Changes in gene regulation are broadly accepted as key drivers of phenotypic differences between closely related species. However, identifying regulatory changes that shaped human-specific traits is a challenging task. Here, we use >60 DNA methylation maps of ancient and present-day human groups, as well as six chimpanzees, to detect regulatory changes that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting vocalization and facial features went through particularly extensive methylation changes. Specifically, we identify silencing patterns in a network of genes (SOX9, ACAN, COL2A1 and NFIX), and propose that they might have played a role in the reshaping of human facial morphology, and in forming the 1:1 vocal tract configuration that is considered optimal for speech. Our results provide insights into the molecular mechanisms that might underlie vocal and facial evolution, and suggest that they arose after the split from Neanderthals and Denisovans.
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