June 18, 2012

Denisovan and Neanderthal proviral DNA

A provirus is a strand of autosomal DNA that was inserted by a virus once upon a time and got lost in our genome as junk DNA, not being anymore active (would it remain active it'd be a retrovirus). Such insertions are thought to be unique phylogenetic events. 

New research has identified a provirus* (HERV-K-Ne1 = HERV-K-De6, inserted in Chromosome 5) shared by Neanderthals and Denisovans but not Homo sapiens. This is consistent with the previous data that placed their autosomal DNA closer to each other than to Homo sapiens.

Lorenzo Agoni et al., Neandertal and Denisovan retroviruses. Current Biology, 2012. Freely accessible (letter with supplementary material) at the time of writing this.

It must be noted however the mitochondrial DNA, inherited by pure matrilineage, is much closer among our species and Neanderthals than either one with Denisovans, what to me suggest that Denisovans are no new species but a hybrid of Neanderthal and Homo erectus. A theory not yet fully testable for lack of DNA from Asian Homo erectus.

Interestingly Denisovans have also several proviruses not found in Neanderthals, what could well support my theory of hybridization. The detected provirus could hence have migrated from Neanderthals to Denisovans in the hybridization episode (along with lots of other autosomal DNA), while the rest could have been retained from the H. erectus ancestors by the maternal line. 

However as the article is both very technical and succinct, I can't be sure right now of how strongly or weakly can this info support the hybridization model (founded opinions welcome). 

In total the researchers detected three Neanderthal proviruses and 12 Denisovan ones, one of which is shared between both nominal species. It is convenient to remind that while the Denisovan genome was very well preserved and sequenced almost completely, the Neanderthal genome is only known in fragmentary form, amounting to about 60% of the actual genome.

25 comments:

  1. FWIW, I find a theory that Denisovians are a relict population of East Eurasian Homo Erectus, whose common retroviral infections may have more to do with the Eurasian range of the retroviruses than with a hybridization with Neanderthals, to be more plausible. But, I don't think that there is enough evidence for any theory to reach a clear conclusion.

    Also, to the extent that there is hybridization, I'm inclined to think that introgression of existing Eurasian Homo Erectus into proto-Neanderthals in general, is probably the more likely theory, than late Neanderthal and other archaic admixture in Denisovians.

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    1. Neanderthals were living side by side with Denisovans, mind you, at the same time in the same district, separated just by a day's walk or so. Hybridization of Neanderthals into Denisovans is not unlikely at all - what is not clear is the other part: that of Homo erectus of which we have no DNA and no recent enough fossils other than H. floresiensis.

      Also it's not retroviruses but proviruses, and either one are just transported by their host: they have no "range" that we know of.

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    2. By "range" I mean that viruses (and pathogens generally) are present in hosts and actively infecting people in some geographic areas and not others. For example, pre-Columbian Europe didn't have modern syphillis. HIV was infecting people in Central Africa thirty years before it became visible in North America, but is almost absent from Tibet. Infection rates for a variety of infectious agents vary dramatically from region to region today.

      And, while we may not have Homo erectus fossils quite that recent, we do have Denisovian genes at fairly high levels in Melanesians, which puts Denisovians precisely located where Homo Erectus is the only pre-existing archaic hominin known to have been present before modern humans from archaeological evidence from both bones and lithic tools, and we have some evidence of incipient speciation of Asian Homo Erectus within the range of fossil variation. We also have an absence of any Neanderthal bones or tools much past India on the Southern Route. I suspect that Denisovians were Homo Erectus mostly for lack of any other pluasible candidates.

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    3. But the provirus is not anymore a virus, but a genetic remnant of what was once one. So it doesn't matter much where it was inserted (which was almost necessarily a single incident) but that it was transmitted as part of the human nuclear DNA since then. So the range is that of the humans that have it in their DNA.

      Agree with the H. erectus thing, as you know, of course, although the position of the nDNA in the ML tree rather suggests a hybrid with Neanderthals, because H. erectus is in principle equally distant from both Neanderthals and us.

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  2. "It must be noted however the mitochondrial DNA, inherited by pure matrilineage, is much closer among our species and Neanderthals than either one with Denisovans, what to me suggest that Denisovans are no new species but a hybrid of Neanderthal and Homo erectus".

