April 6, 2014

Revised Lazaridis study on ancient ancestry of Europeans

The already famous Lazaridis et al. study on the contribution of various ancient populations to modern European genetics has gone through a revision which does not alter the fundamental conclusions reached in the past but does add some interesting nuances, new graphs and some new data.

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans. BioArxiv 2013 (preprint). Freely accessibleLINK (last version) [doi:10.1101/001552]

Most up to date supplementary info → LINK

For background see this previous entry.


Scandinavian hunter-gatherers deviate towards Siberia

Among the new data (or maybe data I skipped in the first read?) is the fact that the ancient Epipaleolithic individuals from Motala (Sweden) deviate towards Mal'ta-1 (Siberia), something that neither Lochsbour (representing Western hunter-gatherers) nor Stuttgart (representing early farmers) do.

This implies that there were already some differences in the Epipaleolithic era among European hunter-gatherers, with those of Magdalenian background lacking the Siberian (ANE) component, which is found however in Scandinavian ones (of Ahrensburgian background?) This may help explaining the extra ANE affinity in Northwest Europe, which is otherwise hard to understand. 

It also suggests that Eastern European hunter-gatherers were already in the Epipaleolithic more akin to Siberian ones than those from the West and South of the subcontinent, as well as those from West Asia (otherwise Stuttgart, which has partial West Asian ancestry would show increased affinity). Of course this can only be confirmed by direct analysis of Eastern European Paleolithic remains but seems quite likely in any case.


Principal component analyses (lots of them!)

Ancient samples projected on the global PCA:

Fig S1-10: projection of ancient samples onto global PCA dimensions 1 & 2

In this global PCA, EEFs overlap well with the reduced modern European sample (Basques and Sardinians only) and the West Asian one (Georgian, Palestinian Bedouins). However projected hunter-gatherers from Europe and Siberia show a clear "other Asian" deviation. Why? For the very same reason that South Asians and Melanesians do, even if they are clearly distinct populations: because the frame gives them no other choice: they are not quite like modern Europeans and they do not have any African tendency either, so the other populations that are somewhat akin to them are other Asians and there they go. 

That's why PCAs must always be taken with a preventive dose of salt: they are very nice visualization tools but they depend too much on the sampling strategy and its intrisical bidimensional limitations. 


Modern West Eurasians projected to a PCA of three ancient samples:

Fig. S10-3 Projection of West Eurasian populations onto the first two principal components
inferred using Loschbour, Stuttgart, and MA1 (full version).

Quite curious: all West Eurasians cluster tightly in comparison to their ancient "ancestors". It is likely that dimension 2 should be scaled down because the second component is always smaller than the first one (often around half). However I could not find a clear datum to proceed so I retained the original equal scale even if it can be a bit misleading. 

While not exactly, Lochsbour and Stuttgart explain the bulk of European (and West Eurasian!) ancestry, at least in comparison to the quite outlying Mal'ta-1 sample, representing ancient Siberians. 

Detail (zoom in) of this PCA:

Fig. S10-4 (I annotated the three ancestral tendencies with arrows for easy of view)

As expected Eastern/SE populations deviate more towards Stuttgart, Western/NW do towards Lochsbour and in general Northern populations deviate slightly towards Mal'ta, also in West Asia (i.e. Iranians, Turks).

Modern European PCA with ancient samples projected on it:

Figure S10.5: Projection of ancient samples onto the “European” PCA (annotations in gray are mine)

Something the authors notice is that their PCA does not approximate a map of Europe, as happens in some cases. They dedicate some time to evaluate this discrepancy, comparing with the PCA of Novembre et al. 2008. The differences are caused because the latter used many more NW and Central European samples and instead had way too little Eastern European ones. 

This highlights that sampling strategy is of utmost importance when analyzing autosomal DNA, not just in PCAs because oversampled populations would tend to cope the axes (or components). This should be obvious but is way too often ignored, what may result in spectacular magic hat tricks but hampers serious science. 

This is one of the reasons why I do not trust too much autosomal DNA analysis: lack of the fundamental rigor. This is of course not a defect in this particular study but it happens often in many others, scholarly and amateur alike. 

The authors believe that the main axis of differentiation in Europe when the subcontinent is considered as a whole may tend to Northeastern Europe rather than SSE/NNW⁸, something that is consistent with their ancient admixture findings elsewhere in the study. 


FineStructure PCA output

A key point in this study is that only Sardinians and Basques can be modeled as simple EEF-WHG admixture, all the rest of Europeans needing of the MA1 component to be explained. This is much easier to visualize in the following graph.
We also processed the ChromoPainter/ChromoCombine output with fineSTRUCTURE1 using 250,000 burnin and 2,500,000 runtime MCMC iterations. Fig. S19.2 shows a Principal Components Analysis by fineSTRUCTURE which strongly resembles that of Fig. 1B.
Fig. S19-2 (annotated in gray by me)
Here we can see that only Sardinians (and quite insistently Canarians), Basques and some populations related to these (North Iberians, South French) are actually close to the Stuttgart-Lochsbour axis. All the rest need a third ancestry for explanation, which is approximated by MA1 (not plotted but whose tendency I annotated).

Notice that in this case the two ancient samples are not projected, as in the previous graphs but actually computed as part of the wider West Eurasian population.

This does not deny that other NE European populations have greater affinity to Lochsbour (fig S19-3) but it seems clear that this affinity must be mediated by another branch of ancient European hunter-gatherers, one that existed in Eastern Europe, rather than in the West, and that it had more ancient Siberian (MA1) affinity. It is also likely that this Eastern European aboriginal population was the one which brought the extra MA1 affinity to the rest of Europe, most likely in the context of Indoeuropean (Kurgan) migrations. Along with it they probably also brought extra WHG-like admixture (but actually from an Eastern European source).

The extra MA1 tendency is also present in West Asia. This may have two alternative or complementary explanations:
  1. There have been also significant Siberian-like intrusions in West Asia after the Neolithic.
  2. This extra ancient Siberian affinity is in fact (largely?) pre-Neolithic but the founder population of West Asian roots which triggered the European Neolithic in Thessaly was particularly removed from this admixture and more akin to Palestinians or peninsular Arabs than to other West Asians.


Sicilians, Maltese and Ashkenazi Jews are different

These three are the only European populations which have a poor fit with the triple admixture model (EFF+WHG+ANE), suggesting that they have fourth party inputs, most likely extra admixture from West Asia. 

This is apparent in the previous graph too (among several).


