February 8, 2012

Splitting hairs with the Neanderthal affinity

John Hawks published today an interesting albeit potentially misleading exercise of comparing (known) Neanderthal DNA (Vi33.16)  to moder humans by HGDP samples.

The first graphic is a for example a very visual representation of why geneticists have concluded that there is a percentage of Neanderthal admixture in non-African humans, a striking visual synthesis of the results of Green 2010 with other modern samples:



It is easy to see for all in this graph that if the median shared Neanderthal variants in Africans is c. 626,000, while in Eurasians is c. 644,000 (visual estimates), then there is something going on and admixture is the most likely explanation.

A simple cross-multiplication exercise shows that the admixture apportion using these medians would be c. 2.9%. However a cautionary use of a higher figure among the African variability range (likely not caused by admixture but retained ancestral diversity) such as 630,000 yields 2.2%.

Green 2010 and later reanalysis by the NGP team estimated 2.4% (although they initially talked of 1-4%), all of which illustrates how is not easy to come with an exact percentage figure and that some uncertainty remains and must remain by the very nature of the exercise and the samples involved.


Splitting hairs

But of course we love to split hairs, at least a bit. I must admit I did it myself back in the day with the handful of samples used by Green et al. originally. Then I was asking rhetorically: are Chinese slightly "more Neanderthal" than other Eurasians?

Not quite because of the uncertainty implied in all the comparison is the real answer: the apparent differences are too small to be significant.

And this more or less what Hawks ponders in his article. As you can see above Europeans appear now slightly more Neanderthal than East Asians. However the difference is actually trivial: approx. 1000 base pairs, what is a variance of 0.12 percentile points of that approx. 2.4% (Hawks writes 'half-percent' when talking of intra-European differences of the same range, but he must be measuring something else than I am: 0.005x2.4%=0.012%, maybe he meant 5%... of that 2.4%? Unsure and, as he does not allow comments, I can't ask).

However, in spite of formally acknowledging this insignificance of the differences, he goes on to state the following unlikely hypothesis:

At present, we can take as a hypothesis that Europeans have more Neandertal ancestry than Asians. If this is true, we can further guess that Europeans may have mixed with Neandertals as they moved into Europe, constituting a second process of population mixture beyond that shared by European and Asian ancestors.

While it's not absolutely impossible, the data does not support any meaningful extra admixture in Europeans but actually what it does support is the lack of any significative difference through Eurasia. IF there was any extra admixture in Europe (or better West Eurasia, what's the obsession with Europe?) it is not detectable and hence was surely hyper-minimal.

We are therefore before yet another case of wishful thinking, of which I have stumbled upon several, much more severe cases in the las weeks alone. The illusion of a Neanderthal admixture or assimilation or even full continuity into, specifically, modern Europeans (usually West Asia is totally ignored even if it was there where most of the Sapiens-Neanderthal interaction must have taken place) is an obsession difficult to put aside for some I am learning.

Hawks is still quite serious and scientific and knows the ropes of genetics quite a bit and, therefore, he does not insist on that too much, showing different angles and comparisons that are interesting albeit unsupportive of his outlined hypothesis. However he does not abandon that unlikely boat so obviously sinking.

I am realizing that it is much harder for some Eurocentric multiregionalists to abandon their old Neanderthalist hypothesis than I would have expected. After all the genetic data is there for all to see and I must say that Hawks provides us with highly informative eye-candy here, which clearly supports the Neanderthal admixture episode and the uniformity of it across the various Eurasian populations.

Yet he seems blinded by the C.I. variation, which is caused, no doubt, mostly or only by local founder effects and/or drift (after the Neanderthal admixture episode).


Illusion of African Neanderthal admixture

A good example is again provided by Hawks himself:


Yorubas here appear some 2000-3000 BPs more Neanderthal than Luhyas. Even Hawks admits to be puzzled by this result, which is obviously attributable to mere ancestral diversity within Homo sapiens (but not for him). He expected the opposite result: that Luhyas, who live in Kenya, would be more influenced by Eurasian back-flow into Africa and display some greater Neanderthal affinity. 

