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Thread: Royal Society Paper Casts Doubt on Neanderthal/Denisovan Genes in Modern Humans

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    Quote Originally Posted by Kale View Post
    r... Africans are not a monolith. If Neanderthal introgression is alleged as an artifact of high homozygosity in Eurasians, why wouldn't different African populations each drifting their merry ways not 'preserve' a unique subset of 'Neanderthal variation' in the areas they hadn't mutated yet? Surely Eurasians after 50,000+ years have not undergone 0 mutation, so Africans should share some 'Neanderthal introgression' that Eurasians don't, just less.

    Not to mention the problem Denisovans and their differential relatedness to Eurasians brings into this.
    I think that some African groups DO show some "Neanderthal introgression" just less. Now I am not sure if it would be introgression that Eurasians "don't show". The idea is that humanity had a certain set of genes that were more "Neanderthal like" at the start, before all the drifting took place. The African groups changed, as you point out in different ways. The OOA group did not because it was super low in diversity. The i So I don't see why it would be a DIFFERENT set of supposed Neanderthal genes. Rather we might expect to see some SUBSET of these genes ALSO more Neanderthal like in isolated African populations. This is EXACTY what had been found, though the study attributes it all to "back migration from Eurasia 20K years ago". https://www.sciencemag.org/news/2020/01/africans-carry-surprising-amount-neanderthal-dna


    Regarding Denisovans, an alternative explanation is that there was more than one OOA population, and the Papuans et al are remnants of an earlier OOA movement that has barely hung on. Going right along with your idea that different African populations would have different signals, this group had a bigger share of genes which looked more Denisovan than Neanderthal. Supporting the idea that this is from lack of drift rather than introgression, Papuans et al also show more NEANDERTHAL than other Eurasians. There is more than one possible explanation for this, but that is also what we would expect to find if the Papuan genes simply evolved slower due to extreme homogeneity in the founding populations. I would add that what they are calling "Denisovan" genes are not really a match for the genes found in the Denisovan, they just look like "they came from a close ancestor".

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    Quote Originally Posted by Cosmo View Post
    Regarding Denisovans, an alternative explanation is that there was more than one OOA population, and the Papuans et al are remnants of an earlier OOA movement that has barely hung on. Going right along with your idea that different African populations would have different signals, this group had a bigger share of genes which looked more Denisovan than Neanderthal. Supporting the idea that this is from lack of drift rather than introgression, Papuans et al also show more NEANDERTHAL than other Eurasians. There is more than one possible explanation for this, but that is also what we would expect to find if the Papuan genes simply evolved slower due to extreme homogeneity in the founding populations. I would add that what they are calling "Denisovan" genes are not really a match for the genes found in the Denisovan, they just look like "they came from a close ancestor".
    Their uniparental haplogroups have Papuans DESCENDED from people who left Africa with almost everybody else.
    That's really the situation for most modern populations, although some left later than that.
    What people did do is to interbreed with some remnants of earlier leavings: Neanderthals, Denisovans we know about. Maybe there were others.
    Last edited by Saetro; 06-20-2021 at 07:35 PM.

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    Their uniparental haplogroups have Papuans DESCENDED from people who left Africa with almost everybody else.
    That is a decent point. Though I do suppose one could make the same point against the idea that Neanderthals or Denisovans contributed any genetic material to any modern humans, or remains of modern humans that we have found for that matter.

    So for example if the ancestors of Papuans in the main came from the SAME OOA group as everyone else, but when they arrived in SE Asia met a few remnants of a modern human group that left earlier, the uniparental markers could have been overwhelmed, yet some nuclear DNA persist. This sounds a lot like what the Introgression camp uses to explain the lack of Neanderthal uniparental markers in modern humans, living or dead.

    Regardless, Dr. Amos thinks the key is the homogeneity in the particular genes in question. Suppose 2,000 modern humans left Africa 50K ago. Almost all of them looked "Neanderthal" in 3% of their genes while a few families numbering 200 people also looked more Denisovan in some of theirs. If a small isolated group heavy in those families headed east first, those genes would lack diversity and thus mutate very slowly. Those with more Denisovan looking genes in the main group would be surrounded by those without them, and thus those genes would "mutate out" of looking like Denisovan genes in the main group, but not in the leading edge group with even lower diversity.

    IOW an echo of exactly what Bill Amos is describing with "Neanderthal" genes vs. African genes in the OOA group would repeat itself regarding "Denisovan" genes in any splinter group from the OOA group.

