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The version of the claim I believed is that Sub-Saharan Africans (especially as of ~2000 years ago) basically don't have any Neanderthal DNA.

Your follow-up doesn't appear to contradict that (of course this wouldn't hold when populations start mixing in modern times and wouldn't have ever held 100%) so I was confused.

However the article does in fact dispute my previous belief:

>The researchers found that African individuals on average had significantly more Neanderthal DNA than previously thought—about 17 megabases (Mb) worth, or 0.3% of their genome.

This is as opposed to 1-4% of genomes for populations outside of Sub-Saharan Africa.

>They also found signs that a handful of Neanderthal genes may have been selected for after they entered Africans' genomes, including genes that boost immune function and protect against ultraviolet radiation.

>The best fit model for where Africans got all this Neanderthal DNA suggests about half of it came when Europeans—who had Neanderthal DNA from previous matings—migrated back to Africa in the past 20,000 years.

"The past 20,000 years" is pretty broad and seemingly includes modern era exchanges, but AFAIK that can't account for selecting Neanderthal genes or for how widespread Neanderthal DNA already is.

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