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Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation
Affiliation:1. State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China;2. Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA;3. Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA;4. Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA;5. Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA;6. Department of Biochemistry, Kampala International University in Tanzania, P.O. Box 9790, Dar es Salaam, Tanzania;7. Department of Biological Sciences, Faculty of Science, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana;8. Department of Biomedical Sciences, Faculty of Medicine, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana;9. Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon;10. Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon;11. Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia;12. Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA;13. Chan Zuckerberg Biohub, San Francisco, CA 94158, USA;14. Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA;1. Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada;2. Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada;3. Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria;4. Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada;1. State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Neurology, the First Affiliated Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361005, China;2. Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong 518057, China;3. Department of Functional Neurosurgery, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361003, China;4. National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China;5. United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen 361103, China;6. State Key Laboratory of Cellular Stress Biology, Cancer Research Center of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China;7. Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA;8. Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, Fujian 361005, China;9. Institute for Brain Science and Disease, Chongqing Medical University, Chongqing 400016, China;1. WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium;2. de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium;3. Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium;4. Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium;5. Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA;6. Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium;7. Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, 91198 Gif-sur-Yvette, France;8. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany;1. Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK;2. Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK;3. Department of Mathematics, Imperial College London, London, UK;4. EPSRC Centre for Mathematics of Precision Healthcare, Imperial College, London, UK;5. Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, D-14195 Berlin, Germany;6. Department of Computer Science, Freie Universität Berlin, Arnimallee 3, D-14195 Berlin, Germany;7. Max Planck Institute for Biology of Ageing, Cologne, Germany;8. Department of Neuroanatomy, Mannheim Centre for Translational Neuroscience (MCTN), Medical Faculty Mannheim/Heidelberg University, Heidelberg, Germany;9. Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, Cologne, Germany;10. Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden;11. Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK;1. Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;2. Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;3. Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;4. Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA;5. Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;6. Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA;7. Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA;8. Division of Cardiovascular Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;9. BioFrontiers Institute and Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA;1. Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland;2. Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000 Neuchâtel, Switzerland
Abstract:
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  • Keywords:African genomics  local adaptation  natural selection  Khoesan  population structure  archaic introgression  gene regulation  human evolution  skin color  African demographic history
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