    The fact that mtDNA, aDNA and, now, the provirus information all give conflicting results indicates to me the the hybridisation involved more than just one event. In other words the three populations are just regional subspecies, capable of interbreeding whenever they met. Just one of those regional populations eventually came to provide most of the modern human genes. Millan Mozota's recent comments posted at your blog on Cantabrian rock art regarding the 'undefinite Early Upper Paleolithic (EUP)' hints strongly that the Neanderthal replacement in Europe was a gradual process. Several fossils can even be interpreted as demonstrating such a gradual transition as modern humans came to predominate in Europe.

    "Hybridization of Neanderthals into Denisovans is not unlikely at all - what is not clear is the other part: that of Homo erectus of which we have no DNA and no recent enough fossils other than H. floresiensis".

    I agree.

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    1. Would it not because of the mtDNA, I would not probably be considering the hybridization scenario at all. First we got the mtDNA which was consistent with a H. erectus (at least for all of us who think that pre-Neanderthal and pre-Sapiens diverged some one million years ago, with the Aucheulean expansion).

      Later we got the autosomal DNA (aka "nuclear DNA" or nDNA, not aDNA, meaning "ancient DNA") and, in those, often misleading, ML trees it became positioned somewhat below the Sapiens-Neanderthal split node, in the Neanderthal branch. This means that it was slightly closer to Neanderthals than to us.

      From experience I know that mixed populations very often end up in high branches in such trees and we had the much more divergent mitochodrial DNA, so I immediately imagined a hybrid. However, lacking a H. erectus genome, this is impossible to verify.

      And now we get these results (which are a subset of the nDNA, not anything truly new), that suggest quite less than 50-50 admixture but are very hard to evaluate, not the less because they may well be an statistical irregularity, i.e. particularly non-representative of the overall genome.

      I would not jump to conclusions really but I felt the need of sharing this in any case. What we really need is an H. erectus genome, even a H. floresiensis could do, I guess.

      I'll reply to your other qualms in a separate comment.

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    2. Arguable gradual technological transition in Europe, possibly occurring within a few Neanderthal communities in the context of general Aurignacoid advance (associated to H. sapiens in Asia at least), does not imply gradual biological replacement, as in hybridization-dilution-dilution-etc. First, there are not enough archaeological cultural waves to justify all that alleged dilution to undetectable homeopathic-like levels. Second, we are finding H. sapiens mtDNA (and only that) since the very Gravettian period, so the homeopathic dilution had to be very very quick, with not enough cultural layers to justify it, or rather not happen at all.

      Incidentally, Millán is skeptic of any such transition, although there are some old-school authors who still don't seem to understand that the Neanderthal introgression into the H. sapiens species was a unique event that happened some 40 or 50 thousand years before the MP-UP transition, affecting all non-Africans (and those Africans who have back-migrant blood).

      What Millán suggested is that either the "Transitional Aurignacian" is a Chatelperronian-like Neanderthal innovation in the UP direction or that, in El Castillo case, it is a confusion of layers because the cave was dug with rather rough methods and poor guarantees in the very early 20th century, that much of that material could well be from the truly "Archaic Aurignacian" layer 16, which is more recent than layer 18.

      There's not enough data to resolve the matter but it can well be argued, based on other sites, that Neanderthals were innovating in an UP direction (much like Chatelperronian but less defined) about the time when H. sapiens showed up in the continent with neat Aurignacoid (Aurignacian 'senso lato') tech (at the very least Proto-Aurignacian, Swabian Aurignacian and true Aurignacian I).

      In any case, if the El Castillo date must be scrapped, we have Proto-Aurignacian in Isturitz just a few decades later, etc. There's no confusing "transition" there, don't worry.

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  3. "Later we got the autosomal DNA (aka 'nuclear DNA' or nDNA, not aDNA, meaning 'ancient DNA')"

    I use 'aDNA' as shorthand for 'autosomal DNA'. I've never seen it used for 'ancient DNA'. Any examples?

    "Second, we are finding H. sapiens mtDNA (and only that) since the very Gravettian period",

    But we have no idea really of what was happening genetically before then.

    "so the homeopathic dilution had to be very very quick",

    Again, not necessarily so. We have the whole TRansitional Aurignacian and Aurignacian proper to fill in.

    "there are not enough archaeological cultural waves to justify all that alleged dilution to undetectable homeopathic-like levels".

    We wouldn't really expect to see 'cultural waves' if we have an increase in the local 'modern human' population and when the earliest cultures of both Neanderthal and Modern are so similar.

    "it can well be argued, based on other sites, that Neanderthals were innovating in an UP direction (much like Chatelperronian but less defined) about the time when H. sapiens showed up in the continent with neat Aurignacoid (Aurignacian 'senso lato') tech (at the very least Proto-Aurignacian, Swabian Aurignacian and true Aurignacian I)".