Actually this comparison does not just illustrate well how such small ranges of variation are normal and a remnant of ancestral diversity within the species (most probably) but also illustrates how Dienekes' hypothesis about Neanderthal admixture being in fact internal structure of Homo Sapiens before the migration out of Africa (or even after, because he has also argued for a greater role for Arabia and what not) is a total fantasy. 

Thanks for the interesting and beautiful graphs, Dr. Hawks, but I cannot agree with your hypothesis because I see zero support for it in your own data. I think you have a clear case of splitting hairs syndrome, probably a symptom of repressed multiregionalist grudge (Eurocentric Neanderthalist variant).

21 comments:

  1. Nothing new...

    He wrote:

    The Tuscans have the highest level of Neandertal similarity of any of the 1000 Genomes Project samples. They have around a half-percent more Neandertal similarity than Brits or Finns in these samples. The CEU sample is slightly elevated compared to Brits and Finns as well.

    This is quite unexpected and odd: whi would the CEU be more neanderthal than Brits and Finns, if they're basically a mixture of the two? And why would some Africans be more neanderthal than others? And some Chinese from the same ethnicity? That makes no sense... but yet: why do we see these "statistically significant" differences between closely related differences? And why do some Africans seem to carry neanderthal DNA?

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  3. Although John Hawks doesn't allow comments (I wish he did, I could see some fascinating conversations developing) his email is in the contact info and in my experience he's pretty good at answering it.

    I'm not competent to take sides in this debate, by the way, just trying to work out at least what you're both saying.

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  4. There are a few more pretty important issues about how you model Neanderthal admixture percentages.

    1. How do you determine if any of the apparent Neanderthal admixture is a product of the Neanderthals having some percentage of modern human admixture that is being reflected back in direct comparisons (which is possible given the age of the Neanderthal DNA sources)? If any modern human DNA had introgressed into Neanderthal populations ancestral to the source of our Neanderthal DNA samples, the Neanderthal admixture estimate would be a little too high. And, there is no good reason, a priori, to assume that Neanderthals would have had any less introgression of modern human DNA than modern humans have of Neanderthal DNA. Indeed, there is suggestive archaeological evidence (although nothing really definitive) that could support some level of modern human DNA introgression into late Neanderthal populations.

    2. A more sophisticated measure adjusted for the fact that a few Neanderthal genes are much more common than all the rest and much more common than would be expected relative to the rest if they were selectively neutral. To do it right one has to back out frequencies that are elevated due to selective effects before doing the cross-multiplication if one wants to get a handle on what the admixture percentages were in the immediate time frame of Neanderthal introgression becoming fixed in the modern human gene pool. The adjustment wouldn't be big, because most of the Neanderthal genes don't show indications of strong selective effects, but an adjustment to reflect this necessarily lowers the estimated Neaderthal admixture percentage by a bit.

    3. I agree that the evidence does not support the hypothesis that Europeans have statistically elevated levels of admixture relative to Asians. But, one has to devise a population model that explains why because what we know from the duration and location of Neanderthal-modern human co-existence, standing alone, should lead to higher levels of admixture in Europeans. Duration of co-existence matters in any reasonable admixture model and Europeans clearly co-existed with Neanderthals much longer than Asians did. My personal conclusion is that the lack of elevated admixture in European is strong evidence that Europeans from the era during which Neanderthal-modern human co-existence continued in Europe but not Asia where diluted to an extreme extend by later waves of modern humans who had not experienced additional admixture in Europe. In other words, Northern European modern humans ca. 30,000 years ago probably did have elevated Neanderthal admixture, but were so diluted by multiple waves of later migration from the Middle East and West Asia, for example, that their contribution to European Neanderthal admixture levels in modern populations is statistically invisible. If that theory is correct, the European populations with the highest Neanderthal admixture levels within the range shown on the chart should be the European relict populations most closely related genetically to Upper Paleolithic, pre-LGM populations (e.g. those populations would also probably be rich in mtDNA haplogroup U5).

