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Is there physical evidence of a Denisovan presence in the Islands of SE Asia?

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  • Is there physical evidence of a Denisovan presence in the Islands of SE Asia?

    Here is an interesting article concerning the possibility that evidence for Denisovans (extinct cousins of us and Neanderthals, who ranged across Asia 30,000 to 100,000 years ago) might already be plentiful in the islands of southeastern Asia, but we haven't looked for it.

    Source: Evolutionary study suggests prehistoric human fossils ‘hiding in plain sight’ in Southeast Asia


    Island Southeast Asia has one of the largest and most intriguing hominin fossil records in the world. But our new research suggests there is another prehistoric human species waiting to be discovered in this region: a group called Denisovans, which have so far only been found thousands of kilometres away in caves in Siberia and the Tibetan Plateau.

    Our study, published in Nature Ecology and Evolution, reveals genetic evidence that modern humans (Homo sapiens) interbred with Denisovans in this region, despite the fact Denisovan fossils have never been found here.

    Conversely, we found no evidence that the ancestors of present-day Island Southeast Asia populations interbred with either of the two hominin species for which we do have fossil evidence in this region: H. floresiensis from Flores, Indonesia, and H. luzonensis from Luzon in the Philippines.

    Together, this paints an intriguing — and still far from clear — picture of human evolutionary ancestry in Island Southeast Asia. We still don’t know the precise relationship between H. floresiensis and H. luzonensis, both of which were distinctively small-statured, and the rest of the hominin family tree.

    And, perhaps more intriguingly still, our findings raise the possibility there are Denisovan fossils still waiting to be unearthed in Island Southeast Asia — or that we may already have found them but labelled them as something else.

    An ancient hominin melting pot

    Stone tool records suggest that both H. floresiensis and H. luzonensis are descended from Homo erectus populations that colonised their respective island homes about 700,000 years ago. H. erectus is the first ancient human known to have ventured out of Africa, and has first arrived in Island Southeast Asia at least 1.6 million years ago.

    This means the ancestors of H. floresiensis and H. luzonensis diverged from the ancestors of modern humans in Africa around two million years ago, before H. erectus set off on its travels. Modern humans spread out from Africa much more recently, probably arriving in Island Southeast Asia 70,000-50,000 years ago.

    We already know that on their journey out of Africa about 70,000 years ago, H. sapiens met and interbred with other related hominin groups that had already colonised Eurasia.

    The first of these encounters was with Neanderthals, and resulted in about 2% Neanderthal genetic ancestry in today’s non-Africans.

    The other encounters involved Denisovans, a species that has been described solely from DNA analysis of a finger bone found in Denisova Cave in Siberia.

    Intriguingly, however, the largest amounts of Denisovan ancestry in today’s human populations are found in Island Southeast Asia and the former continent of Sahul (New Guinea and Australia). This is most likely the result of local interbreeding between Denisovans and modern humans — despite the lack of Denisovan fossils to back up this theory.

    To learn more, we searched the genome sequences of more than 400 people alive today, including more than 200 from Island Southeast Asia, looking for distinct DNA sequences characteristic of these earlier hominin species.

    We found genetic evidence the ancestors of present-day people living in Island Southeast Asia have interbred with Denisovans — just as many groups outside Africa have similarly interbred with Neanderthals during their evolutionary history. But we found no evidence of interbreeding with the more evolutionarily distant species H. floresiensis and H. luzonensis (or even H. erectus).

    This is a remarkable result, as Island Southeast Asia is thousands of kilometres from Siberia, and contains one of the richest and most diverse hominin fossil records in the world. It suggests there are more fossil riches to be uncovered.

    So where are the region’s Denisovans?

    There are two exciting possibilities that might reconcile our genetic results with with the fossil evidence. First, it’s possible Denisovans mixed with H. sapiens in areas of Island Southeast Asia where hominin fossils are yet to be found.

    One possible location is Sulawesi, where stone tools have been found dating back at least 200,000 years. Another is Australia, where 65,000-year-old artefacts currently attributed to modern humans were recently found at Madjebebe.

    Alternatively, we may need to rethink our interpretation of the hominin fossils already discovered in Island Southeast Asia.

    Confirmed Denisovan fossils are extremely rare and have so far only been found in central Asia. But perhaps Denisovans were much more diverse in size and shape than we realised, meaning we might conceivably have found them in Island Southeast Asia already but labelled them with a different name.

