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Thread: Neanderthal and Denisovan interbred with an archaic hominin

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    Neanderthal and Denisovan interbred with an archaic hominin

    Posted this on the news thread:
    https://anthrogenica.com/showthread....l=1#post573223

    https://www.biorxiv.org/content/10.1101/657247v1

    Neanderthal-Denisovan ancestors interbred with a distantly-related hominin

    Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors—members of a “superarchaic” population that separated from other humans about 2 mya. The superarchaic population was large, with an effective size between 10 and 46 thousand individuals. We confirm previous findings that: (1) Denisovans also interbred with superarchaics, (2) Neanderthals and Denisovans separated early in the middle Pleistocene, (3) their ancestors endured a bottleneck of population size, and (4) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (5) Neanderthals interbred with the ancestors of modern humans.
    But maybe it warrants a thread of its own as the implications are pretty big. First of all there is an assesment of Simo de los Huesos teeth that calls for a neanderthal AMH split of 800.000 years ago that seems to fit this scenario pretty well.

    https://advances.sciencemag.org/content/5/5/eaaw1268
    https://www.smithsonianmag.com/scien...ght-180972184/

    Secondly, this will make Heidelberg a typical European species.

    And thirdly this may be evidence that the origin of AMH is in Africa. Hints were given that people like Chris Stringer and Reich considered the possibility of AMH originating outside of Africa. But if Neanderthals and Denisovans received a 1.8 million year old Super-Archaic admixture but AMH didn't, that could mean a post-AMH split migration into Homo Erectus area.

    But maybe other scenario's fit? Any ideas?
    Last edited by epoch; 06-06-2019 at 06:55 PM.

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    Very interesting:

    Abstract [...]


    We show that early in the middle Pleistocene, long before the expansion of modern humans into Eurasia, the “neandersovan” ancestors of Neanderthals and Denisovans undertook a very similar expansion. In both cases, an African population expanded into Eurasia, endured a narrow bottleneck of population size, interbred with indigeneous Eurasians, largely replaced them, and split into eastern and western sub-populations. In the earlier expansion, neandersovans interbred with a “superarchaic” population that had been separate since about 2 mya and may represent the original expansion of humans into Eurasia.
    https://www.biorxiv.org/content/10.1101/657247v1

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    And then we have the recent Ragsdale pre-print with yet another archaic interaction before AMH left Africa.
    https://doi.org/10.1371/journal.pgen.1008204

    I am just an interested amateur currently feeling swamped by these sorts of papers from all directions.
    What limited statistical experience I do have (in another field entirely) leads me to wonder whether these claims can all be right at the same time?
    Or whether one claim might interfere with another?
    And it would be nice to see some sort of overall review of where we are with all of this.
    So much has happened since David Reich's book came out.
    A review might be a big task.
    Anyone aware of one already, or maybe someone working on it?

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    interesting. oddly enough considering my background I score twice as much Denisovan than I do Neanderthal.

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    I read the article itself, and I want to tell fellow non-professionals - just wait.
    What I can clearly understand from the article, that there is no consensus about "molecular clock" coefficents and thus, all the genetic dates of "splits" or genetic exchanges should be viewed as a hypothesis, but not as a proven fact.

    We can be sure about gene flow from Neanderthals and Denisovians to AMHs, because we have Neanderthal/Denisovian DNA that can be compared to modern human's DNA.
    Authors of the article build their method of analysing genetic data, confirming facts of gene flows between populations, estimating dates of gene flow e.t.c. But if the method is new, this means it has not been tested well. It can be all wrong or just not precise. Lets just wait for professional critics.

    P.S. Given what we know about gene flow between AMHs, Neanderthals and Denisovians (and also calculations, showing gene flow between African AMHs and some African Archaics) there is nothing surprising in gene flow between Archaics and Superarchaics.
    Last edited by artemv; 06-13-2019 at 10:48 PM.

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    Quote Originally Posted by JerryS. View Post
    interesting. oddly enough considering my background I score twice as much Denisovan than I do Neanderthal.
    No way! Do you have Eastern Non African related Ancestry (East Asian or Native Americans)?

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    Quote Originally Posted by epoch View Post
    Posted this on the news thread:
    https://anthrogenica.com/showthread....l=1#post573223


    But maybe it warrants a thread of its own as the implications are pretty big. First of all there is an assesment of Simo de los Huesos teeth that calls for a neanderthal AMH split of 800.000 years ago that seems to fit this scenario pretty well.

    https://advances.sciencemag.org/content/5/5/eaaw1268
    https://www.smithsonianmag.com/scien...ght-180972184/

    Secondly, this will make Heidelberg a typical European species.