    I have no problem at all accepting that hypothesis. But I find it unlikely that Neanderthals would be 'innovating in an UP direction' in the absence of any contact with modern humans. Diversification is the usual phenomenon in the ansence of contact. It could be possible to argue 'parallel evolution' of culture but that argument would stand on shakey ground.

    "Would it not because of the mtDNA, I would not probably be considering the hybridization scenario at all".

    Exactly. Hybridization is actually quite difficult to detect without the relevant original populations.

    "And now we get these results (which are a subset of the nDNA, not anything truly new), that suggest quite less than 50-50 admixture but are very hard to evaluate"

    But don't forget that genes are reduced by one half with every back cross. For most breeds of domestic animals 15/16 is sufficient for an individual animal to qualify as 'purebred' of the majority DNA. That is just four crossings: 1/2, 1/4, 1/8, 1/16.

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    1. http://en.wikipedia.org/wiki/ADNA > Ancient DNA (redirected from aDNA)

      Autosomal DNA does not have a shorthand but nDNA is approximate enough (you just have to scrap Y-DNA or W-DNA in the species that have it).

      ...

      "Again, not necessarily so. We have the whole TRansitional Aurignacian and Aurignacian proper to fill in".

      That's still very fast in absence of new Homo sapiens waves. The fact is anyhow that after the MP-UP transition we have exactly the result we would expect if there was absolutely no hybridization in Europe, so the most parsimonious conclusion is that there was no further hybridization worth to mention.

      Anyhow, in real life there's no such thing as homeopathy: it's called "wishful thinking" or "placebo". However in homeopathic practice the gurus actually do all the job of dilution, what requires immense amounts of water (or other non-active component) and in the Aurignacian period there was not enough of that "water". We should see some signals in the Gravettian or even today - and we do not.

      "... when the earliest cultures of both Neanderthal and Modern are so similar".

      Actually they are not.

      "But I find it unlikely that Neanderthals would be 'innovating in an UP direction' in the absence of any contact with modern humans".

      Fair enough. But nobody knows where that contact happened and what dimension had. Also there are some elements in Mousterian that can be precursors themselves (some rustic bladelets), so maybe it's not so easy to characterize mode 4 vs. mode 3 in absolute terms, at least in transitional periods.

      Whatever the case techno-cultural borrowing does not need to imply sex, much less effective reproduction.

      "But don't forget that genes are reduced by one half with every back cross".

      Approximately so (it's not automatic because of recombination). But do you think there were enough H. erectus in Siberia for that? Also, if so, why does the Denisovan nDNA fall within the Neanderthal-Sapiens clade and not outside. I'd say that minor Neanderthal intorgression would not alone cause it.

      So I'd rather think that these specific sites are not representative of the whole Denisovan genome.

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  4. I still think Densisovans are mostly (if not entirely) heidelbergensis-like - all time frames match rather well. Heidelbergensis, and thus also Neanderthals (later on), diverged from humans when climate shut off gene flow between Europe & West Asia versus Africa ~400,000ya. However, heidelbergensis in West Asia might very well have had a much deeper maternal lineage, given the original expanse over three continents (or may have interbred with Asian erectus).

    While it is not clear whether AMHs interbred with ~local Denisovans or perhaps somewhere along a heidelbergensis-like - Asian erectus continuum, if there were several waves of advance, at one point separated by Toba, what now looks like local SE Asian admixture could have very well occurred any place in Pakistan or NW India, instead.

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    1. Not likely because:

      1. That implies a wide front, unconstrained, gene flow, ignoring not just deserts but also seas, cultural barriers and what not. That'd be like a perfect gas, not like real biology, where clades (more or less gradual genetic transitions) also imply clusters (more or less abrupt genetic distinctions).

      2. There is a buffer of neither-this-nor-that hominins between the proto-Neanderthal H. heidelbergensis cluster in Europe and the proto-Sapiens H. rhodesiensis cluster in East and South Africa. This buffer may have been vehicle of very minor genetic flow but mostly would have acted as barrier, as effective buffer.

      http://leherensuge.blogspot.com.es/2010/09/late-human-evolution-maps.html

      Finally I'm not even sure where you get the notion that there was a climate shift at c. 400 Ka ago and not earlier, according to the ice core data the c. 400 Ka BP climate optimum is just one in a cyclical series preceded and followed by many others. Not sure why that one would be special.