Tree modeling for the origins of the ancestral populations

From fig. S16-2 (allowing for five admixture edges)

From fig. 16-4 (full-genome coverage, allowing for 5 admixture edges and using Dai instead of Onge)

The basic topology of the tree is consistent (excepted the partial change of the location of Karitiana Native Americans, which depends on the greater affinity of the East Asian sample used and is essentially neutralized by the admixture edge with Onge or Ma1 respectively). The main admixture events are:
  1. The Karitiana (and Amerindians by extension) are clearly a mix of East Asians plus Ancient Siberians of Western affinity (MA1), which is represented differently in both trees.
  2. Early European Farmers (Stuttgart, Iceman) have clear "Basal Eurasian" admixture (which can be interpreted as North or East African input and/or a residual ancient Arabian element, probably both)
  3. La Braña also has "Basal Eurasian" admixture (surely from NW Africa, what implies that the North African component in Western Iberia is pre-Neolithic)
  4. Motala has Ancient Siberian (MA1-like) admixture
  5. Mal'ta 1 probably has some East Asian admixture
  6. Ötzi the Iceman might have some Western Hunter-Gatherer admixture (~3%)

Of the three Western branches, MA1 is the more distant one. That implies that West Asia and Europe were also exchanging genetics in the Upper Paleolithic, while Siberia remained more isolated in comparison. That stands even when East Asian admixture into MA1 is accounted for. 


A Lochsbour's cousin in West Asia

The authors compare and analyze many models of possible admixture leading to the known ancient and modern populations. They seem to favor this one in the end:

Figure S14.20: A model for Near Eastern populations with Ancient North Eurasian admixture.
Stuttgart is a mixture of Near_East and a sister group of Loschbour (UHG: Unknown Hunter-
Gatherers); A Test population (shown here) is a mixture of Near_East and a sister group of MA1.

This scheme suggests that ancient West Asian ("Near East") populations were closer to ancient Europeans (Lochsbour) than to ancient Siberians (MA1). It also suggests an unknown relative population of Lochsbour (UHG) as partial ancestor of early European farmers (Stuttgart). This population is speculated to have lived in the Balcans. 

An issue here is that most modern West Asians and all Caucasian peoples actually have too much MA1 affinity to be a good fit for the (ancient) Near East proto-population concept. About 12-13% among West Asians (Cypriot, Druze) and as much as 29% among Caucasians. They are actually more like "Test" than like "Near East".

The authors conclude that they don't really know if this extra MA1-like ancestry is old or recent. If old, it would imply either two different populations of West Asians or, as they say, the expansion of a West Asian population with extra "Basal Eurasian" ancestry. 

This brings us to a key question: what is actually "Basal Eurasian"?


What is "Basal Eurasian"?

Notice that "Basal Eurasian" is defined as phylogenetically intermediate between the Mbuti and Eurasian-plus populations. Quite misleadingly the node is described as "Non-Africans" but that does not need to be true at all. It is just downstream of one of the most ancient African sub-branches, that of Pygmies, so it can still represent African populations which are or were closer to the out-of-Africa branch. 

There is no formal ascertainment whatsoever of what is "Basal Eurasian", no comparison with other African populations and no even formal consideration of the (very likely) possibility of various isolate ancient populations existing in NW Africa or Arabia. This is clearly a flaw. 

A key piece of information here is that La Braña (ancient NW Iberian hunter-gatherer) consistently shows "Basal Eurasian" admixture. This admixture is much more likely to have arrived from North Africa than anywhere else. NW African genetic markers are still apparent in Western Iberia in fact and there is strong archaeological support for Iberia-NW Africa interaction in Solutrean/Oranian times. 

We can only consider in fact this "Basal Eurasian" idea as a mere indicator of African-like affinity, even if it's not Mbuti but something else. This something else can be in fact several things:
  • NW African Aterian residual in the case of La Braña
  • Arabian OoA residual influence in the case of EEF
  • Direct NE African admixture in the proto-EEF West Asian population, strongly indicated by the NE African E1b-M78 (notably its subclade E1b-V13) in ancient Neolithic and modern European Y-DNA.
I am particularly inclined to suspect an almost direct migration from Palestine to Thessaly at the origins of European Neolithic. After all both non-European lineages found in early European farmers (E1b-V13 and G) are common in that area. But of course an Anatolian intermediate station cannot be excluded.

In any case I'd suggest to change the terms "Basal Eurasian" and "non-Africans" by something more neutral, maybe "Ultra-Mediterranean" and "Proto-Eurasian" respectively, where both concepts are allowed to be African, at least partly so.


Update (Apr 23): see also here for some curious aspects of Lochsbour's IBD ancestry.

39 comments:

  1. Quite curious: all West Eurasians cluster tightly in comparison to their ancient "ancestors". It is likely that dimension 2 should be scaled down because the second component is always smaller than the first one (often around half). However I could not find a clear datum to proceed so I retained the original equal scale even if it can be a bit misleading.

    Maju, quick note on this, I'm pretty sure the ancient samples are far apart compared to the recent here because of the PCA is largely based on their intra individual variability.

    If you do a PCA based on, for example. 1 each of present day South Asians, Europeans and North Africans, you'd get a similar spread when you projected other present day South Asians, Europeans and North Africans onto it, with each of the populations bunching up near the middle and overlapping noisily and tilting in the direction of their "representative".

    This is because most what the PCA found based on the 1 each of the individuals simply won't be related to population level variation.

    (For another comparison, if we did a Maju-Matt-someone else PCA, then our respective populations wouldn't tilt very much towards either of us, because most of our genetic differences are individual to us, so they'd sit more or less at around 0 and overlap a lot, with only slight tendencies towards us (perhaps unless they were actually close family with one of the 3).)

    IIRC, there's a similar figure in the recent Anzick genome paper that does the same on Anzick vs some other Native American samples to this effect.

    When lots of individuals are included, intra-individual variance gets cancelled out, which is why with more population samples (even 10 individuals from each) we get nice smooth PCA.

    On a similar note, I'm not divided on whether the axes would really need much rescaling here. On the one hand, the null assumption would be there's no reason for more intra-individual variability between any dyad of these individual and so each dimension mostly representing a contrast between one individual and the other two should be about the same size... But if there were, by chance, that would be distorting. It would have been interesting.to know the relative size of each anyway..

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    1. Interesting meditation, Matt. Honestly I can't say if you're right or wrong but I can ascertain that it is not the same "projecting" than factoring samples together, as seems quite obvious from the comparison between the variousprojections and the FineStructure PCA. It is interesting that at least the Lochsbour distinctiveness is enough to get him to dominate one of the polarities on his own, in spite of being a single individual.

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  2. Maju,
    I think you hit the nail on the head questioning the assumptions on "Basal Eurasian". A commentor on Davidski's site suggested the so-called "basal" admixture coming from the Natufians who, among others, were some of the earliest people to be absorbed by the earliest NE farmers. As you mentioned, aboriginal peoples of Arabian peninsula are probably worthy of more scrutiny since their skeletal features would suggest significant African ancestry and they certainly mixed with the early famers.

