Genes Affecting Vocal and Facial Anatomy Went Through Extensive Regulatory Divergence in Modern Humans

David Gokhman; Malka Nissim‐Rafinia; Lily Agranat-Tamir; Genevieve Housman; Raquel García-Pérez; Esther Lizano; Olivia Cheronet; Swapan Mallick; María A. Nieves-Colón; Heng Li; Songül Alpaslan-Roodenberg; Mario Novak; Hongcang Gu; Jason M. Osinski; Manuel Ferrando-Bernal; Pere Gelabert; Iddi F. Lipende; Deus C. Mjungu; Ivanela I. Kondova; Ronald E. Bontrop; Ottmar Kullmer; Gerhard W. Weber; Tal Shahar; Mona Dvir‐Ginzberg; Marina Faerman; Ellen E. Quillen; Alexander Meissner; Yonatan Lahav; Leonid Kandel; Meir Liebergall

doi:10.1038/s41467-020-15020-6

Evolutionary BiologyNature CommunicationsMar 4, 2020

Peer-reviewed journal article

Genes Affecting Vocal and Facial Anatomy Went Through Extensive Regulatory Divergence in Modern Humans

David Gokhman iD, Malka Nissim‐Rafinia, Lily Agranat-Tamir iD, Genevieve Housman iD, Raquel García-Pérez iD, Esther Lizano iD, Olivia Cheronet iD, Swapan Mallick iD, María A. Nieves-Colón iD, Heng Li iD, Songül Alpaslan-Roodenberg iD, Mario Novak iD, Hongcang Gu iD, Jason M. Osinski iD, Manuel Ferrando-Bernal iD, Pere Gelabert iD, Iddi F. Lipende iD, Deus C. Mjungu, Ivanela I. Kondova iD, Ronald E. Bontrop iD, Ottmar Kullmer iD, Gerhard W. Weber iD, Tal Shahar iD, Mona Dvir‐Ginzberg iD, Marina Faerman iD, , Liran Carmel iD

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Abstract

SummaryRegulatory 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.View Full Text