    Given that the earliest evidence for hominin occupation of this region predates the divergence between modern humans and Denisovans, we can’t say for certain whether the region has been continuously occupied by hominins throughout this time.

    It might therefore be possible that H. floresiensis and H. luzonensis (but also later forms of H. erectus) are much more closely related to modern humans than currently assumed, and might even be responsible for the Denisovan ancestry seen in today’s Island Southeast Asia human populations.

    If that’s true, it would mean the mysterious Denisovans have been hiding in plain sight, disguised as H. floresiensis, H. luzonensis or H. erectus.

    Solving these intriguing puzzles will mean waiting for future archaeological, DNA and proteomic (protein-related) studies to reveal more answers. But for now, the possibilities are fascinating.


    Source

    © Copyright Original Source



    Given that roughly 3 to 5% of the DNA found in modern Aboriginal Aussies and Melanesians along with approximately 7% to 8% of the DNA in Papuans is thought to have derived from the Denisovans there is obviously a good reason that at one time the Denisovans had lived in this area in spite of the lack of fossil evidence. And it would not surprise me in the least if in the past some fossils that once they were identified as coming from a Homo were automatically assumed to have been from Homo sapiens if they came from a certain time period. A reanalysis of these remains might uncover a number that actually were Denisovan.

    I'm always still in trouble again

    "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
    "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
    "Of course, human life begins at fertilization that’s not the argument." --Tassman

  • #2
    Originally posted by rogue06 View Post
    A reanalysis of these remains might uncover a number that actually were Denisovan.
    That's pretty unlikely. Denisovans are part of the same branch of the hominin tree that produced Neanderthals, and so we have to assume they were physically similar. In contrast, both H. luzonensis and H. Floresiensis have a fair number of basal traits, including some shared with Australopiths. It's difficult to fit them into the H. erectus lineage, and some have suggested they are an indication of even earlier members of our genus making their way out of Africa. Getting those traits out of what is essentially an early branch off the modern human lineage and a sister branch to the Neanderthals is even more difficult.

    But the fun thing is that we can't rule it out. We don't have DNA for the island species, and we don't have substantial remains for the Denisovans.

    If we ever manage to get DNA out of Homo naledi, it will be immensely informative, given that it also has a similar mix of early/late features as one of these island species.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

    Comment


    • #3
      Originally posted by TheLurch View Post
      That's pretty unlikely. Denisovans are part of the same branch of the hominin tree that produced Neanderthals, and so we have to assume they were physically similar. In contrast, both H. luzonensis and H. Floresiensis have a fair number of basal traits, including some shared with Australopiths. It's difficult to fit them into the H. erectus lineage, and some have suggested they are an indication of even earlier members of our genus making their way out of Africa. Getting those traits out of what is essentially an early branch off the modern human lineage and a sister branch to the Neanderthals is even more difficult.

      But the fun thing is that we can't rule it out. We don't have DNA for the island species, and we don't have substantial remains for the Denisovans.

      If we ever manage to get DNA out of Homo naledi, it will be immensely informative, given that it also has a similar mix of early/late features as one of these island species.
      I could sworn that I read something coming out of a Deciphering the Denisovans symposium from no more than a couple years ago about a skull fragment with unusual thick bones where the closest one with those dimensions is a skull from Pleistocene Java.

      I'm always still in trouble again

      "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
      "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
      "Of course, human life begins at fertilization that’s not the argument." --Tassman

      Comment


      • #4
        Originally posted by rogue06 View Post
        Here is an interesting article concerning the possibility that evidence for Denisovans (extinct cousins of us and Neanderthals, who ranged across Asia 30,000 to 100,000 years ago) might already be plentiful in the islands of southeastern Asia, but we haven't looked for it.

        Source: Evolutionary study suggests prehistoric human fossils ‘hiding in plain sight’ in Southeast Asia


        Island Southeast Asia has one of the largest and most intriguing hominin fossil records in the world. But our new research suggests there is another prehistoric human species waiting to be discovered in this region: a group called Denisovans, which have so far only been found thousands of kilometres away in caves in Siberia and the Tibetan Plateau.

        Our study, published in Nature Ecology and Evolution, reveals genetic evidence that modern humans (Homo sapiens) interbred with Denisovans in this region, despite the fact Denisovan fossils have never been found here.

        Conversely, we found no evidence that the ancestors of present-day Island Southeast Asia populations interbred with either of the two hominin species for which we do have fossil evidence in this region: H. floresiensis from Flores, Indonesia, and H. luzonensis from Luzon in the Philippines.