    Early Southern Europeans, on the other hand, may have already had some early African admixture in the late Paleolithic, at least from a Grimaldi-like population. That, or another source, may have contributed to Mesolithic La Brana's heritage, which was significantly more African shifted that modern European populations. (thanks for posting the thumbnail of La Brana, btw) I believe Coon had originally hypothesized that early brutish Western Eurasians were originally gracialized by African admixture, leading to Mediterranean Caucasoids.
    In any case, I don't think we know for certain that ANE, WHG and EEF are three discrete things instead of one thing, mixed with three unknown things. Given that the EEF people must certainly have been a racially mixed population, I think we may be looking at the latter.

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    1. NW African influence in Europe seems quite restricted to Western Iberia and in any case, other than punctual founder effects like some Welsh village whose name I don't recall, it has remained restricted to the Iberian peninsula or almost so. So it's not something that can be generalized to all Southern Europe.

      "a Grimaldi-like population"...

      Long not heard of Grimaldi! Actually it was demonstrated years ago that Grimaldi is a typical Caucasoid specimen with some misleading post-mortem deformation of the skull, particularly the jaw. It's a bit like the Portuguese boy skull claimed once to be a half-Neanderthal and which is actually post-mortem deformation of the skull by mere gravitational compression under the soil.

      There should not be anything too obvious in the appearance of NW African admixed people because, on one side, NW African themselves are dominantly West Eurasian by origin (and partly Iberian in fact) and, even more importantly, the score of their genetic influence is rather low: less than 10% today, not much more in the past, judging on La Braña and some other scattered data.

      It seems to me that Gravetto-Solutrean South Iberians migrated to North Africa in large numbers at the very genesis of Oranian culture (what has left ~30% Iberian like mtDNA and autosomal legacy in the area) and that, in return, some NW African ancestry reached the Western parts of Iberia (notably Estremadura and Asturias initially, later expanded to all the Western third, which was not as populated).

      Of course I can't exclude that this backflow is of a later date, Neolithic for example, but the La Braña data seems to suggest that it's not the case.

      " I believe Coon had originally hypothesized that early brutish Western Eurasians were originally gracialized by African admixture, leading to Mediterranean Caucasoids".

      I wouldn't bet my money on Coon's Nordocentric theory, really. If he can't discern a Spaniard from a Greek, he's obviously blind to "racial" variation. When I used to read on the subject years ago I rather preferred Lundman, although he also has some of that Nordic bias.

      My own opinion is that a robust individual like Crô-Magnon 1 is simply exceptional, individual variability, and that most other remains are more average. But well, I lost most of my interest on these matters long ago because physical anthropology is a very slippery terrain with low informative value, at the very least when compared with genetics.

      "I don't think we know for certain that ANE, WHG and EEF are three discrete things instead of one thing, mixed with three unknown things".

      Indeed. Particularly ANE seems a bit slippery and is probably rather a proxy for Eastern European Hunter-Gatherers, who must have more ancient Siberian admixture (but otherwise were relatively close to WHG.

      EEFs were for sure a mixed population, however I would not say "racially mixed" because they are the ones who best fit with the modern "Caucasoid race" samples. There's no such thing as a "pure race", only variable mixtures.

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  3. 'Basal Eurasian' has always been right under your nose Maju, so to speak, it is nothing new really, Cavalli Svorza outlined almost 20 years ago that Europeans had 1/3 African Affinity. I had also, as I am sure you do recall, attempted to hammer in the very simple and basic concept that at K=2, West Asians showed significant Affinity to Africans relative to East Asians. This Basal Eurasian statistical concept is part and parcel of this rudimentary and simple observation that is most often ignored (intentionally?) by geneticists, amateur and professional alike, now the proverbial chicken is coming home to roost.

    Global contour map, K=2

    The World at K=2

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    1. But Luigi Cavalli-Sforza was not right, exactly the same you are not: K=2 at the global level is always a function of sample size, just try super-oversampling Australian Aborigines or Khoisan peoples (this was done in fact, as I showed you to no avail) or any other very distinctive population and all the rest will cluster as non-them or intermediate between the super-sample and the "non-them". Of course that the level and pattern of distinctiveness also matter but sample size does too and Admixture/Structure will always be a function of these factors: nothing more, nothing less.

      At K=2 global you have such a brutally bad cross-validation value that nobody would think that means anything at all. But there you go beating the dead horse.

      It's plain and clear.

      West Eurasians have some African and surely also quasi-African (OoA isolates') admixture, many Africans also have West Eurasian admixture, even more than the inverse (for example Ethiopians seem to be a 50-50 mix). But you can hardly tell from a global K=2 because it's just meaningless noise.

      You do some interesting stuff, Ethio but in this issue you are absolutely wrong.

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  4. "We can only consider in fact this "Basal Eurasian" idea as a mere indicator of African-like affinity, even if it's not Mbuti but something else."

    It shows affinities to Mbuti as well, assuming Sardinians as the study seems to show clearly are a good proxy for EEF.


    I also posted this on Davidski's blog, but it might be of some value in discussion here as well. Below is a Chromopainter/FINESTRUCTURE heatmap of world populations from Anders Pålsen's project. The affinity of Sardinians to the African groups, be they Ethiopians, Khoisan, West Africans or Pygmies, is the highest in Europe.

    https://sites.google.com/site/fennobga/CCAggrWorld240413.png

    I fully agree about the study being lacking when it comes to exploring what the hypothesized Basal Eurasian really is.

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    1. "It shows affinities to Mbuti as well"...

      What's your foundation to claim that? All I can see in the TreeMix algorithm is that it is somewhere between Mbuti and West Eurasians, what can be almost anything. I would say, based on the full genome coverage ones that it is quite downstream of the node of Pygmy divergence, something like "North African" (very loose sense) but the matter merits more investigation in any case, no doubt.

      "Below is a Chromopainter/FINESTRUCTURE heatmap of world populations from Anders Pålsen's project."

      That kind of hyper-high resolution image really clutters my computer, and possibly others. I can't see anything with so many tiny names anyhow, even if it manages to load. It's something I've told Anders but to no avail.

      "The affinity of Sardinians to the African groups, be they Ethiopians, Khoisan, West Africans or Pygmies, is the highest in Europe".

      Maybe but that only means an African tendency of the same uncertain kind that we are discussing when talking about this "Basal Eurasian" mystery. I'm quite sure that they are not more akin to Africa than North Africans or Arabs: it's a tendency.

      My question is: is that African-like tendency or minor component wholly African or partly something else (residual aboriginal Arabian, for example, retained in the area since the OoA migration, but very diluted anyhow)? Whatever part is African, can we identify it with the trail left by yDNA E1b-M78/V13?