    And thirdly this may be evidence that the origin of AMH is in Africa. Hints were given that people like Chris Stringer and Reich considered the possibility of AMH originating outside of Africa. But if Neanderthals and Denisovans received a 1.8 million year old Super-Archaic admixture but AMH didn't, that could mean a post-AMH split migration into Homo Erectus area.

    But maybe other scenario's fit? Any ideas?
    How would the Denisovan mtDNA in Cranium 5 Neanderthal fit in with this new information? Perhaps there was not a clean split between Ancestral Denisovans and Neanderthals after the bottleneck ocurs, with intogression of Neanderthal and Denisovans genes going both directions. In my opinion, there is a stronger possibility that the Super-Archaic Hominid in an Homo Erectus like species rather than Homo Heidelbergensis,given our current knowledge about the earliest possible dating of Heidelbergensis (700-300,000 kya). We seriously need aDNA samples from East Asia IMO

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    Quote Originally Posted by Diictodon View Post
    No way! Do you have Eastern Non African related Ancestry (East Asian or Native Americans)?
    no, but I scored 1.1 Denisovan and only .6 Neanderthal, or something like that.
    Last edited by JerryS.; 06-14-2019 at 08:39 AM.

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    Quote Originally Posted by Diictodon View Post
    How would the Denisovan mtDNA in Cranium 5 Neanderthal fit in with this new information? Perhaps there was not a clean split between Ancestral Denisovans and Neanderthals after the bottleneck ocurs, with intogression of Neanderthal and Denisovans genes going both directions. In my opinion, there is a stronger possibility that the Super-Archaic Hominid in an Homo Erectus like species rather than Homo Heidelbergensis,given our current knowledge about the earliest possible dating of Heidelbergensis (700-300,000 kya). We seriously need aDNA samples from East Asia IMO
    The idea is that Neanderthal had some Anatomical Modern Human (AMH) gene flow which introduced a very ancient human mtDNA and some founder effect caused it to overtake the original mtDNA. That would explain why Miguelons mtDNA is closer to Denisovans. It would also explain that calculated Neanderthal-AMH split is dated older than the calculated split between Neanderthal-mtDNA and AMH mtDNA. It's the γ event from the paper. The Hohlenstein-Stadel Neanderthal study elaborates on it.

    https://www.nature.com/articles/ncomms16046

    It raises highly interesting questions. If mtDNA admixted into Neanderthals earlier than 270,000 years ago but later than 430,000 years ago, where was this AMH population? How did it reach Europe? Jebel Irhoud is the nearest Home Sapiens population, conveniently dated 300,000 years old. Oddly enough these have originally been classified as a North African form of Neanderthals based on morphology.


    I'm not sure, but I think that the AMH gene flow that Kuhlwilm detected in Altai neanderthals is more recent, 100,000 years ago, and a separate one.

    EDIT: No, that lates remark was not true. A high coverage Vindija Neanderthal genome saw similar AMH admixture. The idea of Kuhlwilm was that if the AMH admixture was unique to Altai it couldn't have been older than the Altai-Vindija split, which was tought to be 100,000 years ago.
    Last edited by epoch; 06-14-2019 at 04:25 PM.

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    Quote Originally Posted by epoch View Post
    The idea is that Neanderthal had some Anatomical Modern Human (AMH) gene flow which introduced a very ancient human mtDNA and some founder effect caused it to overtake the original mtDNA. That would explain why Miguelons mtDNA is closer to Denisovans. It would also explain that calculated Neanderthal-AMH split is dated older than the calculated split between Neanderthal-mtDNA and AMH mtDNA. It's the γ event from the paper. The Hohlenstein-Stadel Neanderthal study elaborates on it.

    https://www.nature.com/articles/ncomms16046

    It raises highly interesting questions. If mtDNA admixted into Neanderthals earlier than 270,000 years ago but later than 430,000 years ago, where was this AMH population? How did it reach Europe? Jebel Irhoud is the nearest Home Sapiens population, conveniently dated 300,000 years old. Oddly enough these have originally been classified as a North African form of Neanderthals based on morphology.


    I'm not sure, but I think that the AMH gene flow that Kuhlwilm detected in Altai neanderthals is more recent, 100,000 years ago, and a separate one.

    EDIT: No, that lates remark was not true. A high coverage Vindija Neanderthal genome saw similar AMH admixture. The idea of Kuhlwilm was that if the AMH admixture was unique to Altai it couldn't have been older than the Altai-Vindija split, which was tought to be 100,000 years ago.
    If Iím understanding itís implications, it is indicating that Neanderthals and Denisovans developed outside Eurasia, migrated to Eurasia, and once there they interbred with (probably) H. Heidelbergensis which had an extant population in Eurasia at that time.

    Is this on track?

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