Functional characterization of gene regulatory elements shaping human evolution

Despite decades of research, we are still far from understanding how adaptation presents itself at the molecular level, and how these changes affect our current anatomy, physiology, and health. The lion’s share of phenotypic divergence is thought to be encoded in noncoding regions of the genome. However, despite their overwhelming importance, our ability to identify divergent regulation between human lineages is currently limited by 1) the rapid degradation of ancient samples, and 2) our restricted ability to infer the regulatory effect of noncoding variants simply by investigating DNA sequence. Here, we used massively parallel reporter assays to map the functional effect of each of the sequence variants that emerged and spread in human evolution. To this end, we assayed over 400,000 variants that are specific to archaic humans (Neanderthals and Denisovans), modern humans, or the ancestors of all of these groups. We carried out theseassays in four cell types: osteoblasts, neural progenitor cells, adipocytes and fibroblasts, thus illuminating four key aspects of human evolution: skeletal, neural, fat, and integumentary. Using these resources, we identified particularly extensive regulatory changes in genes affecting the anatomy and physiology of the vocal tract and cerebellum of modern humans. In summary, this work provides the first insight into how noncoding variants shaped human evolution.