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  5. 4. The fact that an East African population shows less Neanderthal admixture than s Nigerian one is surprising, at least in the absence of cyptic Euroasian ancestry from Saharan or Colonial sources which isn't really supported by the Y-DNA or mtDNA evidence. Alternately, the founding population of modern Nigerians may have originated in East Africa sometime in the Holocene - although it is still hard to see how Nigerians could be more closely related to Eurasians than East Africans given the abundance of uniparental and autosomal genetic evidence to the contrary.

    Dienekes' surely is right that there must have been considerably population structure in Africa at the point of the Out of Africa migration(s) as you have pointed out in comments at my blog about the mtDNA evidence supporting that conclusion. But, I also agree with you that it is hard to see (particularly in light of the lack of excess Neanderthal admixture in East Africans) how that could account for observed levels of Neanderthal admixture which my hair splitting above only tweaks a little. The Eurasian numbers at the charts illustrate, are entirely outside the range of modern African diversity and it isn't obvious how or why a population within the modern Eurasian range would have gone extinct in Africa while being so successful in the rest of the world, without contributing to African DNA in a notable way.

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  6. The Luhya are Bantu speakers who migrated to the East only 3000 years ago. So they aren't representative of this region, they also could have Archaic/Pygmy admixture which would lower their Neanderthal affinities compared to aboriginal East Africans.

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  7. I went to Hawks' site and read his entire argument. I am also unimpressed with his hair splitting interpretation. Except for the clear void between A/OOA, the other graphs show nearly superimposed bell curves. The differences within each region can be best explained by founder effects and drift.

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  8. Most of the comments queuing up for moderation were from this post. Sorry but I did not see them at all (I expected an email notice I never got).

    Just so you know (if subscribed) that your comments are now up and that I feel really bad about the delay.

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  9. "why would the CEU be more neanderthal than Brits and Finns, if they're basically a mixture of the two?"

    Mormon Neanderthal gene? Or just drift?

    ...

    "his email is in the contact info and in my experience he's pretty good at answering it".

    Ok. I take notice, although I am too shy to generally allow myself to write to someone who has not written to me first (exceptions can be made but I kinda need a good excuse, as I feel like invading the other's privacy without invitation).

    ...

    "The Luhya are Bantu speakers who migrated to the East only 3000 years ago. So they aren't representative of this region"...

    They should be MORE representative than the Yoruba in any case. We do not know anyhow if they actually migrated or just assimilated into a small immigrant farmer group. In Henn's latest paper they cluster with Maasai and not other Niger-Congo peoples, so I have absolutely no reason not to think that they do not represent East Africans in general at least to some extent.

    "they also could have Archaic/Pygmy admixture which would lower their Neanderthal affinities compared to aboriginal East Africans".

    Bushmen and Yoruba were similarly non-Neanderthal in the original Green 2010 paper. Some Yoruba appeared a bit "more Neanderthal" (as they do here in relation to the Luhya) but that was interpreted (correctly I think) as normal meaningless diversity.

    This interpretation is what Hawks seems to be challenging based on nothing but his imagination.

    ...

    "I am also unimpressed with his hair splitting interpretation".

    Thanks Joy, I'm glad that some other people also see it as I do.

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  10. @Andrew

    "... there is no good reason, a priori, to assume that Neanderthals would have had any less introgression of modern human DNA than modern humans have of Neanderthal DNA".

    Yes, that Green et al. could not detect it. This "a priori" can only be seen as "before" Green 2010 but it was Green 2010 which revealed the Neanderthal admixture so I kinda find your sentence self-contradictory (oxymoron).

    "I agree that the evidence does not support the hypothesis that Europeans have statistically elevated levels of admixture relative to Asians. But, one has to devise a population model that explains why because what we know from the duration and location of Neanderthal-modern human co-existence, standing alone, should lead to higher levels of admixture in Europeans".

    The model is known: single admixture event at the exit from Africa (between Africa and South Asia - your choice) within a small population.