        Together, this paints an intriguing — and still far from clear — picture of human evolutionary ancestry in Island Southeast Asia. We still don’t know the precise relationship between H. floresiensis and H. luzonensis, both of which were distinctively small-statured, and the rest of the hominin family tree.

        And, perhaps more intriguingly still, our findings raise the possibility there are Denisovan fossils still waiting to be unearthed in Island Southeast Asia — or that we may already have found them but labelled them as something else.

        An ancient hominin melting pot

        Stone tool records suggest that both H. floresiensis and H. luzonensis are descended from Homo erectus populations that colonised their respective island homes about 700,000 years ago. H. erectus is the first ancient human known to have ventured out of Africa, and has first arrived in Island Southeast Asia at least 1.6 million years ago.

        This means the ancestors of H. floresiensis and H. luzonensis diverged from the ancestors of modern humans in Africa around two million years ago, before H. erectus set off on its travels. Modern humans spread out from Africa much more recently, probably arriving in Island Southeast Asia 70,000-50,000 years ago.

        We already know that on their journey out of Africa about 70,000 years ago, H. sapiens met and interbred with other related hominin groups that had already colonised Eurasia.

        The first of these encounters was with Neanderthals, and resulted in about 2% Neanderthal genetic ancestry in today’s non-Africans.

        The other encounters involved Denisovans, a species that has been described solely from DNA analysis of a finger bone found in Denisova Cave in Siberia.

        Intriguingly, however, the largest amounts of Denisovan ancestry in today’s human populations are found in Island Southeast Asia and the former continent of Sahul (New Guinea and Australia). This is most likely the result of local interbreeding between Denisovans and modern humans — despite the lack of Denisovan fossils to back up this theory.

        To learn more, we searched the genome sequences of more than 400 people alive today, including more than 200 from Island Southeast Asia, looking for distinct DNA sequences characteristic of these earlier hominin species.

        We found genetic evidence the ancestors of present-day people living in Island Southeast Asia have interbred with Denisovans — just as many groups outside Africa have similarly interbred with Neanderthals during their evolutionary history. But we found no evidence of interbreeding with the more evolutionarily distant species H. floresiensis and H. luzonensis (or even H. erectus).

        This is a remarkable result, as Island Southeast Asia is thousands of kilometres from Siberia, and contains one of the richest and most diverse hominin fossil records in the world. It suggests there are more fossil riches to be uncovered.

        So where are the region’s Denisovans?

        There are two exciting possibilities that might reconcile our genetic results with with the fossil evidence. First, it’s possible Denisovans mixed with H. sapiens in areas of Island Southeast Asia where hominin fossils are yet to be found.

        One possible location is Sulawesi, where stone tools have been found dating back at least 200,000 years. Another is Australia, where 65,000-year-old artefacts currently attributed to modern humans were recently found at Madjebebe.

        Alternatively, we may need to rethink our interpretation of the hominin fossils already discovered in Island Southeast Asia.

        Confirmed Denisovan fossils are extremely rare and have so far only been found in central Asia. But perhaps Denisovans were much more diverse in size and shape than we realised, meaning we might conceivably have found them in Island Southeast Asia already but labelled them with a different name.

        Given that the earliest evidence for hominin occupation of this region predates the divergence between modern humans and Denisovans, we can’t say for certain whether the region has been continuously occupied by hominins throughout this time.

        It might therefore be possible that H. floresiensis and H. luzonensis (but also later forms of H. erectus) are much more closely related to modern humans than currently assumed, and might even be responsible for the Denisovan ancestry seen in today’s Island Southeast Asia human populations.

        If that’s true, it would mean the mysterious Denisovans have been hiding in plain sight, disguised as H. floresiensis, H. luzonensis or H. erectus.

        Solving these intriguing puzzles will mean waiting for future archaeological, DNA and proteomic (protein-related) studies to reveal more answers. But for now, the possibilities are fascinating.


        Source

        © Copyright Original Source



        Given that roughly 3 to 5% of the DNA found in modern Aboriginal Aussies and Melanesians along with approximately 7% to 8% of the DNA in Papuans is thought to have derived from the Denisovans there is obviously a good reason that at one time the Denisovans had lived in this area in spite of the lack of fossil evidence. And it would not surprise me in the least if in the past some fossils that once they were identified as coming from a Homo were automatically assumed to have been from Homo sapiens if they came from a certain time period. A reanalysis of these remains might uncover a number that actually were Denisovan.
        UPDATE:

        A new study has found that the Philippine Negrito ethnic group known as the Ayta Magbukon have the highest known level of Denisovan DNA of any group in the world -- considerably more than the Papuan New Guinea Highlanders, who previously held the distinction of having the highest level of Denisovan ancestry.

