Modern populations and neolithic farmers?

joeyc said:

Eurogenes ANE K7. You can find the spreadsheet on Polako's blog.

Have you got those results from Gedmatch? If yes they are wrong and you should use the software from Dodecad.

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Angela said:

I'm sorry to revive an old thread, but questions were raised once again in the ancient British genomes threads about the three ancestral populations of Europe. I think to get into a detailed discussion there about this topic would have been hijacking those threads, so I am posting my thoughts here.

Questions concerning the amount of "WHG" in EEF keep being asked and again. For suggesting that it is a distraction in terms of the discussion of the peopling of Europe, a respected, published author has been attacked on another forum.

I will here speak only for myself. I get the distinct feeling at times that this obsession with quantifying the amount of "WHG" in EEF may, in some people, stem from an attempt to nail down exactly how "European" a group or a person is by taking that figure and adding it to the "regular" WHG in the figures given for modern populations in Lazaridis et al. Apparently, ANE is considered "European" enough not to raise concern, despite its eastern affinities. The short answer is that we are all 100% European, whether we come from France, or Finland, or southern Italy, and whether we can be modeled best with two or three of these ancestral EEF/WHG/ANE populations.

That undertone also is present, imo, in many of these discussions about how much hunter-gatherer is present in groups or individuals. This reflects a fundamental misunderstanding of human history. Everyone is 100% descended from hunter-gatherers as I've said repeatedly on many threads for many years, because all of those groups, Basal Eurasian, UHG, WHG, ANE, and all the others were hunter gatherers before they learned how to farm.

It seems to me that some people obsessed with these questions (of course, not those who merely seek to understand the issues), who are constantly, to use a phrase I'd like to borrow, "massaging" the data through calculators etc. are merely concerned with minimizing, as much as possible, any "Near Eastern" element in them or their groups.

I'm afraid that like it or not, most of EEF was Near Eastern.

Since apparently people forget it, here is the appropriate excerpt, I think, from Lazaridis et al.

"The amount of Near Eastern admixture estimated for Stuttgart can be seen in Table S10.2 and range between 61-98% with estimates increasing as the amount of estimated African admixture in BedouinBincreases.There are reasons to doubt both the lower estimates (near60%), since ALDER provides only a lower bound on African ancestry, but also the )higher estimates (near 100%) since there is direct evidence that Stuttgart has European hunter-gatherer ancestry (Fig. 1B and Table S10.1

Determining the precise levels of Near Eastern admixture in Stuttgart must await further ancient DNA studies from both Europe and the Near East, but we can at least reasonably claim that most of the sample’s ancestry was Near Eastern, consistent with the mtDNA evidence for the Linearbandkeramik, which demonstrated a strong Near Eastern influence3-5"


(So, in Stuttgart, the Near Eastern admixture, according to this excerpt , is somewhere between 60 and 98%. I may have erred in using the 25% figure for the non Near Eastern admixture in Stuttgart (whether you call it UHG or WHG or a combination or anything else) I believe that is the figure for Oetzi. Anyone is free to correct the percentage from the academic literature, not if you please, from amateur "calculators", some of which have already been proved to be unreliable. Regardless, that is why I stated elsewhere that the majority of EEF’s ancestry is from the Middle East.

If any of this is incorrect, in fact, please direct me to a quote from the paper to that effect.

If someone wants to dispute the general statement, then I would suggest that they contact Lazaridis and Reich and point out how their statistical ability is superior to that of the authors. Or, they might want to write a paper and submit it for peer review. )


I also want to make sure that we are comparing similar things. The calculations that were made in the paper as to EEF/WHG/ANE in modern populations were based, to the best of my recollection, on Stuttgart. They certainly were not based on the Gok farmer results. Therefore, it's irrelevant for this purpose that Gok farmers had more WHG than did Stuttgar. The calculator used in the paper is comparing the genomes of modern Europeans to Stuttgart. That is the source of the 50% figure that is used for the EEF level in English people. They are not being compared to the Gok famers Again, if I'm wrong, and the paper is using both Stuttgart and Oetzi, for example, please correctt the record. This shouldn't be all about ego; it should be about getting it right.

