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Thread: Adaptive archaic introgression

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    Adaptive archaic introgression

    It certainly seems to have been of benefit to homo sapiens sapiens as it moved into different locales and their different climates or the genetic material in question wouldn't show such high levels of positive selection.


    See:
    https://science.sciencemag.org/conte.../6463/eaax2083

    "INTRODUCTION

    Characterizing genetic variants underlying local adaptations in human populations is one of the central goals of evolutionary research. Most studies have focused on adaptive single-nucleotide variants that either arose as new beneficial mutations or were introduced after interbreeding with our now-extinct relatives, including Neanderthals and Denisovans. The adaptive role of copy number variants (CNVs), another well-known form of genomic variation generated through deletions or duplications that affect more base pairs in the genome, is less well understood, despite evidence that such mutations are subject to stronger selective pressures.

    RATIONALE

    This study focuses on the discovery of introgressed and adaptive CNVs that have become enriched in specific human populations. We combine whole-genome CNV calling and population genetic inference methods to discover CNVs and then assess signals of selection after controlling for demographic history. We examine 266 publicly available modern human genomes from the Simons Genome Diversity Project and genomes of three ancient hominins—a Denisovan, a Neanderthal from the Altai Mountains in Siberia, and a Neanderthal from Croatia. We apply long-read sequencing methods to sequence-resolve complex CNVs of interest specifically in the Melanesians—an Oceanian population distributed from Papua New Guinea to as far east as the islands of Fiji and known to harbor some of the greatest amounts of Neanderthal and Denisovan ancestry.

    RESULTS

    Consistent with the hypothesis of archaic introgression outside Africa, we find a significant excess of CNV sharing between modern non-African populations and archaic hominins (P = 0.039). Among Melanesians, we observe an enrichment of CNVs with potential signals of positive selection (n = 37 CNVs), of which 19 CNVs likely introgressed from archaic hominins. We show that Melanesian-stratified CNVs are significantly associated with signals of positive selection (P = 0.0323). Many map near or within genes associated with metabolism (e.g., ACOT1 and ACOT2), development and cell cycle or signaling (e.g., TNFRSF10D and CDK11A and CDK11B), or immune response (e.g., IFNLR1). We characterize two of the largest and most complex CNVs on chromosomes 16p11.2 and 8p21.3 that introgressed from Denisovans and Neanderthals, respectively, and are absent from most other human populations. At chromosome 16p11.2, we sequence-resolve a large duplication of >383 thousand base pairs (kbp) that originated from Denisovans and introgressed into the ancestral Melanesian population 60,000 to 170,000 years ago. This large duplication occurs at high frequency (>79%) in diverse Melanesian groups, shows signatures of positive selection, and maps adjacent to Homo sapiens–specific duplications that predispose to rearrangements associated with autism. On chromosome 8p21.3, we identify a Melanesian haplotype that carries two CNVs, a ~6-kbp deletion, and a ~38-kbp duplication, with a Neanderthal origin and that introgressed into non-Africans 40,000 to 120,000 years ago. This CNV haplotype occurs at high frequency (44%) and shows signals consistent with a partial selective sweep in Melanesians. Using long-read sequencing genomic and transcriptomic data, we reconstruct the structure and complex evolutionary history for these two CNVs and discover previously undescribed duplicated genes (TNFRSF10D1, TNFRSF10D2, and NPIPB16) that show an excess of amino acid replacements consistent with the action of positive selection.

    CONCLUSION

    Our results suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation that is absent from current reference genomes."


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    1 members found this post helpful.
    I suppose it makes sense that Melanesians wouldn't have maintained a higher percentage of non-homo sapiens sapiens DNA than most other people for tens of thousands of years unless it was positively selected for. The explanation that they just interbred more with Neanderthals and Denisovans doesn't explain why they still have this DNA when some other populations (such as Europeans) seem to have lost some of their Neanderthal DNA, presumably because it has been selected against.

    The association with autism is interesting. I'm not sure whether the researchers are suggesting that the Denisovan genomic variation at 16p11.2 is associated with autism or is protective against autism. Severe autism is obviously a developmental disorder that would be selected against, but the more common mild form of autism can be associated with high functioning creativity and intelligence (that could be subject to positive selection). It would be interesting to compare the rate of autism in Melanesian populations with the rate in other populations.

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    Quote Originally Posted by Tamakore View Post
    I suppose it makes sense that Melanesians wouldn't have maintained a higher percentage of non-homo sapiens sapiens DNA than most other people for tens of thousands of years unless it was positively selected for. The explanation that they just interbred more with Neanderthals and Denisovans doesn't explain why they still have this DNA when some other populations (such as Europeans) seem to have lost some of their Neanderthal DNA, presumably because it has been selected against.

