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Thread: Did humans really interbreed with Neanderthals (this preprint says maybe not)

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    Did humans really interbreed with Neanderthals (this preprint says maybe not)

    Statistics used to infer inter-breeding between humans and Neanderthals are strongly predicted by flanking sequence heterozygosity.
    William Amos, Cambridge University

    Abstract
    A large and rapidly expanding literature has grown out of the observation that humans carry a genetic legacy reflecting ancient inter-breeding with archaic hominins such as Neanderthals and Denisovans. However, a recent study suggests that a commonly used statistic used to assess legacy size, D, is driven mainly by heterozygous sites in Africa acting to increase divergence from our common ancestor rather than introgressed fragments outside Africa reducing divergence. To test this new model, I analysed how D is influenced by heterozygosity within a kilobase of each putative introgressed base. I find that flanking heterozygosity is a potent predictor of D, with introgression always being inferred as having occurred into the population with lower heterozygosity. This pattern cannot be driven by any introgressed fragments themselves, which simulations show create the exact converse pattern, but instead appears to be generated by heterozygosity acting to drive increased divergence from the ancestral sequence. This new model explains why introgression of haploid or semi-haploid regions is essentially lacking and why introgression is often inferred around immune genes and other regions under strong selection. More generally, these results raise the possibility that reported legacies are largely an artefact arising out of the false assumption that mutation rate is constant.

    A discussion of the preprint on Twitter

    Neanderthal introgression: a case of smoke and mirrors?
    A log the author is keeping on this topic.
    Last edited by pmokeefe; 10-12-2020 at 09:23 PM.
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    Would that mean that say Papuans would have instead gone through considerably higher mutation rates instead of garnering excessive archaic admixture?

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    I think it is saying almost the opposite, though it does not address Papuan. Basically what they have that LOOKS LIKE Denisovan DNA is really just a minor part of the gene pool that was always with Modern H. Sapiens. It is just that they were a small homozygous group and so the genetic oddities they had (relative to Africa where these mutations were such a minority that they dropped out and were overwhelmed by current genotypes) stayed with them much longer. The Africans actually mutated AWAY from the Neanderthal/Denisovan like genes, which were only a small part of the population anyway. The small groups with little variation just kept their oddities. They had a lower mutation rate than the more diverse large populations because genes that are the same have a lower mutation rater than genes that are different when dividing.

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    Quote Originally Posted by Cosmo View Post
    .. Basically what they have that LOOKS LIKE Denisovan DNA is really just a minor part of the gene pool that was always with Modern H. Sapiens. It is just that they were a small homozygous group and so the genetic oddities they had (relative to Africa where these mutations were such a minority that they dropped out and were overwhelmed by current genotypes) stayed with them much longer. The Africans actually mutated AWAY from the Neanderthal/Denisovan like genes, which were only a small part of the population anyway. The small groups with little variation just kept their oddities. They had a lower mutation rate than the more diverse large populations because genes that are the same have a lower mutation rater than genes that are different when dividing.
    Great explanation.
    Do you mind if I quote that to friends?

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    I feel like this should be bigger news, no?

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    OTOH Africans are so diverse it seems less plausible that all of them would have discarded their Neander/Denisovan gene signatures.

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