      On the contrary, we have good reasons to think that the Neanderthal-Sapiens split happened at the Baventian (Pre-Pastonian) stage c. 1.3-0.8 Ma ago, which is the period in which Acheulean tech and Homo ergaster made it out of Africa. But the climatic understanding of those periods is at the very least blurry, so I'd focus on material evidence.

      "While it is not clear whether AMHs interbred with ~local Denisovans"...

      If that would be the case we'd see Denisovan genetics in Siberia and Native America and not in (mostly) Australasian Natives.

      "if there were several waves of advance"...

      We have no evidence of any such several waves. Rather the opposite, although of course some minimal complexity within the single wave must have existed, specially upon arrival to SE Asia, where possible paths seem to multiply.

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  5. "Heidelbergensis, and thus also Neanderthals (later on), diverged from humans when climate shut off gene flow between Europe & West Asia versus Africa ~400,000ya. However, heidelbergensis in West Asia might very well have had a much deeper maternal lineage, given the original expanse over three continents (or may have interbred with Asian erectus)".

    To me that sums the situation up pretty well. We really have just one species that has occasionally developed independently in several different regions and at other times mixed again.

    "But do you think there were enough H. erectus in Siberia for that? [genes are reduced by one half with every back cross]".

    To me it looks as though Siberian H. erectus were eventually outbred by humans carrying genes from Africa. But enough 'Denisova' genes survive to be detectable in some human populations today.

    "Autosomal DNA does not have a shorthand but nDNA is approximate enough"

    OK, nDNA it is.

    "That's still very fast in absence of new Homo sapiens waves".

    The point I was trying to make was that there is no need to postulate new waves. If the first lot in establish a population that expands in numbers and, eventually, in geographic range a single 'invasion' is sufficient. As that population expands its range it will replace the earlier population but quite possibly breeding with them as they expand.

    "The fact is anyhow that after the MP-UP transition we have exactly the result we would expect if there was absolutely no hybridization in Europe, so the most parsimonious conclusion is that there was no further hybridization worth to mention".

    Don't we have evidence that the Gravettian is from at least as far east as Eastern Europe? Perhaps the earliest Aurignacian was carried by Y-DNA I and the Gravettian by Y-DNA R1b.

    "Also there are some elements in Mousterian that can be precursors themselves (some rustic bladelets), so maybe it's not so easy to characterize mode 4 vs. mode 3 in absolute terms, at least in transitional periods".

    And that should lead us to being cautious regarding rapid replacement in Europe. Some level of continuity is quite possible. But humans carrying the African genes (or with parents who ultimately derived from Africa) were more effective at surviving. Perhaps through some aspect of social organisation.

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    1. We are not going to agree, Terry.

      Why would the Denisovan genes survive almost only in Australasia if the admixture was, as in the Neanderthal case, indiscriminate? Illogical thinking here.

      "Siberian H. erectus were eventually outbred by humans"

      "Outbreed" is not in my dictionary. It needs too many special conditions, mostly many successive new waves of immigrants, incapacity to breed of the natives (what mostly happens when you're already dead or expelled to the wastelands, i.e. walking dead) and would in any case leave a signature that we must be able to detect (and we do not).

      It's more a (non-planned) genocide than "outbreeding": "this land now ours, flat-head get out (and die) or stay in and be killed". Probably they did not even talk it at all, as they saw each others as "monsters" or "animals".

      "Don't we have evidence that the Gravettian is from at least as far east as Eastern Europe?"

      From West Asia (not too clear).

      http://forwhattheywereweare.blogspot.com.es/search/label/Gravettian

      "Perhaps the earliest Aurignacian was carried by Y-DNA I and the Gravettian by Y-DNA R1b".

      Perhaps. Again not too clear.

      Whatever the case, the Aurignacian left enough cultural signature through the other layers to be at the origin of Magdalenian (which is fundamentally an elaborate and refined Aurignacian). Similarly there's quite a bit of Y-DNA I today in Europe. So if there was widespread or even significant Neanderthal admixture through the Aurignacian, we should see in Gravettian and modern genetics.

      No outbreeding but gradual genocide. Punctual contact maybe but not much. Perception of each other as "monsters". That's what I think.

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  6. Regarding the last point: here is what Millan wrote on the other post in relation to El Castillo:

    "Me, i just agree with them in one basic point: 90% of their 'Transitional Aurignacian' is of Mousterian and Neanderthal nature. I fact, i think it is of 100% this nature, and it has no correlations to real Protoaurignacian and real Early Aurignacian".