Perhaps I am, knowing the history of certain segments of the amateur community, seeing a problem where none exists, and if that is the case, I apologize, and I certainly don't mean to tar all people who ask these questions or discuss them with the same brush, but it seems to me that a related issue involves all of the discussions and data analysis around how much total UHG/WHG is present in certain populations and people. It sometimes seems to me that the underlying concern for some people is not to have Basal Eurasian. If that's the case, I don't even have the words to express how pathetic I think that is...

In terms of the Near Eastern farmers, I do not recollect that the authors of Lazaridis et al provided a figure for the BE in them. There is a figure for the amount of Basal Eurasian in Stuttgart of 44% plus or minus 10%. So, if anyone wants to figure out their percentage of Basal Eurasian, just, for a rough estimate, take 44% of your group's EEF and there you have it. Now, for those so inclined, you can have a contest over who has the least amount of it. Mazel Tov in advance.

As to the "source" of Basal Eurasian, this is what the authors of the paper have to say:
" The Near East was the staging point for the peopling of Eurasia by anatomicallymodern humans. As a result, it is entirely plausible that it harbored deep Eurasian ancestry which did not initially participate in the northward colonization of Europe, but was later brought into Europe by Near Eastern farmers. More speculatively, some basal Eurasian admixture in the Near East may reflect the early presence of anatomically modern humans7in the Levant, or the populations responsible for the appearance ofthe Nubian Complex in Arabia8, both of which date much earlier than the widespread dissemination of modern humans across Eurasia. Finally, it could reflect continuing more recent gene flows between the Near East and nearby Africa after the initial out-of-Africa dispersal, perhaps associated with the spread of Y-chromosome haplogroup E subclades from eastern Africa 9, 10into the Near East, which appeared at least 7,000 years ago into Neolithic Europe11. "

So far as I can see, the question is still open, and the answers must await further ancient dna and responsible modeling by academics.

To conclude, Jean Manco posted a synopsis of the peopling of Europe which is a model of clearsightedness and logic. I hope she doesn't mind my posting it here for those who don't check in to Anthrogenica occasionally.


"The import of the Lazaridis paper is that there were three migrations into Europe [my notes in brackets]:

1. From the Asian crossroads/Middle East in the Palaeolithic. [mtDNA U and Y-DNA IJ and F]
2. From the Middle Eastern Neolithic heartland in the Neolithic. [mtDNA U3, H, I, J, V etc and Y-DNA G, with a bit of E]
3. From the Asian steppe in the Copper Age. [Y-DNA R]

As each of the waves reached Europe it mixed with descendants of the previous wave(s). "

All of the other comments in this post are my own and not to be attributed to her.

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Angela said:

Well, since the academics say over and over again that the ancient samples we have cluster with modern day Sardinians, I suppose they're the best candidate.

Here's the PCA from Lazaridis et al:
https://lh4.googleusercontent.com/-...t_three_ancestral_populations_Fig1b_small.png

It's too small an image, but if you enlarge it on your computer you can see what I mean.
Probably better to take a look at it in the paper.
http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

Or we can go with EEF levels:
View attachment 6673

Ashkenazi 93%, Sicilians 90%, Sardinians 82%, Spanish 81%, Greeks 79% and down from there.

The Sicilians score higher because of additional "doses" they got later, probably mostly, although not only during the Metal Ages through mainland Greece and the Islands as vectors. (The Maltese would fit in here as well.)

The Ashkenazi are a special case. It's complicated. They may be preserving the genetic signal of the ancient Near East better than other populations.

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Aberdeen said:

That was an excellent summary, Angela, and it helped clarify some things for me. But I have a question. If we eventually have detailed information about the genetic history of North Africa, do you think it could reveal the possibility that "basal European" could be gene flow from North Africa during the Neolithic? Given that Neolithic people were apparently much better sailors than was once assumed, we have two probable access routes, one from what is now Libya and one from what is now Morocco. IMO, if "basal European" is a yet undiscovered "ghost population", the ghosts might be hiding in the one place nobody has yet looked.

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Angela said:

Please don't assume quite yet that it's an excellent summary...the criticisms have yet to appear. I may have gotten some of it wrong, and if I did, I hope it is pointed out...civilly, of course!