    The admixture event probably implied that the migrant pop. absorbed an already hybrid bunch, maybe from the Galilee group. Other hybrids would have gone effectively extinct, assuming they existed at all.

    The key is understanding that coexistence does not imply hybridization, even if it remains as a possibility. There can be cultural and/or biological factors involved, probably both.

    "Dienekes' surely is right that there must have been considerably population structure in Africa"...

    Why don't we see it today anywhere? I mean: there is diversity and structure in Africa but not in the sense Dienekes proposes. There is no significant signal of "Neanderthalism", so to say, among any Africans (not admixed with Eurasians) but the signal is hyper-strong and homogeneous among non-Africans.

    You, Dienekes and Hawks can build on thin air all you want but the evidence is not there and once cartoon physics yield to real physics, your hypotheses falls to the abyss like ol' good Wile E. Coyote for lack of anything supporting them.

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  11. I'd like to add:

    If Tuscans are more neandertal than Brits and Finns, how does this deal with the Neolithic demic diffusion model? As far as we know, Tuscans share more affinities with Middle Easterners than Brits and Finns do, yet if Hawks is right with his nearly complete replacement in the Holoce, we'd expect to see opposite, that's it, North-western euros being more neandertal.

    Hawks also said the Yoruba may be admixed, yet we know they are no more than 5% "non-african" according to several ADMIXTURE runs and mtDNA.

    Some authors have suggested that, based on their anatomy, Vindija neanderthals may be mixed to some extent, yet their DNA don't show any admixture coming from modern humans, so I really don't know what to think.

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  12. I don't know what to think about the alleged lack of Sapiens admixture in Neanderthals. Unlike what happen with our kin, there was not so much to compare within the Neanderthal species, so maybe Green et al. missed something?

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  13. "I don't know what to think about the alleged lack of Sapiens admixture in Neanderthals. Unlike what happen with our kin, there was not so much to compare within the Neanderthal species, so maybe Green et al. missed something?"

    I think it's quite possible. After all, we know modern humans have been living there for more than 100.000 years, and unidirectional gene flow doesn't seem too realistic. It'd be interesting to extract DNA from Amud, Kebara or one of these "progressive" neanderthals althought I'm not sure if that's possible at all.

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  14. "The model is known: single admixture event at the exit from Africa (between Africa and South Asia - your choice) within a small population. The admixture event probably implied that the migrant pop. absorbed an already hybrid bunch, maybe from the Galilee group. Other hybrids would have gone effectively extinct, assuming they existed at all. The key is understanding that coexistence does not imply hybridization, even if it remains as a possibility. There can be cultural and/or biological factors involved, probably both."

    Co-existence produced hybridization once, but only once, despite superficially very similar circumstances in the later instances. So, what changed? What made the later co-existence different than the first one? That is a very interesting question in my mind and demands more than an "it seems to be what happened" explanation.

    "I mean: there is diversity and structure in Africa but not in the sense Dienekes proposes. There is no significant signal of "Neanderthalism", so to say, among any Africans (not admixed with Eurasians) but the signal is hyper-strong and homogeneous among non-Africans."

    I don't think we disagree much on this score. Yes, there was surely population structure in Africa, and no it doesn't seem to have been very important in Neanderthal admixture percentages. Indeed, the emerging evidence seems to point instead to admixture with various non-Neanderthal archaic hominins as one possible sources of what genetic distinctiveness there is in Bushmen, Pygmies and Melanesians, respectively, compared to their regional neighbors. This in turn implies that there AMH ancestors of these peoples may have been somewhat less distinct than their modern descendant populations are from their regional neighbors.

    In particular, Dienekes seems to be thinking about African population structure with time depths on the order of 300kya+, while I'm inclined to think that most of the population structure in Africa today has a time depth of 150kya or less, and that the African population structure at OOA would have had considerably less time depth and hence considerably less distinctiveness. In my view, with the exception of something on the order of three to six relatively minor percentage of descendent-wise archaic admixture events (Neanderthal, Denisovian, at least one in Africa, and perhaps a few more than are not well established yet), that modern humans have a pretty tree-like lineage from an African Adam and an African Eve within the last 150 kya and perhaps even more recently, with the earlier part of the modern human era being less geographically dispersed and not huge in effective population.

