonization. (One possible wild guess could be 50%EEF+40%ANE+10%WHG, or in Admixture terms aproximately: 40% Atlantic_Med, 40% North_European, 20% West_Asian).

I don't understand how one can claim that Bronze age invaders did not alter the autosomal admixture. Check almost every important admixture run around, for instance the most recent one from the paper. Check out the light yellow color from K=14..20 which peaks in all Caucasus peoples (Georgians, Lezgins, Chechens, Abkhazians,...) and you'll see that it occurs in all european countries except Basques and Sardinians. But this is no news actually as K12b for instance was telling basically the same for some time already.

The inconsistencies are minimal: The R1b in Basques is a big inconsistency for a long time already, but I think they have been impacted only partially by the invaders, namely by the male Y-line only but not maternal (see their high U5 frequency), such that their autosomal has been changed much less than surrounding peoples and the mothers kept speaking Basque. K12b still showed Gedrosian in them, while Lazaridis et al Admixture runs show no West Asian at all. I think this incompletely appearing West Asian signal in Basques could be the hint for their weaker yet non-zero Bronze-age impression. The Finns and Saami do have some West Asian like other Volga-Ural peoples, but it must come from an aboriginal non-IE source (from more 'pure' ANE-hunter-gathers) because they are so low in EEF.

And any West_Asian admixture was completely absent in paleolithic and neolithic finds so far, except Ötzi showed 20% in K12b where even Sardinians showed 20%. If K12b was not too oversensitive here, it might indicate that very very tiny part West_Asian was present in some neolithic peoples already.
 

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