        The co-lead author, Maximilian Larena of Uppsala University's Department of Organismal Biology, also noted that

        "We made this observation despite the fact that Philippine Negritos were recently admixed with East Asian-related groups—who carry little Denisovan ancestry, and which consequently diluted their levels of Denisovan ancestry. If we account for and masked away the East Asian-related ancestry in Philippine Negritos, their Denisovan ancestry can be up to 46 percent greater than that of Australians and Papuans."


        The researchers think that the fact that the Ayta Magbukon possess the highest level of Denisovan ancestry in the world, along with the recent discovery of a small-bodied hominin, called Homo luzonensis, suggest that there were multiple archaic species of Homo that inhabited the Philippines prior to the arrival of modern humans, and that these archaic groups could have been genetically related.

        Source: New clue to human evolution's biggest mystery emerges in Philippines


        The only definitive fossil evidence that points to the existence of Denisovans -- an enigmatic group of early humans first identified in 2010 -- comes from five bones from the Denisova cave in the foothills of Siberia's Altai mountains.

        The fragments are so tiny that they can all fit in the palm of one person's hand.

        Now, DNA from 3,000 miles (4,828 kilometers) away in the Philippines is shedding more light on human evolution's biggest mystery.

        New research published Thursday has found that a Philippine ethnic group known as the Ayta Magbukon has the highest known level of Denisovan ancestry in the world.

        Denisovan DNA lives on in some humans today because, once our Homo sapien ancestors encountered the Denisovans, they had sex with them and gave birth to babies -- something geneticists call admixture. By analyzing current-day genetic data, we can look back into human history.

        The "admixing" happened more than 50,000 years ago, as modern humans moved out of Africa and likely crossed paths with both Neanderthals and Denisovans. But pinning down exactly where it happened has proven difficult -- particularly in the case of Denisovans.

        It's especially puzzling that the only Denisovan fossils were found in Siberia (with the potential exception of a jaw bone on the Tibetan plateau). Genetic evidence has tied the archaic humans most closely to places much farther south.

        "The fact that Ayta Magbukon have the highest amount of Denisovan ancestry of anywhere in the world is unexpected, and I am intrigued, as previous studies did not report such high amounts in other Philippines populations," said Joăo Teixeira, a visiting fellow at the Australian Centre for Ancient DNA at The University of Adelaide. He was not involved in the study.

        Researchers from the Philippines and Sweden stumbled on the new findings as part of a wider study on human history in the Philippines that involved studying the genetic makeup of 118 different groups in the country. The study was published in the journal Current Biology on Thursday.

        The study found that the Ayta Magbukon had around 5% Denisovan ancestry, more than Aboriginal Australians and Papuans, whom previous research found to have around 4%, said Mattias Jakobsson, a geneticist at Uppsala University in Sweden and an author of the study.

        Denisovan ancestory is also present in many East Asian people -- although at a much lower level, other studies have found.

        Ayta Magbukon belong to a wider group of people in the Philippines that identify as Negritos, Jakobsson said.

        The findings are further evidence that Denisovans once lived all throughout Asia and were likely living in the Philippines long before any Homo sapiens arrived, the authors said. It also suggests that different Denisovan populations mixed and intermingled with Homo sapiens in multiple locations and various points in time.

        "If the results are accurate, then human colonizations of the Philippines and surrounding regions were even more complex than we thought up to now," said Chris Stringer, a professor and research leader in Human Origins at The Natural History Museum in London. He was not involved in research.

        It also appears that our ancestors may have interacted more widely with Denisovans than Neanderthals -- a much more deeply studied early human who lived in Europe and some parts of Asia until about 40,000 years ago, Stringer said.

        "Relatively small groups of early modern humans interbred with Neanderthals in western Eurasia and then spread across Eurasia and beyond, passing on that level of acquired Neanderthal DNA to descendant populations," he said.

        "In the case of the Denisovans, it looks like they were genetically much more diverse, and they intermixed separately in different locations with differentiating early modern populations, hence the more varied patterns we see today."

        Why so few Denisovan fossils?

