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Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans

David Gokhman, Lily Agranat-Tamir, Genevieve Housman, Raquel García-Pérez, Malka Nissim-Rafinia, Swapan Mallick, Maria A. Nieves-Colón, Heng Li, Songül Alpaslan-Roodenberg, Mario Novak, Hongcang Gu, Manuel Ferrando-Bernal, Pere Gelabert, Iddi Lipende, Ivanela Kondova, Ronald Bontrop, Ellen E. Quillen, Alexander Meissner, Anne C. Stone, Anne E. Pusey, Deus Mjungu, Leonid Kandel, Meir Liebergall, María E. Prada, Julio M. Vidal, Kay Prüfer, Johannes Krause, Benjamin Yakir, Svante Pääbo, Ron Pinhasi, Carles Lalueza-Fox, David Reich, Tomas Marques-Bonet, Eran Meshorer, Liran Carmel
doi: https://doi.org/10.1101/106955
David Gokhman
1Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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Lily Agranat-Tamir
1Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
2Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 91905, Israel.
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Genevieve Housman
3School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA.
4Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA.
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Raquel García-Pérez
5Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.
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Malka Nissim-Rafinia
1Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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Swapan Mallick
6Broad Institute, Cambridge MA 02138, USA.
7Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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Maria A. Nieves-Colón
3School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA.
4Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA.
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Heng Li
6Broad Institute, Cambridge MA 02138, USA.
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Songül Alpaslan-Roodenberg
7Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Mario Novak
9Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia.
22Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.
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Hongcang Gu
6Broad Institute, Cambridge MA 02138, USA.
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Manuel Ferrando-Bernal
5Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.
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Pere Gelabert
5Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.
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Iddi Lipende
10Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania.
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Ivanela Kondova
11Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands.
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Ronald Bontrop
11Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands.
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Ellen E. Quillen
12Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 85287, USA.
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Alexander Meissner
6Broad Institute, Cambridge MA 02138, USA.
13Harvard Stem Cell Institute, Cambridge, MA 02138 USA.
14Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138 USA
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Anne C. Stone
3School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA.
4Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA.
15Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA.
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Anne E. Pusey
16Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
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Deus Mjungu
10Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania.
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Leonid Kandel
17Orthopaedic Department, Hadassah – Hebrew University Medical Center, Jerusalem, Israel.
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Meir Liebergall
17Orthopaedic Department, Hadassah – Hebrew University Medical Center, Jerusalem, Israel.
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María E. Prada
18I.E.S.O. ‘Los Salados’. Junta de Castilla y León, Spain.
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Julio M. Vidal
19Junta de Castilla y León, Servicio de Cultura de León, Spain.
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Kay Prüfer
20Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig D-04103, Germany.
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Johannes Krause
21Max Planck Institute for the Science of Human History, 07745 Jena, Germany.
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Benjamin Yakir
2Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 91905, Israel.
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Svante Pääbo
20Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig D-04103, Germany.
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Ron Pinhasi
22Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.
23Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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Carles Lalueza-Fox
5Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.
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David Reich
6Broad Institute, Cambridge MA 02138, USA.
7Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
8Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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Tomas Marques-Bonet
5Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.
24Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
25Centro Nacional de Análisis Genómico (CRG-CNAG), 08028 Barcelona, Spain.
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Eran Meshorer
1Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
26The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
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Liran Carmel
1Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.
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Summary

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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Posted October 03, 2017.
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Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans
David Gokhman, Lily Agranat-Tamir, Genevieve Housman, Raquel García-Pérez, Malka Nissim-Rafinia, Swapan Mallick, Maria A. Nieves-Colón, Heng Li, Songül Alpaslan-Roodenberg, Mario Novak, Hongcang Gu, Manuel Ferrando-Bernal, Pere Gelabert, Iddi Lipende, Ivanela Kondova, Ronald Bontrop, Ellen E. Quillen, Alexander Meissner, Anne C. Stone, Anne E. Pusey, Deus Mjungu, Leonid Kandel, Meir Liebergall, María E. Prada, Julio M. Vidal, Kay Prüfer, Johannes Krause, Benjamin Yakir, Svante Pääbo, Ron Pinhasi, Carles Lalueza-Fox, David Reich, Tomas Marques-Bonet, Eran Meshorer, Liran Carmel
bioRxiv 106955; doi: https://doi.org/10.1101/106955
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Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans
David Gokhman, Lily Agranat-Tamir, Genevieve Housman, Raquel García-Pérez, Malka Nissim-Rafinia, Swapan Mallick, Maria A. Nieves-Colón, Heng Li, Songül Alpaslan-Roodenberg, Mario Novak, Hongcang Gu, Manuel Ferrando-Bernal, Pere Gelabert, Iddi Lipende, Ivanela Kondova, Ronald Bontrop, Ellen E. Quillen, Alexander Meissner, Anne C. Stone, Anne E. Pusey, Deus Mjungu, Leonid Kandel, Meir Liebergall, María E. Prada, Julio M. Vidal, Kay Prüfer, Johannes Krause, Benjamin Yakir, Svante Pääbo, Ron Pinhasi, Carles Lalueza-Fox, David Reich, Tomas Marques-Bonet, Eran Meshorer, Liran Carmel
bioRxiv 106955; doi: https://doi.org/10.1101/106955

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