As to your specific question about where Basal Eurasian was "hiding", if I may rephrase it that way, I really don't know. Lazaridis et al seem to be hinting toward Arabia, but the "Red Sea" area might be more precise? That would include the North African side of the Red Sea.

As for movement during the Neolithic, we don't have the genome of a Near Eastern farmer. However, we have a genome from the LBK farmer, and we are told she was 44% Basal Eurasian, plus or minus 10%. We also know from the yDna and mtDna and archaeology and papers like Paschou et al, that the Neolithic farmers moved from the Near East north and then north west into Europe.

They also, of course, moved east toward India, as one of the recent archaeology papers with very accurate dating pointed out. The prevailing opinion seems to be that they also spread west along the coast of North Africa and eventually deeper south into Africa itself as pastoralists.

Now, whether some of them also crossed the straits of Gibraltar into the Iberian peninsula, that argument has been made to explain some of the E-M81 in Spain, as I pointed out on the thread about Iberian genetics. I know that there has been some speculation that perhaps some R1b also made that trip. It's certainly possible, I would think, for something like R1b V88. Perhaps, some intrepid souls braving the currents in the Mediterranean also made the trip to Sicily or Sardinia directly from the coasts of North Africa, and that could explain the presence of that particular clade in those islands.

However, as to the P-312 in Europe, it seems to me that the current evidence is heavily in favor of that type of R1b being an ANE derived lineage that mixed with farmers and WHG/UHG somewhere to the east and then moved into Europe from there.

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John Doe said:

Is LBK Stuttgart?

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Angela said:

Stuttgart is a place in Germany where an LBK community was found. The bones of the inhabitants, one in particular, were analyzed. The genome of one of these LBK people from that site has been used as the model for EEF.

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Angela said:

......................

Now, whether some of them also crossed the straits of Gibraltar into the Iberian peninsula, that argument has been made to explain some of the E-M81 in Spain, as I pointed out on the thread about Iberian genetics. I know that there has been some speculation that perhaps some R1b also made that trip. It's certainly possible, I would think, for something like R1b V88. Perhaps, some intrepid souls braving the currents in the Mediterranean also made the trip to Sicily or Sardinia directly from the coasts of North Africa, and that could explain the presence of that particular clade in those islands.

However, as to the P-312 in Europe, it seems to me that the current evidence is heavily in favor of that type of R1b being an ANE derived lineage that mixed with farmers and WHG/UHG somewhere to the east and then moved into Europe from there.

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Aberdeen said:

That would certainly seem like a plausible theory, provided Basques and Sardinians have high levels of ANE, but they don't. I'm not personally convinced that the only R1b to migrate to Africa was V88. Perhaps whatever (possibly climate related) event pushed most of the V88 south pushed other R1b subclades into Europe. The problem is that Neolithic North African DNA seems to be pretty much unresearched at present, so there's no way to prove or disprove the idea.

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Angela said:

I agree with you that North African yDna has not been sampled extensively, but there are some pretty good studies, and the P-312 does not seem to show any kind of phylogenetic trail from the Middle East.

I think another thing to consider is that by the time the R1b got to places in the far south or southwest it might have been to a large degree rather de-coupled from the ANE autosomal component. We just need to look at the British for example, who have very high levels of R1b, and comparatively very low levels of ANE.

Also, the Basque do have some ANE...11% according to the chart in Lazaridis et al. It is the Sardinians who lack it, scoring under 1%, while having some R1b. My personal theory is that R1b in Sardinia is very recent, and mostly from the Italian mainland, where the levels are under 12% for ANE for the Tuscans, for example. I could see that getting diluted through progressive intermarriage with Sardinians in a very isolated setting, while the yDna would survive.

That's just a theory, though, and I am used, by now, to being surprised by ancient dna findings, so I'm certainly keeping an open mind.

Ed. Oh, one thing that I definitely think could have happened, is that some R1b L23 people, perhaps in the late Neolithic/Copper Age, as just an example, could have set sail from the eastern Mediterranean and gone across to Iberia, even perhaps stopping for some time on the coast of North Africa.

