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

  1. #21
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    @Andrewid,

    I guess I have not heard of a recent Zavala study on archaic introgression.

    Regarding the one that you linked to, given its premises my first reading is that it is reasonable, but the premises are exactly what is being questioned here. Whatever happened to "convergent evolution"? It seems to go away when studying these matters. For example the paper assumes that Mastiffs in Tibet got a "different version" of a high-altitude" gene from wolves that had it. Why didn't they evolve similar genes in response to similar environmental pressures? That is what would normally be assumed. I think I linked to it earlier in this thread, but there was a study where Neanderthals and Mammoths evolved a similar set of genes as an adaptation to cold. That wasn't from "introgression", it was from two mammals having a similar response to similar selection pressures.

    I did notice the study you linked to at least tried to filter out "false positives" and found some. But it could only do so in cases where the limited ancient African samples found a similar gene. Seems like the more ancient African samples we get, the more of those "probably false positives" we will find. Dr. Amos is basically saying if we had enough such ancient African DNA we'd find close relatives of ALL of the genes purported to be from "introgression". They are leftovers that Africans drifted away from in some cases, and in other cases were selected AGAINST in Africa while selected FOR in an environment like the one Neanderthals lived in.

  2. #22
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    Quote Originally Posted by Cosmo View Post
    @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?
    The study is not yet published. But this genome, no doubt, will provide some new information regarding questions that you interested in.

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    Quote Originally Posted by Cosmo View Post
    @Andrewid,

    I guess I have not heard of a recent Zavala study on archaic introgression.

    Regarding the one that you linked to, given its premises my first reading is that it is reasonable, but the premises are exactly what is being questioned here. Whatever happened to "convergent evolution"? It seems to go away when studying these matters. For example the paper assumes that Mastiffs in Tibet got a "different version" of a high-altitude" gene from wolves that had it. Why didn't they evolve similar genes in response to similar environmental pressures? That is what would normally be assumed. I think I linked to it earlier in this thread, but there was a study where Neanderthals and Mammoths evolved a similar set of genes as an adaptation to cold. That wasn't from "introgression", it was from two mammals having a similar response to similar selection pressures.

    I did notice the study you linked to at least tried to filter out "false positives" and found some. But it could only do so in cases where the limited ancient African samples found a similar gene. Seems like the more ancient African samples we get, the more of those "probably false positives" we will find. Dr. Amos is basically saying if we had enough such ancient African DNA we'd find close relatives of ALL of the genes purported to be from "introgression". They are leftovers that Africans drifted away from in some cases, and in other cases were selected AGAINST in Africa while selected FOR in an environment like the one Neanderthals lived in.
    Convergent evolution versus introgression can be determined by looking at the segment around the mutation of interest to see whether it more closely resembles other members of the population or a member of the potential introgressing population.
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    Quote Originally Posted by Kale View Post
    Convergent evolution versus introgression can be determined by looking at the segment around the mutation of interest to see whether it more closely resembles other members of the population or a member of the potential introgressing population.

    That is true when the flanking genes are unique to the introgressed group and not part of their "parent" population, but it is much harder when one is saying, as Amos is, that the parent population started with all of these seemingly introgressed genes but evolved out of them over time while the daughter population, due to a low mutation rate driven by high homogeneity, kept more of them the same.

    He actually devised a test for this, to see if the signal from the flanking genes made it look more like introgression or more like mutation. His results were one-sided in favor of it coming from mutation. Here is his paper https://www.biorxiv.org/content/10.1101/2021.01.21.427635v1.full

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    In that case, in a daughter population where the allele in question is not fixed, wouldn't you expect adjacent segments for both 'carriers' and 'controls' to be equally different from the 'parent' population? Low mutation rate > high homogenity > etc. isn't going to differentially affect members of the same population.
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    @Kale,

    Not sure I get what you are saying here, or you me. It is the high homogenity which leads to the low mutation rate. It is true that if an allele is variable in the daughter population to the degree it is in the parent population that the mutation rate should be the same, but that's not where the alleged "introgression" is. Instead, it seems the higher the homogenity in a gene segment of Eurasians the greater the odds it will show up as "introgressed". That makes no sense as archaic introgression should greatly DECREASE homgenity. Amos says "More than 80% of the observed ABBA - BABA count difference can be attributed to sites where the Neanderthal B allele is ancestral to archaics (Neanderthal = Denisovan) and fixed in non-Africans (!!). "

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    Would archaic introgression decrease homogenity? Neanderthals were a lot more homogenous than modern humans, and if a Neanderthal segment were introgressed and kept around for 40,000 years, it probably would be because it's beneficial and would lead to positive selection which I think also would increase homogenity (two copies of a beneficial gene generally better than one?)
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    @Kale,

    ??Would archaic introgression decrease homogenity?//

    I feel certain it would so long as the following conditions are met: So long as the archaic genes were different from those of the introgressed population and their parent group it would by necessity decrease homogeneity. You are putting different genes into the population, so by necessity the genes would be less alike after that was done than before. Now if those genes were already present in the parent population, even at low frequency, it would not necessarily decrease homogeneity, but then you would not need introgression to explain the presence of the genes either!

    The other possible exception is what you alluded to.... What if the introgressed genes rise to fixation? If there were multiple alleles to start with but an introgressed allele pushes them out over time then that would NOT decrease homogeneity. It could increase it.

    But you have to ask yourself how often is an introgressed gene going to come to dominate a population? It is very unlikely to occur unless it provides some strong benefit- such as disease resistance. But that brings us right back to the issue of how the gene got there- whatever happened to convergent evolution? A beneficial mutation will spread and it doesn't need introgression from another species to do it- they had similar mutations that were beneficial that "took" because they faced similar pathogens, no introgression needed. But most supposed Neanderthal alleles are neutral or even slightly deleterious. Yet they are almost all at fixation in Eurasians. That doesn't sound like introgression. It sounds like a homogenous population that had so little diversity they couldn't shed their inferior alleles, and shared some mutations with another species which ALSO could not shed such alleles due to high homogeneity. I realize this is a less intuitive explanation, but the norm for introgression should indeed by that it decreases homogeneity yet the supposed "Neanderthal" alleles are usually at fixation and therefore INCREASE it.
    Last edited by Cosmo; 07-01-2021 at 03:15 AM.

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