Entirely deserved. Pääbo is the main guy in the team that discovered Europeans have 2-4% Neanderthal ancestry in 2014 and East Asians have up to 6% Denisovan ancestry. That is, the humans who lived around the world before the Out of Africa event about 60kya, dating back to 1 or even 2 million years out of Africa themselves, contributed some genes to our current makeup, even though they have been eliminated as a species by Homo sapiens. (We weren't smarter, we were probably just meaner and better able to work together in groups.) You can listen to John Hawks talk about him with Steve Hsu and Corey Washington or catch up with Quillette's (very good) take on the award. I would only note that the description of those who believed in the theories that he essentially disproved is oversimplified, and they deserve more credit for nuance and interpretation. Many others who study this material look at his work and say "Just as we always said. If there is any Neanderthal genetic material, it didn't have any important effects and mostly vanished." They're not wrong. The simplest Out of Africa models of 50 years ago are still 95% of the story.
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