Newly analyzed ancient DNA shows significant population structure in the settlement of the Americas by the founding population and multiple waves of internal migration include the extinction of some branches of the founding population of the Americas. For example, the ancestors of modern high altitude occupants of the Andes mountains split from low altitude residents of the region about 9,000 years ago.
There is a wealth of new detail in the three new papers discussed in the linked New York Times story. I don't have time to give those papers a full treatment now, but will update this post and make new posts when I do.
A much clearer picture emerges.
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