      And also: why do modern West Asians appear to lean less in that direction (excepted Palestinians and peninsular Arabs? Is that because the European founding farmers arrived from Palestine, maybe in a coastal migration, or is it that the demographics of West Asia has changed quite a bit since those times?

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    2. The Chromopainter affinity, and assumption that Sardinians are basically a WHG-shifted EEF-population, is my foundation for the claim. Sardinians show more Mbuti affinity than any other Europeans. It does not need to be direct Mbuti admixture though, any kind of African is enough to increase the affinity to Pygmies and Khoisan given the diversity of their autosomal haplotypes.

      "Maybe but that only means an African tendency of the same uncertain kind that we are discussing when talking about this "Basal Eurasian" mystery. I'm quite sure that they are not more akin to Africa than North Africans or Arabs: it's a tendency."

      It still has to come from somewhere, the problem is that modern North Africans and Arabs can be expected to also have recent Sub-Saharan admixture which complicates investigations. As for modern West Asians showing the shift, depends a lot. Cypriots or Druze show more African affinity than Sardinians in Chromopainter/FINESTRUCTURE and do have more Middle-Eastern like ancestry. One would have to go to Caucasus to find ones with equivalent shift to Sardinians, and I don't think there's any doubt about demographic shifts happening there. Same goes for Anatolia, mesolithic aDNA from there would no doubt be informative about the spread of farmer ancestry.

      "My question is: is that African-like tendency or minor component wholly African or partly something else (residual aboriginal Arabian, for example, retained in the area since the OoA migration, but very diluted anyhow)? "

      I think it's residual African in Middle East. I wouldn't go as far as to say it's been preserved since original OOA, there's more likely been several African-ME contacts with small effects between Neolithic and the OOA event. I'm a bit wary about linking autosomal DNA and haplogroups, but let's say that in this case I don't see other possible links to Y-DNA for the pre-neolithic Africa-ME mixtures than E1-variants. After it got spread into the Middle Eastern population any migration from the area would have carried it.

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    3. I would need a screen of the side of the wall (and a better computer possibly) to be able to study such a huge image. Or at the very least I would need the graphic's coordinates and key ID of the populations mentioned to find it. Or simpler: I will take your word for it because once you refined your original statement, it does not seem different from what I can appreciate in the data from this study: an African-like (or negative-Eurasian) tendency, which can be anything African or para-African.

      "It still has to come from somewhere, the problem is that modern North Africans and Arabs can be expected to also have recent Sub-Saharan admixture which complicates investigations".

      If an amateur like myself could find it in the first relevant Admixture tries, any researcher with the insight can, using much more powerful tools (or the same ones but refinedly so). Naturally you do not stay at K=2, K=5 or K=8 levels, you need to go beyond K=10. You also need a wise sampling strategy: what is what I want to study, possible comparisons. And you need to evaluate the relative Fst distances between components. There's no point on doing a K=5 or K=8 global Admixture graph each time we analyze something: the resulting graphs are shallow and the populations studied unnecessarily too large, complicating things a lot. That's OK for a preliminary or generic study but not for "microscoping" this kind of stuff.

      That's why in this Lazaridis' paper Admixture takes such a low prominence: it merely says nothing we did not know already. Maybe if they had tried another sampling strategy approach... we would be looking at different images with similar results.

      "As for modern West Asians showing the shift, depends a lot. Cypriots or Druze show more African affinity than Sardinians in Chromopainter/FINESTRUCTURE and do have more Middle-Eastern like ancestry. One would have to go to Caucasus to find ones with equivalent shift to Sardinians"...

      That's not the data-point I gathered: ~10% MA1-shift in Cypriot and Druze (they don't mention others). From the PCAs, particularly figh. S19-2, Turks and Iranians are even more shifted, with ANE affinity not far from that of Caucasians, for which is reported ANE affinity levels of as much as 29% (higher than any European). This is of course just a preliminary assessment because without ancient West Asian genotypes for comparison all becomes quite blurry, but that's at least what seems from comparison with EEF and WHG, for whatever is worth. Naturally Turks and Iranians are the most steppe-influenced populations in the area but they should also be more influenced than Caucasian peoples, which are believed to be refuge populations, so... still confusing.

      It's not impossible that Northern Ancient West Asians from the Zagros-Taurus arch were more ANE-like than those from the Levant. They were almost certainly two distinct populations and it's even possible that Eastern Europe had influenced the former at some point. If this is correct, then the EEFs had a founder effect from the Levant rather than from the Northern Highlands. But much of this can only be speculative until ancient West Asian genomes are studied in greater depth than just mtDNA sequences.

      ....

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    4. ...

      "I think it's residual African in Middle East. I wouldn't go as far as to say it's been preserved since original OOA"...

      I tend to that idea because of E1b-M78. However, I am also reasonably certain that Saudi Arabians and some Low Egyptians (but not others) retain a component that appears equally distant (at "continental" distance scores) from Africans and West and East Eurasian main components alike.

      The same happens in NW Africa (particularly Southern Morocco) but it is a different component (ref. links in main entry). So I believe that isolate OoA populations existed in these two regions but were eventually overrun by mostly West Eurasian (UP) and possibly some secondary African expansions, remaining however in form of a very diluted component and some more or less notorious mtDNA lineages (whose L(xM,N) adscription make them appear as "African" but are often distinctive).

      Sadly, it will take time for academic research to confirm this because those areas are not so well studied as Europe is (neither in the genetic nor in other aspects like archaeology) but I am personally very persuaded that it is the case: there is an "Aterian" and a distinct "early OoA" residuals in these two regions and they can be found if you pay attention, if you study the genome with sufficient depth and the proper sampling strategies (just overloading your samples is of no help: better to select just specific controls and a good sample of the studied regional population).

      "there's more likely been several African-ME contacts with small effects between Neolithic and the OOA even"...

      That I do not know, except for the Eurasian back-migration to parts of Africa, which seems confirmed by just looking at haploid DNA (and confirmed by autosomal DNA) as follows:
      1. West Asian flow into NE Africa, probably in the early UP, leading to the LSA.
      2. Iberian flow into NW Africa, surely at the Oranian genesis, of Solutrean influence.

      But in what regards to secondary flows from Africa to those areas, I can only discern the E1b (and related mtDNA) current, which seems rather Mesolithic than Paleolithic (and some backflow in West Iberia related to point #2).

      "I'm a bit wary about linking autosomal DNA and haplogroups".