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  15. "The model is known: single admixture event at the exit from Africa (between Africa and South Asia - your choice) within a small population. The admixture event probably implied that the migrant pop. absorbed an already hybrid bunch, maybe from the Galilee group. Other hybrids would have gone effectively extinct, assuming they existed at all. The key is understanding that coexistence does not imply hybridization, even if it remains as a possibility. There can be cultural and/or biological factors involved, probably both."

    Co-existence produced hybridization once, but only once, despite superficially very similar circumstances in the later instances. So, what changed? What made the later co-existence different than the first one? That is a very interesting question in my mind and demands more than an "it seems to be what happened" explanation.

    "I mean: there is diversity and structure in Africa but not in the sense Dienekes proposes. There is no significant signal of "Neanderthalism", so to say, among any Africans (not admixed with Eurasians) but the signal is hyper-strong and homogeneous among non-Africans."

    I don't think we disagree much on this score. Yes, there was surely population structure in Africa, and no it doesn't seem to have been very important in Neanderthal admixture percentages. Indeed, the emerging evidence seems to point instead to admixture with various non-Neanderthal archaic hominins as one possible sources of what genetic distinctiveness there is in Bushmen, Pygmies and Melanesians, respectively, compared to their regional neighbors. This in turn implies that there AMH ancestors of these peoples may have been somewhat less distinct than their modern descendant populations are from their regional neighbors.

    In particular, Dienekes seems to be thinking about African population structure with time depths on the order of 300kya+, while I'm inclined to think that most of the population structure in Africa today has a time depth of 150kya or less, and that the African population structure at OOA would have had considerably less time depth and hence considerably less distinctiveness. In my view, with the exception of something on the order of three to six relatively minor percentage of descendent-wise archaic admixture events (Neanderthal, Denisovian, at least one in Africa, and perhaps a few more than are not well established yet), that modern humans have a pretty tree-like lineage from an African Adam and an African Eve within the last 150 kya and perhaps even more recently, with the earlier part of the modern human era being less geographically dispersed and not huge in effective population.

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  16. "So, what changed?"

    We can't know. We can speculate but that is best done before som beers and maybe a joint or two... I mean: we won't go anywhere that way, we can't prove anything... but we can have some laughs.

    Rather than thinking in what changed in normal temporal direction anyhow my speculation is what was exceptional early on allowing the admixture events (two considering the "Denisovan" one) to have such an effect.

    One element is population size maybe. Probably when those hybridization events happened the proto-Eurasian and proto-Australasian populations respectively were very small, so a few hybrids caused a lot of impact. Later the population of Sapiens would be so large that any exceptional hybridization episode would cause no visible impact anymore.

    The archaic populations would also decrease, rather rapidly in many places, so the opportunities for hybridization would be less and less common.

    But there may have been other reasons, for example, as Sapiens became more common in Asia, they may have felt growingly hostile, xenophobic, racist... toward other populations, which may have been culturally and even cognitively different (the cultural part may well apply to other sapiens) and certainly be easy to identify visually and by other senses (smell, sound - Neanderthals had different voices probably). That may have also been the case in the Neanderthal side of the equation: "those swarthy skinny sapiens that occupy our ancestral hunting grounds!"

    I think that in general mistrust and hostility grew because of the Sapiens (and to lesser extent also Neanderthal) success that left so little land open for newer expansion pitting the clans against each other and toward marginal lands more and more.

    "the emerging evidence seems to point instead to admixture with various non-Neanderthal archaic hominins as one possible sources of what genetic distinctiveness there is in Bushmen, Pygmies"...

    I have not seen any evidence just a modeling and models are not evidence but "toys". As far as I am concerned it's not impossible but there is absolutely no evidence as of now.