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Aberdeen said:

I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.[/QUOTI]

It certainly would, although, of course, they would be the product of admixtures along the way as well.

I suppose part of what underlies my reasoning is the finding that Mal'ta, who is by definition 100% ANE, was "R" or pre "R". Therefore, I guess it seems logical to me that both R1b and R1a are related to ANE.

I also think there's something to be said for the formulation of Jean Manco and others that this group then moved southwest (tracking micolith technology), with R1a perhaps further north and R1b further south.

The path that R1b took from there is an open question as far as I'm concerned.

I've seen some people speculate that R1b was the haplogroup of Maykop, or Cucuteni, for example, and got scattered when steppe invasions began in earnest. I've wondered if that's true, whether that could also have led to a migration west by sea.

I think the only way we're going to know is with lots and lots of ancient dna. As recent threads have shown, a few results don't answer all the questions.

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Angela said:

Aberdeen said:

I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.[/QUOTI]

It certainly would, although, of course, they would be the product of admixtures along the way as well.

I suppose part of what underlies my reasoning is the finding that Mal'ta, who is by definition 100% ANE, was "R" or pre "R". Therefore, I guess it seems logical to me that both R1b and R1a are related to ANE.

I also think there's something to be said for the formulation of Jean Manco and others that this group then moved southwest (tracking micolith technology), with R1a perhaps further north and R1b further south.

The path that R1b took from there is an open question as far as I'm concerned.

I've seen some people speculate that R1b was the haplogroup of Maykop, or Cucuteni, for example, and got scattered when steppe invasions began in earnest. I've wondered if that's true, whether that could also have led to a migration west by sea.

I think the only way we're going to know is with lots and lots of ancient dna. As recent threads have shown, a few results don't answer all the questions.

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I understand your point about Mal'ta Boy, and whatever surviving relatives of his became the ancestors of R1a and R1b people, but I haven't seen any data showing whether the ANE stayed strong in R1b or whether it was diluted to the point of disappearance, although it wouldn't surprise me if that was the case for the V-88 subclade. IMO, whether or not other subclades retained a strong ANE profile would depend on how they reached Europe. If R1b wasn't part of proto-IE but instead reached western Europe by way of Anatolia and from there further westward by sea, I wouldn't expect to see much of an ANE signature in the earliest examples of R1b in western Europe. And I wouldn't expect a high level of ANE if R1b took the Balkan route from Anatolia. However, if the earliest examples of R1b were high in ANE, I would assume R1b was likely part of the proto-IE population.

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Aberdeen said:

I agree that if R1b was originally ANE, that would have been diluted as it travelled west, but since Sardinia is nearly 20% R1b and well under 1% ANE, that's a lot of dilution, especially since the small amount of ANE could have come from other haplotypes. And I know of nothing that gives us an ANE connection to R1b of the kind we have for R1a. I can't find anything on line about an autosomal analysis of the two oldest R1b samples we have for Europe (which are also the only two Y DNA samples we have for Bell Beaker). It would be interesting to see whether such ancient R1b was ANE.

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Silesian said:

Same example could be made from R1a Shammar bedouins. By your logic they should have a fair amount of ANE, the Shimar sample carried two main haplogroups—J1 (at 52.3%) and R1a1 (at 42.8%)—with a small percentage of G2 (4.76%).
What about groups/regions like Lezgins/Tabassarans from where did they get there ANE J/R1a/G?

http://en.wikipedia.org/wiki/Y-DNA_haplogroups_by_ethnic_group

https://docs.google.com/spreadsheet...R62NHPbMRySUJ2J48_Q/edit?pli=1#gid=1410860471

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Mars said:

I agree with Angela, many people on antro boards tend to minimize the near eastern identity of the early farmers, probably for some political agenda, I think. Political wannabeism and science always clash, genetics are not exception to this rule Leaving aside "hobby" calculators, according to Genographic and FamilyTreeDNA I'm around 16% "Asia minor". It's a trace of neolithic expansion from the Fertile Crescent into Europe according to them - and we know they're right - and the very most europeans have (variable) amounts of this component in their DNA. It's part of us since 8,000 years.
My MTDNA haplogroup is HV, genographic project associates it to neolithic expansion, too.

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