    Mind you, he does consider the possibility that the few 'Aurignacian' features have been specially selected or that they may have been derived from upper levels. A further of his comments from the same post:

    "On the bright side of things, i think that at least they've helped to highlight the many elements of continuity between lastest MP and first EUP industries, even if they were made by diferent human populations (Neandertal, AMH...)and even when they are not derived one from another. For example: The use of bones and antler as tools are quite ususal on Late MP (even if they are quite different from the typican 'bone industry' of 'sagaies' and awls. Also, during Proto/Aurignacian there is an important 'less ellaborated' industry in bone and antler, quite similar to the objets from MP, which is frecuently undestimated".

    Sounds like a fairly gradual transition to me. Another comment suggestive of gradual change:

    "From l'Arbreda i've seen both drawings and a few materials. I'll say that teh older so called Aurignacian level it is more an 'undefinite Early Upper Paleolithic (EUP) level' that a clear Aurignacian or Protoaurignacian. Yes, it has some affinities, is quite old and it is under a more typical Aurignacian, if i recall correctly, son it is a reasonable guess that vein... but it cant be assured from the lithic point of view (my opinion)".

    'Indefinite Early Upper Paleolithic' sounds fairly transitional.

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    1. But in other paragraphs he suggests that much of the material attributed to layer 18 may be misplaced (the dig is from a century ago and was a bit brutish, megalomaniac, not at all acceptable by modern standards) and be from layer 16, which is clearly Aurignacian already. It was a lengthy discussion and there was no unequivocal conclusion.

      "Sounds like a fairly gradual transition to me".

      If you wish to read it that way. That's exactly what the current El Castillo research team claims BUT Millán thinks they are wrong, and so do I. He criticized their continuity theory in fact as product of little evidence and much wishful thinking. First of all wishful thinking that the original diggers had done everything right, what in his opinion is most unlikely.

      "Indefinite Early Upper Paleolithic' sounds fairly transitional".

      In this case the impression he transmitted was it may be a Chatelperronian-like Neanderthal local UP tech. However, as it's already more recent than nearby Proto-Aurignacian of Isturitze, it can't be ruled out it's a Sapiens industry either. Whatever the case, the Catalan caves are much more solid than El Castillo, which must be put in the map with a big bold-type question mark.

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  7. "We are not going to agree, Terry".

    Wrong Maju. We agree on that statement.

    "Why would the Denisovan genes survive almost only in Australasia if the admixture was, as in the Neanderthal case, indiscriminate? Illogical thinking here".

    Certainly not illogical thinking. If the Denisova genes were in fact distributed from the Altai to SE Asia, but absent through South Asia that would suggest a widespread H. erectus population through Central Asia from Altai to SE Asia. That is precisely the region Mousterian technology failed to penetrate so we probably have two H. erectus species: one through the above region and H. ergaster through Africa, SW Asia and South Asia. We know that periodic ice ages have depleted homo populations through Central Asia, if not eliminated them entirely. Surely that explains why the Denisovan genes would survive only in region accessed early from SE Asia. Elsewhere the genes have been replaced by later immigration or by extinction through climate change. Someone who posted a comment at one of your blogs had a link to Central Asian H. erectus that claimed East asia H. erectus had moved through Central Asia rather than north from SE Asia. I can't remember the name of the commenter (a new person) or the blog. Sorry.

    "'Outbreed' is not in my dictionary".

    Outbreeding usually means the opposite of inbreeding so it should be in your dictionary. However in this case I meant the ability to produce a greater number of offspring that survive in turn to breed.

    "It needs too many special conditions, mostly many successive new waves of immigrants"

    It certainly does not require 'many successive new waves of immigrants'. The mallard has succesfully outbred the native grey duck in New Zealand without any such new waves of releases. And don't bother claiming that humans are not ducks. All species obeey much the same biological laws. It is perfectly possible that a particular group of humans could be more effective at raising offspring than another group. Especially if it had taked over particularly desirable habitat.

    "incapacity to breed of the natives"

    Again we find the mallard and grey duck perfectly capable of forming fertile hybrids, and very often do. But the mallard is still replacing the grey duck, almost certainly because of differences in their breeding habitat. Human population numbers can hardly have remained the same or else increased at a constant rate. In all species numbers fluctuate with population groups periodically expanding to fill the gaps by population groups that have become extinct, or nearly so.

    "would in any case leave a signature that we must be able to detect (and we do not)".

    But we do. Haven't you been mentioning all along that we find Neanderthal and Denisova genes in modern humans?