    The association with autism is interesting. I'm not sure whether the researchers are suggesting that the Denisovan genomic variation at 16p11.2 is associated with autism or is protective against autism. Severe autism is obviously a developmental disorder that would be selected against, but the more common mild form of autism can be associated with high functioning creativity and intelligence (that could be subject to positive selection). It would be interesting to compare the rate of autism in Melanesian populations with the rate in other populations.
    That's exactly how I see it.

    I'm glad I'm not the only one who couldn't quite figure out what they were getting at in reference to autism. :)

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    Quote Originally Posted by Tamakore View Post
    I suppose it makes sense that Melanesians wouldn't have maintained a higher percentage of non-homo sapiens sapiens DNA than most other people for tens of thousands of years unless it was positively selected for. The explanation that they just interbred more with Neanderthals and Denisovans doesn't explain why they still have this DNA when some other populations (such as Europeans) seem to have lost some of their Neanderthal DNA, presumably because it has been selected against.

    The association with autism is interesting. I'm not sure whether the researchers are suggesting that the Denisovan genomic variation at 16p11.2 is associated with autism or is protective against autism. Severe autism is obviously a developmental disorder that would be selected against, but the more common mild form of autism can be associated with high functioning creativity and intelligence (that could be subject to positive selection). It would be interesting to compare the rate of autism in Melanesian populations with the rate in other populations.
    I have hard time to make sense of all those positive / negative selection things. Obviously because i'm an amateur. But nature dont seem to be that accurate in selecting things. If we follow the unmentionable amount of studies that advocate Meat as pure Sickness of the human being, why are we eating that much of it, why our ancestors survived and evolved eating that much of it, wouldn't our body make us distate it?

    And why would Creativity being selected from the beginning. With their respect, do Autistic people give the feels to being able of Adaptation in different type of situations? I thought they had kinda their " own rituals " and everything going against it are disturbing them. Hard to survive in the wilderness like that. And if Autism was positively selected that far in times, it probably would have been way more common.

    Sounds more likely that Creativity in respect of the Autistic spectrum could have been favorised into a human group for whatever social reasons.

    Thing apart, i have read that a lot of Polynesians and maybe Melanesians? Suffers from modern times excess and have some of the biggest rate of Obesity of the world. Would be interesting to know if there is a genetic issue toward this reality and if archaic genes might be linked to it.

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    A meat diet may clog our arteries and kill us in the long run, but by then we've usually had whatever children we were going to have anyway, so we've already passed on our meat craving genes to the next generation.

    Natural selection is a blind process without foresight. A mutation didn't have to be perfect to be selected, its disadvantages just had to be outweighed by its advantages. For example, some people in tropical areas have a sickle cell mutation that is protective against malaria, but if they get a double dose of the mutation it causes sickle cell anemia.

    Perhaps something similar applies to genes for autism, although that's only an unproven hypothesis.

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    Quote Originally Posted by Tamakore View Post
    A meat diet may clog our arteries and kill us in the long run, but by then we've usually had whatever children we were going to have anyway, so we've already passed on our meat craving genes to the next generation.
    I am not sure if meat carving is something relating to genes, or more to cultural habits.
    Overall, humans seem to be highly adaptive species and would change their diet on things that are available. During pre-historic times, the reason why people ate meat was rather straightforward - in cold climate (long white winters or living on plains) there was no other choice for Palaeolithic people if they wanted to adapt.
    On the other hand, switching to non-meat diet should not be something out of reach now, as there is variety of food available and we can adapt if want to. The genetic link, if there is such one, should work something like that:


    Fish - European WHG component
    Cereals - Farmers
    Diary/Meat - Herders


    https://www.dailymail.co.uk/sciencet...mily-tree.html


    Culturally, for instance, not eating meat is difficult for people in Mongolia.
    "With annual consumption of meat topping 200 pounds per person and livestock outnumbering people 14 to 1, Mongolia is a carnivore’s paradise"

    Genetically though Mongolians are most closely linked with Northern Han Chinese, and Han people are very much farmers and culturally prevalently rice eaters

    I am a Lithuanian with 53% pastoralist/herders genes, but switching to non-meat diet was very easy to me. So again, matters of diet are not that simple to connect to genetic make-up.

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    I agree that since farming began many people have chosen a non-meat diet for cultural or personal reasons without too much trouble. Culture can override genetic tendencies. It may be that humans have fat craving genes rather than specifically meat craving genes.

    However, I think animals generally do have genes that dispose them to desire the food that their ancestors ate and that their digestive systems have evolved to process. As you noted, Paleolithic people were omnivores who included meat in their diet. Their ancestors may have been omnivores for millions of years, ever since they parted company with the ancestors of chimpanzees. Bonobos and chimpanzees are also omnivores who seem to get particularly excited when they have an opportunity to eat meat. The common ancestor of all three species may have already evolved a similar taste for meat.

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    Regarding animals, my dog is fully an opportunistic eater. There is hardly anything that he would not want to eat actually. Adores pancakes with apples for instance. I should do an experiment about his preferences: a piece of raw beef vs a pancake.

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