ArticleNature communications2020
Differential DNA methylation of vocal and facial anatomy genes in modern humans.
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Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64citing papers in PubMed
120.8field-weighted citation impact, top 1% of its field
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Who cites it
64 citing papers in PubMed, 112 citations in OpenAlex.
- Genomic structural variations distinguishing archaic and modern humans are associated with neurodevelopment.iScience · 2026Article
- Regulatory Evolution and the Genetic Basis of Human Brain Expansion.Journal of molecular evolution · 2026Review
- The gene-regulatory evolution of the human skeleton.Nature · 2026Article
- Local ancestry inference identifies robust evidence of selection in Neolithic Europe.Molecular biology and evolution · 2026Article
- Dynamic NFIX Promoter Usage Shapes Stem and Committed Myogenic States.International journal of molecular sciences · 2026Article
- Population epigenetics: deciphering DNA methylation diversity and its implications for health, disease, and evolution.Molecular biology and evolution · 2026Review
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- Optimal Reference Panel Design in Ancient DNA Imputation from Coalescent Theory, Simulation, and Real Data Application with an Ancient Reference Panel.bioRxiv : the preprint server for biology · 2026Article
- Profiling the epigenomic landscape of late embryonic and adult mouse hind limb muscles.Scientific reports · 2026Article
- Neanderthal-derived variants increase SOX9 enhancer activity in craniofacial progenitors that shape jaw development.Development (Cambridge, England) · 2025Article
- The rise of historical epigenomics and temporal analysis of gene regulation.Genome biology · 2025Review
- RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions.Genome biology · 2025Article
- Candidate Denisovan fossils identified through gene regulatory phenotyping.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Rethinking Hominin Air Sac Loss in Light of Phylogenetically Meaningful Evidence.Evolutionary anthropology · 2025Article
- The genetic history of Portugal over the past 5,000 years.Genome biology · 2025Article
- Whole-genome ancestry of an Old Kingdom Egyptian.Nature · 2025Article
- Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.Genome biology · 2025Article
- Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies.Molecular ecology resources · 2025Review
- Regulatory Plasticity of the Human Genome.Molecular biology and evolution · 2025Article
- Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk.bioRxiv : the preprint server for biology · 2025Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
41 authors at 16 institutions in 9 countries.
David GokhmanDepartment of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel. david.gokhman@mail.huji.ac.il.
Malka Nissim-RafiniaDepartment of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
Lily Agranat-TamirDepartment of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
Genevieve HousmanSchool of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA.ORCID http://orcid.org/0000-0002-3482-7511
Raquel García-PérezInstitute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain.
Esther LizanoInstitute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain.ORCID http://orcid.org/0000-0003-3304-9807
Olivia CheronetDepartment of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria.ORCID http://orcid.org/0000-0001-6760-1204
Swapan MallickBroad Institute, Cambridge, MA, 02138, USA.
Maria A Nieves-ColónSchool of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA.
Heng LiBroad Institute, Cambridge, MA, 02138, USA.
Songül Alpaslan-RoodenbergDepartment of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
Mario NovakInstitute for Anthropological Research, 10000, Zagreb, Croatia.
Hongcang GuBroad Institute, Cambridge, MA, 02138, USA.
Jason M OsinskiDepartment of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA.
Manuel Ferrando-BernalInstitute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain.
Pere GelabertInstitute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain.ORCID http://orcid.org/0000-0003-3019-0725
Iddi LipendeGombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania.
Deus MjunguGombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania.
Ivanela KondovaBiomedical Primate Research Centre (BPRC), Rijswijk, Netherlands.ORCID http://orcid.org/0000-0003-2745-6094
Ronald BontropBiomedical Primate Research Centre (BPRC), Rijswijk, Netherlands.ORCID http://orcid.org/0000-0003-0874-6467
Ottmar KullmerDepartment of Palaeoanthropology and Messel Research, Senckenberg Center of Human Evolution and Paleoecology, Frankfurt am Main, Germany.ORCID http://orcid.org/0000-0002-5929-8070
Gerhard WeberDepartment of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria.
Tal ShaharDepartment of Neurosurgery, Shaare Zedek Medical Center, Jerusalem, Israel.
Mona Dvir-GinzbergLaboratory of Cartilage Biology, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, 91120, Jerusalem, Israel.ORCID http://orcid.org/0000-0003-3089-6875
Marina FaermanLaboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel.
Ellen E QuillenDepartment of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 85287, USA.
Alexander MeissnerBroad Institute, Cambridge, MA, 02138, USA.ORCID http://orcid.org/0000-0001-8646-7469
Yonatan LahavOtolaryngology - Head & Neck Surgery Department, Laryngeal Surgery Unit, Kaplan Medical Center, Rehovot, Israel.
Leonid KandelOrthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.
Meir LiebergallOrthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.
María E PradaI.E.S.O. 'Los Salados'. Junta de Castilla y León, León, Spain.
Julio M VidalJunta de Castilla y León, Servicio de Cultura de León, León, Spain.ORCID http://orcid.org/0000-0002-5309-0586
Richard M GronostajskiDepartment of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA.ORCID http://orcid.org/0000-0003-4264-208X
Anne C StoneSchool of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA.ORCID http://orcid.org/0000-0001-8021-8314
Benjamin YakirDepartment of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel.
Carles Lalueza-FoxInstitute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain.ORCID http://orcid.org/0000-0002-1730-5914
Ron PinhasiDepartment of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria.ORCID http://orcid.org/0000-0003-1629-8131
David ReichBroad Institute, Cambridge, MA, 02138, USA.ORCID http://orcid.org/0000-0002-7037-5292
Tomas Marques-BonetInstitute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain.ORCID http://orcid.org/0000-0002-5597-3075
Eran MeshorerDepartment of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel. eran.meshorer@mail.huji.ac.il.ORCID http://orcid.org/0000-0003-4777-986X
Liran CarmelDepartment of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel. liran.carmel@huji.ac.il.ORCID http://orcid.org/0000-0003-0225-8550
Hebrew University of Jerusalem · ILBroad Institute · USInstitut de Biologia Evolutiva · ESArizona State University · USUniversity of Vienna · ATBiomedical Primate Research Centre · NLHadassah Medical Center · ILJunta de Castilla y León · ESThe Jane Goodall Institute · TZUniversity at Buffalo, State University of New York · USHarvard University · USInstitució Catalana de Recerca i Estudis Avançats · ESSenckenberg Centre for Human Evolution and Palaeoenvironment · DEShaare Zedek Medical Center · ILTexas Biomedical Research Institute · USUniversity College Dublin · IE
Funding
The Southwest National Primate Research Center Supplement- Infrastructure improvements of ABSL2 holding areasP51OD011133 · OD · TEXAS BIOMEDICAL RESEARCH INSTITUTE · PI Larry S. Schlesinger · 2012 to 2026
$129.7MMolecular Epidemiology and Natural History of SIVcpzR01AI058715 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HAHN, BEATRICE H · 2004 to 2013
$6.1M2/2 Somatic mosaicism and autism spectrum disorderU01MH106874 · NIMH · YALE UNIVERSITY · PI SESTAN, NENAD · 2015 to 2019
$4.0MHoward Hughes Medical InstituteNIAID NIH HHS R01 AI058715NIH HHS P51 OD011133NIMH NIH HHS U01 MH106874
Abstract
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated 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.
Indexed as
DNA, AncientDNA MethylationPhenotypeAdultAgedAnimalsCells, CulturedChildChondrocytesEvolution, MolecularFaceFemaleGene Regulatory NetworksGenetic SpeciationHumansLarynxDNA, Ancient
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