    "... and Melanesians"...

    Obviously "what genetic distinctiveness there is in"... Melanesians is not just product of the hybridization episode with "Denisovans" or Erectus. That's only a small part of the picture. Most of their distinctiveness is there because they have diverged in relative isolation through a long time, as happens with all populations that we can consider "distinct" in similar manner (races or whatever).

    ...

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  17. ...

    "In particular, Dienekes seems to be thinking about African population structure with time depths on the order of 300kya+, while I'm inclined to think that most of the population structure in Africa today has a time depth of 150kya or less, and that the African population structure at OOA would have had considerably less time depth and hence considerably less distinctiveness".

    I am rather with you in the time frame, although I browse older time figures as possible too. The main issue is that for some the genetic hunches (based in totally wrong assumptions) of Neanderthal divergence between 800 Ka (Green, not a bad figure) and as littl as 300 Ka (crazy!) are right. In reality Neanderthal divergence is more in the 0.9-1.3 million years and that makes the time depth differences you mention less important.

    What really matters is imagining that the Neanderthal divergence is a late and not an old phenomenon. That's a key disagreement that distorts everything else.

    And a disagreement they won't discuss: they just repeat the short chronologies, as short as possible, once and again, Goebbels style. That is not science but propaganda.

    A major key (in all genetic age estimates) is the issue of Pan-Homo divergence ages. As I have mentioned once and again in this blog and its predecessor (each time mentioning a different study, all them convergent), genetic modelings systematically underestimate the Pan-Homo divergence age, producing therefore estimates that must be 15-100% lower than reality (assuming everything else is ok).

    Another issue is the divergence of the Trinkaus school that claims a hyper-short Neanderthal divergence of maybe as little as 350 Ka. and extensive admixture (nowhere to be found) and what not and the, IMO much more solid, Atapuerca school that states that Sapiens-Neanderthal divergence is probably of the order of 1.3 million years. When you follow Trinkaus' ideas things don't make sense, contradictions pile up, clearly indicating that the popular scholar is less wise than his fame would suggest.

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  18. It seems like the new trend in trying to explain away African genetic diversity is by invoking hybridization with some archaic hominini, when there is a simple and easy explanation of the origin of the species as evidenced by the sole continent on earth where MRY, mtDNA and fossil evidence meet together, which would therefore imply a higher effective population size for a longer amount of habitation time than anywhere else on earth, this would therefore be the most plausible scenario leading to modern Africans harboring more genetic diversity than non-Africans, no need to invoke the Gods of the now dead multi-regionalists.

    It seems quite simple to me, modern human beings have been outside of Africa for only less than half the time since the origin, from which they separated and filled all the corners of the world, and say one does not delineate the origin by 'speciation', then the time humans have been outside of Africa would even further decrease to a very small fraction.

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  19. What happens is that at the very genesis of the species, say some 190-160 Ka ago based on the fossil record (Omo, Idaltu, Irhoud, etc.) there must have been other Homo sp. (Homo ergaster/rhodesiensis, I guess, closely related to H. sapiens in any case, closer than Neanderthals) living in other areas of Africa. As our kin expanded in Africa (first wave: L0, L1 specially, possibly c. 160 Ka. if Irhoud is a product of it) it must have met them. Whether they hybridized or not is another story and the evidence so far is not yet there in any case.

    What I recollected in Sep 2010 in one of my last Leherensuge posts titled 'Late human evolution maps', is that, before Homo sapiens, in the c. 400-200 Ka ago parenthesis, in Africa there was a population of H. ergaster ("erectus" in the maps, following the source's nomenclature) in North Africa (and the Levant), while in East Africa we have H. rhodesiensis and the Eyasi hominid, dated 240 Ka. which is probably transitional towards our species. We also know of previous H. rhodesiensis in Southern Africa and no reason to think it went extinct. As always the jungle areas of West and Central Africa are lacking any fossils but it's legitimate to imagine they were inhabited by some kind of Homo sp. as well.

