Archaic and modern bone DNA methylation maps from the Neanderthal, Denisovan, modern human and chimpanzee

Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract DNA methylation maps were reconstructed from several human groups, including two Neanderthals, one Denisovan and five anatomically modern humans (Ust Ishim, Stuttgart, Loschbour, I1583 and La Braña 1). Additionally, present-day DNA methylation maps were produced from two present-day human bones (WGBS) and two chimpanzee bones (WGBS and RRBS). The metadata for the following samples are included in the supplementary file 'GSE96833_metadata_reanalysis_samples.xls': - Altai Neanderthal Reconstructed Methylome - Denisovan Reconstructed Methylome - Modern Human (Ust Ishim) Reconstructed Methylome - Modern Human (Stuttgart) Reconstructed Methylome - Modern Human (Loschbour) Reconstructed Methylome - Vindija Neanderthal Reconstructed Methylome