Genes Affecting Vocal and Facial Anatomy Went Through Extensive Regulatory Divergence in Modern Humans
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Summary: 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.
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XYLT1 is among the top differentially methylated genes compared to archaics.
“are among the top differentially methylated genes compared to archaics and were also highlighted in a recent study on regulatory changes that shaped the modern human facial and vocal anatomy (tables S1 and S3) (43)”
AMH-specific hypermethylation has been identified in the regulatory region of BAZ1B itself.
“This is also reinforced by the recent identification of AMH-specific hypermethylation in the regulatory region of BAZ1B itself (43).”
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Zanella, M., Vitriolo, A., Andirko, A., Martins, P. T., Sturm, S., O’Rourke, T., Laugsch, M., Malerba, N., Skaros, A., Trattaro, S., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw7908 · Cited by 101 · see citing works
The cis-regulatory effects of modern human-specific variants
Weiss, C. V., Harshman, L., Inoue, F., Fraser, H. B., Petrov, D. A., Ahituv, N., & Gokhman, D. (2021) · eLife · doi:10.7554/elife.63713 · Cited by 70 · see citing works
Self-citation
- Authors
- Gokhman, D., Nissim-Rafinia, M., Agranat-Tamir, L., Housman, G., García-Pérez, R., Lizano, E., Cheronet, O., Mallick, S., Nieves-Colón, M. A., Li, H., Alpaslan-Roodenberg, S., Novak, M., Gu, H., Osinski, J. M., Ferrando-Bernal, M., Gelabert, P., Lipende, I., Mjungu, D., Kondova, I., Bontrop, R., Kullmer, O., Weber, G., Shahar, T., Dvir-Ginzberg, M., Faerman, M., Quillen, E. E., Meissner, A., Lahav, Y., Kandel, L., Liebergall, M., Prada, M. E., Vidal, J. M., Gronostajski, R. M., Stone, A. C., Yakir, B., Lalueza-Fox, C., Pinhasi, R., Reich, D., Marques-Bonet, T., Meshorer, E., & Carmel, L.
- Affiliations
- Hebrew University of Jerusalem (IL)
- Arizona State University (US)
- Consejo Superior de Investigaciones Científicas (ES)
- University of Vienna (AT)
- Broad Institute (US)
- Harvard University (US)
- University College Dublin (IE)
- University at Buffalo, State University of New York (US)
- The Jane Goodall Institute (TZ)
- Biomedical Primate Research Centre (NL)
- Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE)
- Shaare Zedek Medical Center (IL)
- Texas Biomedical Research Institute (US)
- Hadassah Medical Center (IL)
- Junta de Castilla y León (ES)
- Corresponding author
- Gokhman, David
- Meshorer, Eran
- Carmel, Liran
- ORCID
- Gokhman, David
- Agranat-Tamir, Lily
- Housman, Genevieve
- García-Pérez, Raquel
- Lizano, Esther
- Cheronet, Olivia
- Mallick, Swapan
- Li, Heng
- Alpaslan-Roodenberg, Songül
- Novak, Mario
- Gu, Hongcang
- Osinski, Jason M.
- Ferrando-Bernal, Manuel
- Gelabert, Pere
- Lipende, Iddi
- Kondova, Ivanela
- Bontrop, Ronald
- Kullmer, Ottmar
- Weber, Gerhard
- Shahar, Tal
- Faerman, Marina
- Quillen, Ellen E.
- Meissner, Alexander
- Lahav, Yonatan
- Kandel, Leonid
- Liebergall, Meir
- Vidal, Julio M.
- Gronostajski, Richard M.
- Stone, Anne C.
- Pinhasi, Ron
- Reich, David
- Meshorer, Eran
- Carmel, Liran
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2017-02-08
- Volume
- 11
- Issue
- 1
- Pages
- 1189-1189
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7055320
- OpenAlex
- W3009791849
- Cited by
- 144
- References
- 86
- Citations by year
- 2026: 37 · 2025: 23 · 2024: 13 · 2023: 14 · 2022: 21 · 2021: 18 · 2020: 10 · 2019: 6 · 2018: 1 · 2017: 1
- FWCI
- 5.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Dipòsit Digital de Documents de la UAB (Universitat Autònoma de Barcelona) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- National Science Foundation (MH106874, 1052693)
- Howard Hughes Medical Institute
- Paul G. Allen Family Foundation
- Leakey Foundation
- Nacey Maggioncalda Foundation
- New York State Stem Cell Science (C030133)
- Centres de Recerca de Catalunya
- Clore Israel Foundation
- Generalitat de Catalunya (BFU2017-86471-P)
- Israel Science Foundation (ISF 1430/13)
- Max-Planck-Gesellschaft
- National Institutes of Health (MH106874, P51OD011133)
- School of Human Evolution and Social Change, Arizona State University
- National Institute of Mental Health (U01MH106874)
- National Institute of Allergy and Infectious Diseases (R01AI058715)
- Division of Materials Research
- FP7 Ideas: European Research Council (263441)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- DNA methylation, differentially methylated regions, human evolution, Neanderthals, Denisovans, human-specific traits, vocal tract anatomy, SOX9, aggrecan, COL2A1, NFIX, XYLT1, hypermethylation, epigenetic regulation, chimpanzees
- MeSH terms
- DNA, Ancient, Adult, Aged, Animals, Cells, Cultured, Child, Pan troglodytes, Face, Female, Humans, Larynx, Male, Middle Aged, Phenotype, Phonation, Tongue, Vocal Cords, Vocalization, Animal, Evolution, Molecular, DNA Methylation, Chondrocytes, Genetic Speciation, Gene Regulatory Networks, Neanderthals, Primary Cell Culture
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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