    While it's probable that the origin of our species is localized in a single area, which I presume, based on mtDNA and fossil record, is the Upper Nile (but notice that Y-DNA and autosomal genetics may contradict this picture somewhat), the process of interaction with the other closely related species (or subspecies) upon expansion is open to speculation and some admixture can't be discarded indeed.

    But the data so far demonstrates nothing anyhow. And I doubt we will have any clear data in a long time (if ever) because it looks difficult in principle to extract DNA from those other hominin remains.

    I just would like to add that Jebel Irhoud has often been considered "hybrid" of some sort (very controversial) and maybe he was indeed, just that not with Neanderthals but maybe with H. ergaster "mauritanicus" (just made up the subspecies label, don't take it too seriously, please). It's even possible that what we see as "Neanderthal admixture is H. ergaster admixture instead, as both Neanderthal and us descend from H. ergaster or can even be considered subspecies of H. ergaster. These North African Ergasters would be indeed similarly distant from us as from Neanderthals.

    But of course, as you can see in the last map, the Sapiens-Neanderthal physical proximity in Palestine later on is very hard to ignore (and for some reason I forgot to map Shanidar), so the Neanderthal admixture explanation looks like the best one anyhow.

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  20. Those are nice maps Maju.
    I never questioned the genetic evidence that modern humans and Neandertals were breeding in trace amounts, I don't think it was in any significant amount however, if it was, we would likely have found very different looking mtDNA (or possibly YDNA as well), I just think this whole 'breeding with archaics' thing is being overestimated and overblown in describing the current genetic variation around the world , which is still a function, by and large, of modern humans migrating out of Africa, not withstanding the trace amounts of non-HSS admixture the early migrants encountered.

    However, when this 'breeding with archaics' frenzy is being applied to Africa I think a different approach has to be taken, mainly because HSS transitioned from 'archaic' to 'modern' probably within Africa, not outside, unlike the Neandertal/HSS pre existing divergence. Telling who was archaic and who was modern thus becomes more murky, like the difference in morphology between Idlatu and OmoI, or even between OmoI and OmoII while all of these are <200 KYA some are considered archaic some modern. Could Africans have bred with archaics that diverged >200 KYA, sure, but probably in trace amounts like the eurasian case, again, there is no evidence in Africa of MRY or mtDNA being present that is older than 200KYA.

    By the way, could the qafzeh skulls be a result of hybrids (HSS/Neandertals) too? Neandertals have had a long presence in the Israel area.

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  21. I understand that the evidence of admixture with Neanderthals is very difficult to question. I looked at it back in the day with maximum care (I was initially skeptical) and there are no faults: the data is there and it's clear: Eurasians-plus (non-Africans or whatever) have c. 2.4% of Neanderthal admixture.

    Is it 2.2.% instead of 2.4%? Maybe, that's the part of hair-splitting that can't be determined but that there is significant (>2% is not insignificant or "trace", even if it's not a lot either) admixture is undeniable. For some it's "great", for others troublesome maybe... but for me it's just a fact of life, like gravity or the need to pee.

    But I totally agree, I think, with what you say of hybridization in Africa. It's murky, the "archaics" involved (if any) were necessarily closer relatives and, crucially, we have no direct evidence, just reasonable speculation (reasonable maybe but speculation in any case).

    "could the qafzeh skulls be a result of hybrids (HSS/Neandertals) too?"

    That has been speculated specially with Skhul 5. However, when I mentioned Irhoud earlier I had also in mind that it is very similar to Skhul5, so maybe it's admixture with Ergaster instead (???)

    It's perfectly possible that (if I'm correct about this Ergaster admixture, so far speculative) that it was mostly lost anyhow after the OoA and that the Neanderthal admixture episode happened elsewhere (Persian Gulf?) It is also possible, I guess, that what we see as Neanderthal admixture is in fact (in all or part) admixture with other Homo ergasters.

    But getting sure about all these matters would require having a bunch of archaic genomes available, and that is not the case as of now (maybe never because of preservation issues).

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