      Me too but, on one side, mtDNA seems to show often a good correlation with autosomal DNA (probably because mothers carried both on in spite of fathers' changes) and, on the other, yDNA usually shows relationship with minor autosomal elements in populations which have gone through such extensive admixture that their patrilineal origins are hard to recognize beyond the yDNA (examples: Native Americans, Uralic peoples, Palestinian-European Neolithic vector of African origin). So it is not so thoughtless when properly pondered: there may be and often are relationships, just that we have to look at them from all angles before reaching to conclusions.

      " I don't see other possible links to Y-DNA for the pre-neolithic Africa-ME mixtures than E1-variants. After it got spread into the Middle Eastern population any migration from the area would have carried it".

      Yes. But E1b variants in West Asia are only important in the Levant and Arabia Peninsula, precisely the populations which show the least ANE-like drift. Turkey for example only has c. 10% E1b, much less than Greece or Albania. So this, like the generic "Basal Eurasian" issue, points to a Palestinian affinity of EEFs, which may be interpreted as either direct origin or as radical population changes further North after the Early Neolithic.

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  5. "I would need a screen of the side of the wall (and a better computer possibly) to be able to study such a huge image. Or at the very least I would need the graphic's coordinates and key ID of the populations mentioned to find it."

    Odd, I don't have any problems doing it with my 4 years old laptop using the scroll feature.

    "That's not the data-point I gathered: ~10% MA1-shift in Cypriot and Druze (they don't mention others). From the PCAs, particularly figh. S19-2, Turks and Iranians are even more shifted, with ANE affinity not far from that of Caucasians, for which is reported ANE affinity levels of as much as 29% (higher than any European)."

    I'm specifically talking about African shift of Cypriots and Druze being > that of Sardinians. African shifts don't show on West Eurasian PCA's with no Africans though. They have more ANE than Sardinians, but are much more Middle Eastern and less WHG, so they are more African shifted than Sardinians in global PCA's. To make the African shift of a West Asian or Middle Eastern population lower than that of Sardinians, lots of ANE is needed. This can be found in Caucasus.

    You can see the African shift of Georgians (higher than Basques but lower than Sardinians) in Dimension 1 of Fig S1-10.
    Any high-resolution global PCA will show Middle Eastern and Caucasus populations as African-shifted compared to non-Southern Europeans. ANE-shift of West Asians (and WHG shift of Europeans) is more visible on the Sardinians vs East Eurasians axis (usually dimension 2 of any global PCA that has Sardinians).

    Personally I think some small admixture events with Africans between OOA and Neolithic are the most plausible explanation for the creation of "ancient Middle Eastern" or "Basal Eurasian" which is the African-shifted non-WHG component in Stuttgart. If there was no African beyond the initial event into the Middle Eastern population, an OOA isolate would look as diverged from Africa as Mal'ta boy who, I assume, had no African influences beyond OOA from his ancestors and places accordingly compared to Africans. The WHG component the farmers could have acquired in Europe. Only ancient autosomal DNA from Middle East and North Africa can settle this though. To prove existence of OOA isolates in the Middle East into the neolithic or Mesolithic, much more ancient DNA is also needed to find out what an OOA looks like in the first place. The Ust-Ishim genome might not be old enough.

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    1. "I'm specifically talking about African shift of Cypriots and Druze being > that of Sardinians."

      Alright. It's true that the African-like shift is not captured on those graphs but it does seem to be in general opposite to the Siberian (ANE-like) shift. So Sardinians who have a very low ANE score (c. 4%) correspondingly show a relatively high African-like score. On the other hand WHG (La Braña excepted) do not show either deviation, their distinctiveness is unique of their own, so they probably had no meaningful Siberian nor African input yet (at the very least they are a reference baseline).

      "They have more ANE than Sardinians, but are much more Middle Eastern and less WHG"...

      Logical, isn't it? The West Asian ancient populations surely were only distantly related to WHG, barely more than MA1, judging on reconstructive models. The non-European element in EEFs (and hence in Sardinians) seems to be made of Ancient West Asian plus some "Basal Eurasian" (i.e. African-like). To that we should add the UHG which would be related to Lochsbour but possibly Balcanic by origin.

      "they are more African shifted than Sardinians in global PCA's"

      I don't perceive that, sincerely. In the main PCA (see previous entry), Bedouins are clearly African-shifted but Cypriots or Druze are about the same as Norther-NE Europeans in this regard. Difficult to judge because there are no African-specific controls but that's the main stretch axis of West Asians: between the African-shift o Bedouins and the Siberian-shift of Caucasian peoples and other "highlanders".

      "You can see the African shift of Georgians (higher than Basques but lower than Sardinians) in Dimension 1 of Fig S1-10".

      You must mean S10-1 (there's no S1-10), the global plot. That is probably misleading in fact, exactly the same of what I said about South Asians, Melanesians and ancient hunter-gatherers looking as intermediate towards East Asia. Other studies using West Eurasian and North African populations do not show such tendency in fact. Sampling strategy is crucial, global analyses are relatively shallow and potentially misleading. In this case they are probably pulled in the African direction by Mozabite and other African "West Asianness" rather than by any genuine "Africanness".

      "Any high-resolution global PCA will show Middle Eastern and Caucasus populations as African-shifted compared to non-Southern Europeans".

      Maybe but it's only an illusion caused by the unspecific globality of such sampling strategy. As I just said: it's almost certain that what pulls them towards Africa is the "West Asianness" of some Africans rather than the opposite. Global comparisons alone are not too informative. Please don't be misled by them without due contrast.

      ...

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    2. ...

      "If there was no African beyond the initial event into the Middle Eastern population, an OOA isolate would look as diverged from Africa as Mal'ta boy"...

      No! Because Mal'ta, as WHG, etc. belongs to the Asian clade which migrated to South Asia (and possibly even reached SE Asia in some instances, only to turn back at some point). That is the "Eurasian" clade. Everything else will look as partly African-like, just because it was neither this nor that: neither "Eurasian" nor "African". Actually the category "African" is extremely diverse, even in spite of the semi-homogeneization caused by Bantu expansion, and includes all non-Eurasian basal populations of Humankind. These aboriginal Arabs (OoA remnant) would look on first sight "African" or partly so just because they diverged before the Eurasian expansion proper, which began only when their descendants reached South Asia. The same happens with NW African aboriginal population isolates of Aterian roots, which may have remained on their own for some 100,000 years. So they look "African" because "African" means everything before the Eurasian-specific expansion, which began in South Asia c. 100 Ka ago (judging on the latest archaeological data).

      Comparatively there is such a strong founder effect in the Eurasian-plus macro-population that all the rest looks like a single amorphous clade by (shallow) comparison and we identify it with Africa, logically. But part of that pre-Eurasian may well have been in Arabia since the OoA.

      "To prove existence of OOA isolates in the Middle East into the neolithic or Mesolithic, much more ancient DNA is also needed to find out what an OOA looks like in the first place".