    "From West Asia (not too clear) [Gravettian]".

    In any case they represent a later population wave that would have helped reduce the Neanderthal proportion of the population's genes. THat would lead to the homeopathic level of Neanderthal and Denisovan genes surviving in the modern population.

    "No outbreeding but gradual genocide. Punctual contact maybe but not much. Perception of each other as 'monsters'. That's what I think".

    And I think that is merely your preferred option. Other explanations than genocide are entirely possible. Simple tribalism is sufficient.

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    1. "Denisovans" used Mousterian (probably learned from their Neanderthal side), South Asian MP instead is not Mousterian but otherwise Acheulean-derived. The classical definition of the whatever-his-name line is not operational without some adjustments.

      "Someone who posted a comment at one of your blogs had a link to Central Asian H. erectus that claimed East asia H. erectus had moved through Central Asia rather than north from SE Asia".

      I think you misunderstood the data. You usually do.

      "Outbreeding usually means the opposite of inbreeding"...

      Actually by Wikitionary it means only what you said first: "to breed more successfully than"...

      What I mean is that mere biological outbreeding is not in the menu, it's not realistic: a species or population outbreeds another mostly by physically displacing them from the land. There may be other complementary reasons but it's essentially a matter of resources: if you have resources your children survive, if you do not they die.

      So outbreeding without competence for the resources, the land normally, is not in my dictionary, so to say.

      "Again we find the mallard and grey duck perfectly capable of forming fertile hybrids, and very often do. But the mallard is still replacing the grey duck, almost certainly because of differences in their breeding habitat".

      If there were so many successful hybrids, it should be a hybrid population the result, right? What brings me to think that there are not as many hybrids as the sentence "very often [they] do" may suggest. It is anecdotal, not "very often".

      "But we do. Haven't you been mentioning all along that we find Neanderthal and Denisova genes in modern humans?"

      No Denisovan genes except in very specific populations, unlike Neanderthal ones. You always have to 'cheat' and dissolve the distinctions, even when they are very clear as in this case.

      "In any case they represent a later population wave that would have helped reduce the Neanderthal proportion of the population's genes".

      We do not know how much is a new population wave and how much is mere cultural diffusion. There's a lot of Aurignacian-to-Gravettian transitional and hybrid layers. I'm of the opinion that it was mostly cultural but depending on region. I'd say that in Southern Iberia it was probably demic and the source of the modern main Iberian genetic cluster (disregarding the less important Neolithic top layer) but in the Franco-Cantabrian region I'm not so sure.

      In any case we should still see Neanderthal remnants in our genes such as much greater apportion of Neanderthal genes than among Chinese (nope), exclusive European/West Asian Neanderthal-derived lineages (nope) or at least these in the Gravettian or other UP burials (nope).

      So there was not any meaningful new Neanderthal admixture upon our migration westward.

      "THat would lead to the homeopathic level"...

      There's no such thing as homeopathic dilution (1:1000 or less): it's a myth. Never mind the massive amounts of "water" needed, impossible to gather in the real biological structure of Homo sp. in Europe and West Asia back in the day. Even if Homo sapiens outnumbered Neanderthals 1:9, as has been recently claimed, that's still too far from the 1:1000 or 1:1 million needed to erase all tracks.

      As for me, there are no tracks: there was no relevant admixture. You can speculate all you want but without evidence it's nothing but wild speculation.

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  8. "'Denisovans' used Mousterian (probably learned from their Neanderthal side), South Asian MP instead is not Mousterian but otherwise Acheulean-derived".

    Sorry. Yes it was Acheulean that failed to spread to Central, East and SE Asia. So we still have two H. erectus populations.

    "I think you misunderstood the data. You usually do".

    You obviously didn't bother to look at the commenters blog, and certainly didn't follow any links he provided there. The argument provided in the link was that much of the region between South Asia and SE Asia was densely forested and mountainous and so basically inaccesible. Exactly as I've been trying to tell you from day one. I'll make another effort to find the comment on your blog and follow it to the link. About 2006 paper if I remember correctly.

    "it's not realistic: a species or population outbreeds another mostly by physically displacing them from the land".

    Rubbish. It happens quite frequently. Often not replacement by memebers of the same species I'll grant, but often of similar species, and almost always by species with much the same ecological requirements.

    "it's essentially a matter of resources: if you have resources your children survive, if you do not they die".

