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Neandertals went extinct! Their features disappeared in later humans! How can any of their genes have survived?

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Neandertals went extinct! Their features disappeared in later humans! How can any of their genes have survived?

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This is my favorite one to answer, because it invokes the true paradox of introgression. The features that we recognize as Neandertal features, were defined as Neandertal features by virtue of the fact that they are mostly gone! That means that any alleles correlated with Neandertal morphological features were almost certainly selected against, or were at best neutral. That means that those recognizably Neandertal genes are gone! But here we have a gene that looks to have come from some archaic population. Adaptive introgression occurs when adaptive alleles are selected, and broken apart from their genetic background. So even as many (perhaps most) Neandertal alleles disappeared, some of their alleles began to increase in frequency — slowly at first, then very rapidly. Some adaptive introgressions may already have been fixed, particularly in Europe (from Neandertals). Others, like microcephalin, are still growing in frequency.

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