      Not necessarily so. As I said I believe I found it in modern autosomal DNA: a minor component that has continental-size Fst distances to both Eurasians and Africans alike. Same in NW Africa. I also think it is apparent in mtDNA and even in some Y-DNA like A00 and A0, which must have arrived to NW Africa in very ancient times, judging only on their frequencies and rarity.

      → http://forwhattheywereweare.blogspot.com/2011/12/north-african-genetics-through-prism-of.html
      → http://forwhattheywereweare.blogspot.com/2012/01/egyptian-genetics-in-regional-context.html

      Is it enough evidence? Maybe not yet but it is a quite strong principle of evidence.

      Anyhow there's no reason to think that the ancient populations of Arabia or NW Africa left zero legacy. They may have been overrun by others, even repeatedly so, but there was no inter-species barrier of any sort as happened with Neanderthals, which hindered admixture. So in principle some of their legacy must remain. We just have to look for it.

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  6. " In the main PCA (see previous entry), Bedouins are clearly African-shifted but Cypriots or Druze are about the same as Norther-NE Europeans in this regard. "

    That PCA is not informative regarding sub-saharan African affinity because they are not present on the plot. For that matter, to truly explore relationship of Eurasians and sub-saharans, we need sub-saharans in the comparison. IBS and Finestructure, and PCA's all require this.

    "No!..."

    My point is that there is additional African output in the Middle East and North Africa including pre-neolithic Middle East compared to the original OOA event which would also have brought with it everything that is in the "Eurasian expansion" and MA-1. If we leave the special case of Oceanians out, everything Eurasian is ultimately African + drift (and some Neanderthal but that is equal for MENA and wider Eurasia) and any hypothetical OOA isolate would have drifted as far from Africa as something like Mal'ta did unless it had additional African input.

    "As I said I believe I found it in modern autosomal DNA: a minor component that has continental-size Fst distances to both Eurasians and Africans alike. Same in NW Africa. I also think it is apparent in mtDNA and even in some Y-DNA like A00 and A0, which must have arrived to NW Africa in very ancient times, judging only on their frequencies and rarity. "

    The problem is that we'd need ancient DNA to compare such results with, as well as more distant African groups and East Asians. That analysis is within Mediterranean context without wide comparisons.

    In any case, my views about what so-called Basal Eurasian is are clear. I doubt further analysis of Stuttgart will change them.

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  7. "That PCA is not informative regarding sub-saharan African affinity because they are not present on the plot".

    We know from other tests in this study that Bedouins have African affinity or admixture but otherwise you are correct, I mean: in purely abstract terms.

    But there are other studies, for example check this old entry: the Mediterranean divide is pretty neat and more or less equal for all populations, even Asturians who have greater E1b-M81 than the rest.

    Check also this one, which includes Sardinians in the pop-res analyses. Sardinians are not significantly more Yoruba-like than CEU at all.

    "My point is that there is additional African output in the Middle East and North Africa including pre-neolithic Middle East compared to the original OOA event"...

    According to my own research, see links above, Palestinians have 1.2% East African ancestry and Turks, Saudis, etc. 0% or such a tiny residual that is effectively zero. North Africans like Egyptians or Moroccans have a greater amount: 8-12%. Instead the "Arab2" component, which fits with an OoA origin, is 12% among Saudis and 11% in one but not the other Egyptian sample.

    Also the South Moroccan component (Aterian IMO) is almost 15% strong in Southern Morocco, where pseudo-Khoisanid phenotypes are found, but only ~1% in other parts of North Africa. Southern Moroccans are also outstanding in West African (Mandenka) affinity: c. 15%, while other North Africans have variable figures around just 5%. In The North African study Saudis showed 0.4% of Mandenka affinity plus a 0.2% of Fulani affinity and a 3.4% of Ethiopian affinity (however this last component is clearly a mix of West Asian and East African and only shows up intermittently).

    The direct Tropical African influence is not that important in West Asia or even in much of North Africa. And certainly is not more important in many cases than the aboriginal regional components from OoA times (estimated on Fst distances).

    "... any hypothetical OOA isolate would have drifted as far from Africa as something like Mal'ta did unless it had additional African input".

    Not at all: the direction of Ma1 and other Eurasian hunter-gatherers in the PCA (projected, remember!) is caused by their intrinsic Eurasianness, i.e. founder effect at the South Asian origin of the expansion: they have something to attach to: Eurasian populations. However the OoA residuals have nothing to attach to, so, if they existed as such pure individuals, they would split their allegiance (nil) between Eurasia and Africa, hanging between them both, just like Ethiopians.

    "... we'd need ancient DNA"...

    Sure: the more, the merrier.

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  8. Would this "basal Eurasian" admixture explain why Davidski's work was showing La Brana as having SE Asian / Melanesian admixture? http://eurogenes.blogspot.ca/2014/03/4-ancestors-oracle-results-for-anzick-1.html

    That's the deepest split in the Out-of-Africa tree, isn't it? Would other OoA isolates cluster with groups like Melanesians and Adamanese simply by virtue of not being on the same branch as the "derived" Eurasians.

    La Brana was Y haplogroup C-V20 though. C-V20's closest relative is C-M8, which is found in Japan and believed to be associated with the Jomon culture. I'm not sure how that can be reconciled into this picture.

    With regards to admixture from an OOA isolate or directly from tropical Africa, couldn't both be correct to some degree? The Sahara wasn't exactly a huge barrier during the timeframe we're talking about.

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    1. It could be the case: I have seen (and commented here) various apparent minor component affinities of La Braña in the past, mostly towards Africa (varied subgroups) but sometimes also towards Asia. This fluctuation may well be because none of them really represents at all the original population behind that component, which could well be Aterian, so it sticks to some oddball rather randomly instead.

      "That's the deepest split in the Out-of-Africa tree, isn't it?"

      I'd say it's not a perfect tree but if we want to simplify the Eurasian population (excluding ancient Arabian left-behind remnants) it is probably best to set the first split between East and West at approx. the Indian-Burmese border. Then the Eastern branch splits between continental and Australasian and the Western one between South Asian and West Eurasian, probably some time later.

      But it's a bit more complex than that. Personally I think that the division between West (originally South Asia) and East was blurry and included some migrations forth and back between parts of India and SE Asia. It only consolidated later on, about at the same time when the Western Eurasian colonization began (early UP) and the first outreach to NE Asia did as well. All three processes were probably caused by demographic growth, which limited migrations within the (sub-)Tropical Asian core areas and pushed some groups to explore the ultimate frontiers.

      " C-V20's closest relative is C-M8, which is found in Japan".

      I was not aware of this phylogenetic affiliation until now. It is indeed interesting.

      "I'm not sure how that can be reconciled into this picture."