    Exactly the point I've been trying to make. If a family (tribe) gains control of a highly desirable region it will survive more effectively than one pushed into more marginal regions. Isn't that exactly what you mean whenever you claim that Africa may have been some sort of 'population pump' at times. It certainly seems to me exactly the sort of situation that has led to the expansion of various haplogroups at various times.

    "If there were so many successful hybrids, it should be a hybrid population the result, right?"

    In many regions that is exactly what has happened, and it certainly happened in the Marianas Islands in pre-European times. However even where the duck population is largely 'greylards' (as they are called) eventually the mallard genotype comes to dominate. Mariana duck:

    http://en.wikipedia.org/wiki/Mariana_Mallard

    Quote:

    "The taxonomic status of the Mariana Mallard is disputed, since it resembles an intermediate of the Mallard and the Pacific Black Duck, two closely related allopatric species which frequently hybridise. Its males had two intergrading color morphs, called the 'platyrhynchos' and the 'superciliosa' types after the species they resembled more".

    "What brings me to think that there are not as many hybrids as the sentence 'very often [they] do' may suggest. It is anecdotal, not 'very often'".

    No. 'Very often' is the fact. I know from experience as I have been trying for some years to conserve the native grey duck. We have released 'pure' greys here several times and they often return with ducklings. Very seldom are these pure greys but show evidence of hybridism. These hybrids in turn often bring in their own crop of ducklings. In fact one is outside at the moment with ducklings although it is extremely early in the season. And by far the majority of ducks (up to 60) that come in here in the morning for a feed are hybrids, and resemble the photo of the Mariana drake.

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    1. "You obviously didn't bother to look at the commenters blog".

      How do you want me to "look" at anything if you only provided your vague memories as reference, c'mon!

      You said: "Someone who posted a comment"... without any link. Don drive me crazy, ok?

      "Mariana duck"...

      Great! An extinct apparently hybrid duck, for which no DNA evidence exists. A pretty useless example!

      "We have released 'pure' greys here several times and they often return with ducklings. Very seldom are these pure greys but show evidence of hybridism"...

      So how come are there are "pure greys" anymore? You just want to drive me crazy diving into messy anecdotal pseudo-evidence of nothing.

      "And by far the majority of ducks (up to 60) that come in here in the morning for a feed are hybrids"...

      So they are not anymore "pure greys" but hybrids. Then what are you talking about?

      Driving me nuts about ducks?!

      Delete
  9. "No Denisovan genes except in very specific populations, unlike Neanderthal ones. You always have to 'cheat' and dissolve the distinctions, even when they are very clear as in this case".

    It is you who are cheating here. Denisova genes are found in modern humans, 'specific populations' or otherwise. It is still found in modern humans as 'a signature we are able to detect'.

    "We do not know how much is a new population wave and how much is mere cultural diffusion".

    True, but I would expect and cultural diffusion to also involve at least some genetic diffusion, including haplogroup diffusion.

    "There's a lot of Aurignacian-to-Gravettian transitional and hybrid layers".

    As we would expect. Complete population replacement is probably quite rare. Even Neanderthal replacement wasn't complete. They have left traces in modern humans.

    "In any case we should still see Neanderthal remnants in our genes such as much greater apportion of Neanderthal genes than among Chinese (nope), exclusive European/West Asian Neanderthal-derived lineages (nope) or at least these in the Gravettian or other UP burials (nope)".

    I think you grossly under-estimate the amount of prehistoric population movement. Dienekes once mentioned something to the effect that he was surprised that anyone could still believe that Paleolithic humans arrived in some region and have remained there until the present day. We can tell from haplogroup distribution that humans have been very mobile for quite some time.

    "As for me, there are no tracks: there was no relevant admixture".

    Because that is how you choose to interpret the evidence. Other interpret it differently. Try having a look for the tracks. You will see them easily enough although you consistently look for an alternative explanation for some reason. You seem uncomfortable with the concept of hybridism. Beliefs of 'racial purity'?

    ReplyDelete
    Replies
    1. "It is you who are cheating here. Denisova genes are found in modern humans, 'specific populations' or otherwise."

      Specific populations, very specific ones in a very specific global region.

      This is very different from Neanderthal genes, which are evenly widespread among all non-Africans.

      In case there was any doubt, the Neanderthal genes dispel it quickly because these are evenly distributed, while the Denisovan ones are not (at all).

      That difference is very important and informative.

      "I think you grossly under-estimate the amount of prehistoric population movement. Dienekes once mentioned something to the effect that he was surprised that anyone could still believe that Paleolithic humans arrived in some region and have remained there until the present day".