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    Quote Originally Posted by Cosmo View Post
    I think that some African groups DO show some "Neanderthal introgression" just less. Now I am not sure if it would be introgression that Eurasians "don't show". The idea is that humanity had a certain set of genes that were more "Neanderthal like" at the start, before all the drifting took place. The African groups changed, as you point out in different ways. The OOA group did not because it was super low in diversity. The i So I don't see why it would be a DIFFERENT set of supposed Neanderthal genes. Rather we might expect to see some SUBSET of these genes ALSO more Neanderthal like in isolated African populations. This is EXACTY what had been found, though the study attributes it all to "back migration from Eurasia 20K years ago". https://www.sciencemag.org/news/2020/01/africans-carry-surprising-amount-neanderthal-dna


    Regarding Denisovans, an alternative explanation is that there was more than one OOA population, and the Papuans et al are remnants of an earlier OOA movement that has barely hung on. Going right along with your idea that different African populations would have different signals, this group had a bigger share of genes which looked more Denisovan than Neanderthal. Supporting the idea that this is from lack of drift rather than introgression, Papuans et al also show more NEANDERTHAL than other Eurasians. There is more than one possible explanation for this, but that is also what we would expect to find if the Papuan genes simply evolved slower due to extreme homogeneity in the founding populations. I would add that what they are calling "Denisovan" genes are not really a match for the genes found in the Denisovan, they just look like "they came from a close ancestor".
    There is the problem of a lot of Africans having Taforalt-like ancestry. We'd have to look at specific locai, to see if Africans only possess Neanderthal variants shared with Eurasians or if they have different ones.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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    This was published today

    Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

    https://www.nature.com/articles/s41586-021-03675-0

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    Quote Originally Posted by Andrewid View Post
    This was published today

    Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

    https://www.nature.com/articles/s41586-021-03675-0
    Interesting 80kybp change:

    "fragments of Denisovan mtDNA recovered from the middle Middle Palaeolithic layers deposited in Denisova Cave after 80 ka consistently show the highest similarity to the mtDNA of Denisova 3 and Denisova 4, as do mtDNA fragments retrieved from sediments at Baishiya Karst Cave on the northeastern flank of the Tibetan Plateau that are broadly contemporaneous in age (70–45 ka)27. This pattern suggests that this lineage was the most abundant mtDNA type carried by Denisovans after 80 ka. Palaeontological studies25 have suggested that Pleistocene mammals migrated from southeast Asia, along the eastern foothills of the Himalayas, to the northwest Altai. These faunal migrations may have spurred the dispersal of Denisovans into the region in which their remains were first discovered."

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    Hmmm. We have no Denisovan fossils from SE Asia. They are all very far away- unless.......I wish we had some DNA date on the mysterious Red Deer Cave people.

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    Quote Originally Posted by Cosmo View Post
    Hmmm. We have no Denisovan fossils from SE Asia. They are all very far away- unless.......I wish we had some DNA date on the mysterious Red Deer Cave people.
    I have good news for you, via Arza on Eurogenes.blogspot.com:

    https://www.ebi.ac.uk/ena/browser/view/PRJEB43715

    Much remains unknown about the population history of early modern humans in Southeast Asia, where the archaeological record is sparse, and the tropical climate is inimical to the preservation of ancient human DNA. Here we report the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (mainland Southeast Asia and the continental islands of western Indonesia) and Pleistocene Australia-New Guinea (Sahul). We extracted genetic material from the petrous bone of a young hunter-gatherer woman who was buried 7274–7078 calibrated years before present at Leang Panninge, a limestone cave in South Sulawesi, Indonesia. The individual shares most genetic drift and morphological similarities with present-day Papuan and Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between Papuan and Australian populations ~37 thousand years ago5. We also describe Denisovan- and deep East Asian-related ancestries in the Leang Panninge genome and infer their large-scale displacement from the region today

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    Apart from SedaDNA in the Zavala et al study published yesterday, we also have this from last month using AI from the Gower et al paper:

    Detecting adaptive introgression in human evolution using convolutional neural networks

    https://elifesciences.org/articles/64669

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    @rozenfeld,

    I can't get in on that one. They are not claiming anything about the Red Deer Cave people are they? If it is from 37K ago that is so close to the supposed time of Denisovan introgression (two proposed introgression one from 50 and one from about that time) that they should see massive identical segments. If introgression is so, then a Denisovan parent or grandparent would not be out of the question.

    Do the results indicate anything like that? Or is it basically just an extinct group of modern humans that had a somewhat about the higher end of "Denisovan" genes? IOW, Papuans today are alleged to have up to 6%. Did this group have higher purported "Denisovan" heritage than that?

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