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The thing about Neanderthals and Denisovans is that they had a very, very high recessive mutational load from being isolated from everyone else for so long, living in small nuclear families, reproducing with their sisters and their mothers, etc. To the point where they were highly genetically and anatomically removed from Homo sapiens. For instance, Neanderthals have tiny mastoid processes, with a crest. Modern humans and chimpanzees are similar to eachother and different from Neanderthals in this regard, in that they have comparatively larger mastoid processes, and completely lack the crest that is found in Neanderthal skulls behind the ear lobe. Although Neanderthals have a lot of primitive features, they also have other features which are quite derived and very different from chimpanzees. When you get down to the minutia they are very different from chimpanzees. The smaller mastoid process is also an example of Neanderthals being more evolved than modern humans, because this is considered a primitive trait.
If Africans are closer to Chimpanzees, I would expect that to be because they lack archaic Eurasian ancestry and haven't . There is no need for them to have archaic African ancestry of any kind. If Native Americans are farthest from Chimpanzees, I would expect that to be due to retention of more archaic introgression, plus additional population bottlenecking from living in America and being isolated for so long.
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