      I don't believe half of half of half of half of half of what Dienekes says out of his own head. The main or possibly only interest that blog has is the coverage of many different publications. He's too ideological 99% of the time.

      "You seem uncomfortable with the concept of hybridism".

      Not at all. I am just uncomfortable with the dramatic lack of evidence supporting hybridization beyond the well known minor flows. You don't build a theory on baseless speculations and all you have is that.

      Delete
  10. "How do you want me to 'look' at anything if you only provided your vague memories as reference, c'mon!'

    You become more ridiculous every day. You've been on at me to create my own blog yet when you had a new commnter on your own blog you obviously couldn't be bothered checking his blog out. If you had you would have immediately found the paper I mentioned. I presume that if I went to the trouble of finding the article you wouldn't bother reading it and so would be able to cling to your conservative views.

    "Great! An extinct apparently hybrid duck, for which no DNA evidence exists. A pretty useless example!'

    Yet another extremely ridiculous comment. What would DNA tell us about the duck that we don't already know? We would certainly find they are a hybrid between the Pacific black duck (grey duck in NZ) and mallard. The Wiki article is a bit dated in the respect it claims we don't know the species involved.

    "So how come are there are 'pure greys' anymore?"

    They are present in isolated, hilly, forested regions, much the same as Neanderthals were present in isolated, hilly forested regions long after modern humans had entered regions where Neanderthals had previously lived.

    "So they are not anymore 'pure greys' but hybrids. Then what are you talking about?"

    Not all are hybrids. When a pure grey comes in with ducklings we pen them so they survive. several clutches of these turn out to be pure as well and we repeat the process next season. Otherwise, as you say, we would finish up with hybrids and eventually a mallard phenotype with some grey genes, including mtDNA.

    "Driving me nuts about ducks?!"

    Because you are obssessed with some sort of 'exclusivity of humans' theory.

    "Specific populations, very specific ones in a very specific global region".

    Humans are always basically specific populations in specific regions, as are all other species.

    "I am just uncomfortable with the dramatic lack of evidence supporting hybridization beyond the well known minor flows".

    They appear now as 'minor flows' because much has changed since the hybridization occurred.

    ReplyDelete
    Replies
    1. "You've been on at me to create my own blog yet when you had a new commnter on your own blog you obviously couldn't be bothered checking his blog out".

      You assume others know what you're talking about by telepathy or something. And you insist on that line... falling again in borderline trollish behavior, decorating all with insults and pretense of knowing but failing to document your claims and statements.

      Do you know why you need a blog? To leave me alone and to see the matter from the other side. But I doubt you'll ever learn at your age, so never mind.

      And then you talk of a population of ducks (ducks?!) which are all (or most hybrid), unlike Homo sp.

      I'm certainly losing interest in reading what you have to say... again. :(

      Delete
  11. "Do you know why you need a blog? To leave me alone and to see the matter from the other side. But I doubt you'll ever learn at your age, so never mind".

    It's your turn to learn. The following 2009 study is obviously related to the one your commenter linked to although it is not the actual paper:

    http://blogs.discovermagazine.com/80beats/2009/03/11/the-date-of-birth-for-peking-man-gets-pushed-back-200000-years/

    Quote:

    "In a comment accompanying the new study, [anthropologist Russell] Ciochon and Iowa geologist Arthur Bettis III hypothesize that H. erectus populations in or just outside of Africa took two separate routes eastward into Asia. Ciochon and Bettis propose that an initial migration followed Asia’s southern coast to Java, which was at the time connected to the mainland. Later, H. erectus passed through central Asia and southern Mongolia to reach the Zhoukoudian vicinity [Science News]. Researchers also note that a huge swath of primeval forest separated the two populations, which they say supports the double-migration theory".

    The authors obviously consider the 'huge swath of primeval forest' was basically impassable.

    This 2005 paper also claims a connection between Altai and Mongolian H. erectus (specifically Middle Paleolithic), and even claims a connection into Northern China:

    http://ejournal.anu.edu.au/index.php/bippa/article/viewFile/85/76

    ReplyDelete
    Replies
    1. I'm not going to dignify you with any answers or attention at all unless you first apologize, not just for insulting but also for being so manipulative and non-scientific, non-cold-headed in general.

      Delete

Please, be reasonably respectful when making comments. I do not tolerate in particular sexism, racism nor homophobia. Personal attacks, manipulation and trolling are also very much unwelcome here.The author reserves the right to delete any abusive comment.

Preliminary comment moderation is... ON (sorry, too many trolls).