        Denisovan DNA, along with Neanderthal DNA, was sequenced completely for the first time in 2010, which led to the initial discovery that they were interbreeding with our Homo sapien ancestors.

        DNA sequenced from the few fossilized bones found in the Siberian cave they were named after has allowed us to learn more about the Denisovans. But we still don't know what these extinct hominins looked like.

        It's not clear why we have so few fossilized remains of Denisovans, but several factors could be at play. Unlike Europe, southeast Asia isn't a region that's been well studied by archaeologists. Also, some locations in the region that might harbor a rich fossil record are now submerged under the sea.

        Tantalizingly, the fossils could also be hiding in plain sight -- in museum or university collections -- but misidentified because we know so little about Denisovan morphology. There are remains in China, Taiwan and other places that could be Denisovan, but it has not yet been possible to extract any DNA, which does not preserve well in tropical heat, from those fossils.

        "What if we have been looking at them all along and calling them something else? The recognized fossil evidence for Denisovans includes fossils for which DNA or proteins have confirmed it to be the case. But how can we tell for sure what a Denisovan is supposed to look like?" Teixeira said.This finding -- along with the recent discoveries of new types of archaic humans in the Philippines and Indonesia -- suggest that Southeast Asia may play a key role in untangling the human story.

        "Island Southeast Asia is still relatively underrepresented. However this may change in the future given the increased interest in the region. Our study, together with the recent discoveries on Homo luzonensis and Homo floresiensis, brings Island Southeast Asia at the forefront of research in human evolutionary history," said Maximilian Larena, study author and researcher at Uppsala University.



        Source

        © Copyright Original Source



        As indicated in the above article, the full paper Philippine Ayta possess the highest level of Denisovan ancestry in the world by clicking on either hyperlink.

        Here is the "abstract":

        Highlights
        • Comprehensive analyses of archaic ancestry among 118 Philippine ethnic groups
        • Ayta Magbukon display ∼30%–40% greater Denisovan ancestry than Australopapuans
        • The model is explained by a distinct admixture event into Negritos from Denisovans
        • Prior to modern humans, Islander Denisovans may have been present in the Philippines

        Summary

        Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world—∼30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

        I'm always still in trouble again

        "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
        "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
        "Of course, human life begins at fertilization that’s not the argument." --Tassman

        Comment


        • #5
          Yeah, it's an interesting finding. The difference is still pretty small - ~8% Denisovan vs. ~6% Denisovan in related island populations. The question is why it's there at all.

          Since we know island populations have more Denisovan DNA in general, it's simple to say "well, the Denisovans were in the islands, too". But that doesn't explain why this one Philippine group has more than others in the same islands, and you can't rule out drift in a group that might have been pretty isolated in the past or even some selective advantage to some Denisovan DNA in the specific environment this group occupied.

          In short, fascinating levels of uncertainty.
          "Any sufficiently advanced stupidity is indistinguishable from trolling."

          Comment


          • #6
            Originally posted by TheLurch View Post
            Yeah, it's an interesting finding. The difference is still pretty small - ~8% Denisovan vs. ~6% Denisovan in related island populations. The question is why it's there at all.

            Since we know island populations have more Denisovan DNA in general, it's simple to say "well, the Denisovans were in the islands, too". But that doesn't explain why this one Philippine group has more than others in the same islands, and you can't rule out drift in a group that might have been pretty isolated in the past or even some selective advantage to some Denisovan DNA in the specific environment this group occupied.

            In short, fascinating levels of uncertainty.
            The only tentative conclusion I would consider is, like Neanderthals, the Denisovans were relatively wide spread and absorbed by our dominant ancestors as we Migrated through Eurasia, They were probably similar enough to be called human if they lived today.
            Last edited by shunyadragon; 08-26-2021, 01:11 PM.
            Glendower: I can call spirits from the vasty deep.
            Hotspur: Why, so can I, or so can any man;
            But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

            go with the flow the river knows . . .

            Frank

            I do not know, therefore everything is in pencil.

            Comment


            • #7
              Originally posted by shunyadragon View Post

              The only tentative conclusion I would consider is, like Neanderthals, the Denisovans were relatively wide spread and absorbed by our dominant ancestors as we Migrated through Eurasia, They were probably eimilarenough to be called human if they lived today.
              They were obviously similar enough to interbreed with us so yeah it would be safe to say they are human.

              I'm always still in trouble again

              "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
              "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
              "Of course, human life begins at fertilization that’s not the argument." --Tassman

              Comment

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