      Me neither honestly. Do you know which is the recent study which redefined the C phylogeny; it seems a very interesting study to read and discuss.

      "With regards to admixture from an OOA isolate or directly from tropical Africa, couldn't both be correct to some degree?"

      It's possible indeed but I would not think that the two or three components potentially hidden behind the "Basal Eurasian" label are the same at all: they just share the quality of not belonging to the main Eurasian macro-population but otherwise they are quite different from each other as far as I can tell.

      Personally I'd expect a NE African element in EEFs via Palestine, associated to yDNA E1b and also maybe an Aboriginal Arabian one. The NW African Aboriginal element would be the third potential candidate and it should only be found in La Braña and modern West Iberians - unless there are confounding factors at play, for example if Iberians scored closer to EEF because of La Brana-like influence, what would be a total artifact.

      The issue of what exactly is "Basal Eurasian" in each case really merits further study.

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    2. This seems to be the study: http://www.nature.com/jhg/journal/v58/n4/full/jhg2012159a.html

      Sadly it is pay per view. I would appreciate if someone with access could send me a copy, really.

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    3. @Ryan
      "La Brana was Y haplogroup C-V20 though. C-V20's closest relative is C-M8, which is found in Japan and believed to be associated with the Jomon culture. I'm not sure how that can be reconciled into this picture."

      I can imagine two possibilities

      1) A population starting at point A (India?) expands both west to point B (La Brana) and east to point C (Jomon). Later two distinct populations develop and expand in between point A and B (Egypt-Arabia) and in between point A and point C (China) thus splitting the populations at A, B and C into three separate populations.

      2) As before but the population expanding west to point B (La Brana) reached the mammoth steppe sooner as it extended furthest south at the western end and those mammoth hunters spread east to point C (Jomon) directly across the mammoth steppe.

      mammoth steppe: http://img571.imageshack.us/img571/6525/7dt9.png

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    4. I must mention here that, for what was explained to me recently in a private exchange, the reorganization of the C tree detaches first of all former C3 (now C2), and then another subclade including all other C sublineages (there is doubt about the exact affiliation of Australian former C4). So C still seems to expand from the Far East, even more solidly than before.

      It is true than within this new C1 subclade, European hyper-rare C-V20 and Japanese (also very rare) C-M8 are most closely related but my most parsimonious tentative conclusion is that C-V20 migrated westwards, rather than C-M8 doing the opposite.

      Nothing is certain anyhow but I must say that neither La Braña nor Ainu are known for hunting mammoths (rather deer and fish respectively). I wouldn't build much on mammoth hyping because, other than is some specific areas, these were not the main prey of Paleolithic hunter-gatherers.

      Sadly there's no published study of any sort on the new classification (seems all FTDNA findings), so I decided to leave discussion on this reorganization of Y-DNA hap. C for the future.

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    5. "Nothing is certain anyhow but I must say that neither La Braña nor Ainu are known for hunting mammoths (rather deer and fish respectively)."

      Yeah I am more inclined to the first explanation - both expanded from the same start location (somewhere south of both La Brana and Jomon) and then separated by later expansions.

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  9. In terms of Siberian affinities, the Eurasian steppe runs straight from the Ukraine across to Lake Baikal, so I don't see why it should be all that surprising the populations living adjacent to it would have some greater affinities to people living there.

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    1. First of all the Altai "Aurignacian" is contemporaneous with the earliest European "Aurignacoid" cultures, both surely stemming from West Asia or somewhere around Pakistan or Uzbekistan. They are "sibling" cultures but quite apparently each has its own distinct founder effects and such.

      Between the Asian and the European steppe it is one of the largest Eurasian rivers, the Volga, which is a natural barrier, and also some quite desertic areas. It's not exactly a "highway", although it's not impossible either that there were some occasional contacts.

      There is no clear evidence of interaction between Europe and Central Asia in the Paleolithic, excepted maybe the Gravettian period (Mal'ta boy belongs to that era), which could also have been centered in West Asia.

      Personally I would indeed expect some European flow to Altai and backflow from there within Gravettian particularly but I would also expect both populations to have kept much of their original distinctiveness (for example modern Altaians still retain lots of yDNA Q1, while in Europe this is extremely rare). I may be wrong in this of course.

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    2. Yah, I definitely agree with that assessment. Only thing I'd caution is re: assuming today's river system is representative of what it was like earlier. During the LGM the river system would have been very different. There's a theory out there that Lake Baikal may have had to drain west first to the Aral, then the Caspian, and then to the Black Sea and beyond. The Volga's drainage basin would have been much smaller, and not yet included the Kama. Many areas that now drain south would have drained north initially, only shifting direction as isostatic rebound takes its course after the glaciers retreated. There would have been much less rainfall in the area too. The Volga may not have been a big barrier at the time, but there could have been other less obvious barriers. Perhaps other opportunities as well for people to fish along these river systems as well as along the massive lakes that would be formed by the retreating ice.



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    3. See: → http://donsmaps.com/icemaps.html

      Scroll down for the North Eurasian Ice Age maps, which are extremely good AFAIK. However the river systems appear to be the same, just that there were huge glacial lakes and inner seas that are not any more (or have been reduced, like the Caspian Sea). The Kama was anyhow a Volga affluent, at least in those high quality maps.

      But maybe you know something Don doesn't...

      A clear barrier at the LGM was the huge glacial lake fed by the Obi and to lesser extent the Yenisei, at some times feeding to Aral Sea (and this one to the Caspian). But otherwise the mighty Volga was there in any case, as well as a much enlarged Caspian Sea.

      An even more mighty barrier was probably the ice corridor going between Tibet and NE Siberia via Lake Baikal, according to another map in that series. That would have kept West and East Asia clearly segregated at the LGM and may have accelerated the proto-Amerindian "orientalization" process, as they were already East of it by all accounts.

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    4. Bah, I was getting different glaciations confused. The Kama was captured in the previous interglacial. My mistake.

      All I know is from reading a few articles on Google Scholar. Apparently the exact details of the Volga during the Last Glacial Maximum are a bit unknown as the Soviets obscured much of the information when they built hydro electric dams in the area.

      The map does correspond to what I read (though the exact extent of Siberian glaciation seems to be a matter of debate still). The climate was much drier though. The Volga may not have been as wide or as fast.

      Amerindians were likely cut-off from the Siberian population, with the Siberians more connected to central Asia and Europe, at least according to that map. Thanks for the link - the maps I saw were of lower quality.

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    5. "A clear barrier at the LGM ... An even more mighty barrier"

      Did these barriers separate mammoth into distinct east and west populations?

      If not I doubt they separated the mammoth hunters.

