Evolutionary switches: How regulatory variants shaped human evolution

Changes in gene regulation are key drivers of human evolution. However, how and which regulatory changes shaped human adaptations remains largely unknown. Here, we employed massively parallel reporter assays (MPRAs) in skeletal and neural cells to uncover the function of the 71,443 variants distinguishing Neanderthals and Denisovans from modern humans. This extensive catalog allowed us to discover hundreds of variants that altered human expression, providing the first insight into the function of noncoding variants in recent human evolution. We use these MPRAs to identify evolutionary trends and detect several examples of convergent evolution. For example, both lineages completely silenced an enhancer of KDM8, a gene involved in tumor progression, but Neanderthals and Denisovans achieved this through motif disruption, while modern humans did so through hypermethylation. Finally, we developed a method to reconstruct morphological profiles from DNA sequence and methylation and used it to reconstruct Denisovan anatomy. Using the profile, we scanned the fossil record and identified unclassified specimens matching the Denisovan profile. We found that Harbin and Dali were likely Denisovans, and that Kabwe might have been related to the ancestor of Neanderthals and Denisovans. Overall, our work helps shed light on the key regulatory changes underlying human evolution.