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  10. "This implies that there were already some differences in the Epipaleolithic era among European hunter-gatherers, with those of Magdalenian background lacking the Siberian (ANE) component, which is found however in Scandinavian ones (of Ahrensburgian background?) This may help explaining the extra ANE affinity in Northwest Europe, which is otherwise hard to understand."

    mammoth steppe

    http://img571.imageshack.us/img571/6525/7dt9.png

    If you assume ANE -> WHG ->(EEF) -> "Basal Eurasian" go from north to south then it makes perfect sense.

    If ANE was mammoth steppe (northern) and not Siberian (eastern) - which is what makes the most sense - then it is a latitudinal distinction not a longitudinal one and the extra ANE in NW Europe is easy to understand. It was already there from the end of the LGM.

    The map also explains why you would expect a higher proportion of ANE east of the Black Sea than west of the Black sea. There are physical geographical barriers in the east: Black Sea, Caucasus, Caspian but not in the west. If ANE and WHG were latitudinal bands then as the ice retreated after the LGM then west of the Black Sea you would expect both ANE and WHG to move north because there are no physical barriers but from the Black Sea eastwards there are geographical barriers stopping the more southerly HG populations moving north hence mostly ANE.

    So WHG/ANE in north western europe and mostly ANE in north eastern Europe pre-Kurgan with additional ANE coming west with the Kurgans.

    #

    "The authors believe that the main axis of differentiation in Europe when the subcontinent is considered as a whole may tend to Northeastern Europe rather than SSE/NNW⁸, something that is consistent with their ancient admixture findings elsewhere in the study."

    Alternatively there were two (or more): an earlier SSE/NNW cline and a later NE cline with the later one(s) partially over-writing the earlier ones.

    #

    "This brings us to a key question: what is actually "Basal Eurasian"?"

    Afro-Asiatic (Egypt/Arabia) imo.

    north to south:
    - ANE (mammoth steppe) (northern HG across all of Eurasia)
    - WHG (western *branch* of southern HG) (southern Europe, north Africa, near east)
    - EEF (mix of WHG and "Basal") (Levant)
    - "Basal" (Afro-Asiatic) (Egypt-Arabia)

    The labeling of the populations has tilted the axis of the debate; it's north to south not east to west.

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    1. I would expect ANE and EHG (Eastern-European Hunter Gatherers) to be somewhat different. I.e. EHG should look as a "mix" of WHG and ANE, a bit like Motala but more towards ANE maybe. That's because the core origin of ANE should be from West Asia, while the core origin of EHG should be from Central Europe, much as WHG - of course this ultimately comes from West Asia too but there is an intermediate downstread node in Central Europe which is not shared by ANE.

      So when we see that Lithuanians, for example, are very high in the WHG component, we must ponder how much of that appearance is actually directly from Lochsbour-like ancestry or a more distant relationship via EHGs. The ANE component (absent in WHG) gives us an important clue but even more important is probably the IBD ancestry analysis, which I forgot to discuss but I plan to, maybe today.

      In the last supp. material article, we can see that, while Sardinians share both the greatest number of segments and length of them with the EEF population (represented by Stuttgart), Baltic Europeans only share the greatest amount of segments with WHG, the ones who share the lengthiest segments with Lochsbour are the French, what implies a difference in the patterns of ancestry: French are less % Lochsbour but more recent descendants of the population he represents, Finns or Balts are more % of Lochsbour but more distant descendants, surely because their ancestry is mediated by EHGs, who diverged from Lochsbour before the LGM.

      Probably a comparison with La Braña or Motala would generate different results, because Lochsbour can't represent single-handedly the complex genetics of European Paleolithic. Ideally an Eastern European hunter-gatherer would illuminate this matter even better. We need more research on this matter.

      Just because we only have three clades with known samples, it does not mean that there aren't more. In fact there must be greater complexity in the European ancestry, from Europe and, of course, from outside it (still unexplored in any direct way other than ANE).

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    2. "Afro-Asiatic (Egypt/Arabia) imo."

      Not in the case of La Braña at least. In the case of EEFs "Basal Eurasian" can and probably is partly that, but I cannot exclude "aboriginal Arabian" (OoA residual) from it. In the case of La Braña, it should be an aboriginal NW African element (Aterian residual, today only detectable at significant amounts in Southern Morocco).

      "If you assume ANE -> WHG ->(EEF) -> "Basal Eurasian" go from north to south then it makes perfect sense".

      I can't assume that (all archaeological and genetic evidence is against it). Your map (which exaggerates the extent of the steppe-tundra, a better name than "mammoth steppe") is meaningless unless you can identify the ecology with archaeological evidence, which is at least quite hard.

      Actually:

      West Eurasian → ANE
      West Eurasian → Paleolithic European (WHG but also UHG, EHG, etc.)
      West Eurasian → West Asian HGs (WAHG),

      In some cases WAHG+OoA residue = "Basal Eurasian" (at least one possible such element), in other cases WAHG+NE African ="Basal Eurasian", finally it is also possible to see "Basal Eurasian" as WAHG+OoA residue+NE African.

      In the case of La Braña instead it's nothing of that: just Aterian residue via NW Africa.

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    3. Fair points. I over stress the mammoth steppe point because it seems to me the labeling of the Laziridis components leads people to forget the mammoth zone extended from France to Siberia, not just Siberia.

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  11. Update: new entry on Lochsbour's IBD relatedness, which I forgot to mention here but I find quite interesting: → http://forwhattheywereweare.blogspot.com/2014/04/lochsbours-ibd-in-modern-europeans-is.html

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    1. Those Somali samples are not actually representative of Somalis, they seem to be some sort of strange intermediate between Somalis and "Southern"/ Borana Oromos.

      I explain this here:

      http://www.forumbiodiversity.com/showthread.php/43408-Lazaridis-quot-Kenyan-Somalis-quot-not-representative-A-mix-between-Boranas-and-Somalis

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    2. Is there any sample of Somalis in the Lazaridis study? Why should it even matter if they are a bit more this of that when it is a study on European origins? Sorry, but it seems you mixed this entry with some other.

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    3. Yeah, in the supplemental... In that very plot you share in this blog post. My point is that about 8 to 6 of those 13 samples are seemingly to possibly mixed with Borana Oromos who have "Omotic" admixture and are seemingly less Middle Eastern admixed than your average Somali so my point was simply that I figured you'd be interested in their mixed-ness.

      It would also be liking sharing Amhara samples that are seemingly half Somali and acting like they fully represent Amharas.

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    4. Look again. No Somalis in this entry, Awale (and nothing to do with the thread discussed, which is European origins based on ancient DNA). Please search for the entry you're interested in.

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  12. This comment has been removed by a blog administrator.

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    1. ^^ There are highly irrelevant commercial links (spam) in your comment: hence I have to delete it. Try reposting without them, please.

      Delete

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