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Key FM, Khadka VD, Romo-González C, Blake KJ, Deng L, Lynn TC, Lee JC, Chiu IM, García-Romero MT, Lieberman TD. On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis. Cell Host Microbe 2023; 31:593-603.e7. [PMID: 37054679 PMCID: PMC10263175 DOI: 10.1016/j.chom.2023.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/14/2023] [Accepted: 03/10/2023] [Indexed: 04/15/2023]
Abstract
The opportunistic pathogen Staphylococcus aureus frequently colonizes the inflamed skin of people with atopic dermatitis (AD) and worsens disease severity by promoting skin damage. Here, we show, by longitudinally tracking 23 children treated for AD, that S. aureus adapts via de novo mutations during colonization. Each patient's S. aureus population is dominated by a single lineage, with infrequent invasion by distant lineages. Mutations emerge within each lineage at rates similar to those of S. aureus in other contexts. Some variants spread across the body within months, with signatures of adaptive evolution. Most strikingly, mutations in capsule synthesis gene capD underwent parallel evolution in one patient and across-body sweeps in two patients. We confirm that capD negativity is more common in AD than in other contexts, via reanalysis of S. aureus genomes from 276 people. Together, these findings highlight the importance of the mutation level when dissecting the role of microbes in complex disease.
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Affiliation(s)
- Felix M Key
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Veda D Khadka
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carolina Romo-González
- Experimental Bacteriology Laboratory, National Institute for Pediatrics, Mexico City, Mexico
| | - Kimbria J Blake
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Liwen Deng
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Tucker C Lynn
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jean C Lee
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Isaac M Chiu
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | | | - Tami D Lieberman
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; Ragon Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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3
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Khadka VD, Key FM, Romo-González C, Martínez-Gayosso A, Campos-Cabrera BL, Gerónimo-Gallegos A, Lynn TC, Durán-McKinster C, Coria-Jiménez R, Lieberman TD, García-Romero MT. The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment. Front Cell Infect Microbiol 2021; 11:720674. [PMID: 34631601 PMCID: PMC8498027 DOI: 10.3389/fcimb.2021.720674] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background Atopic dermatitis (AD) is characterized by an altered skin microbiome dominantly colonized by S. aureus. Standard treatment includes emollients, anti-inflammatory medications and antiseptics. Objectives To characterize changes in the skin microbiome during treatment for AD. Methods The skin microbiomes of children with moderate-to-severe AD and healthy children were investigated in a longitudinal prospective study. Patients with AD were randomized to receive either standard treatment with emollients and topical corticosteroids or standard treatment with the addition of dilute bleach baths (DBB) and sampled at four visits over a three-month period. At each visit, severity of AD was measured, swabs were taken from four body sites and the composition of the microbiome at those sites was assessed using 16S rRNA amplification. Results We included 14 healthy controls and 28 patients. We found high relative abundances of S. aureus in patients, which correlated with AD severity and reduced apparent alpha diversity. As disease severity improved with treatment, the abundance of S. aureus decreased, gradually becoming more similar to the microbiomes of healthy controls. After treatment, patients who received DBB had a significantly lower abundance of S. aureus than those who received only standard treatment. Conclusions There are clear differences in the skin microbiome of healthy controls and AD patients that diminish with treatment. After three months, the addition of DBB to standard treatment had significantly decreased the S. aureus burden, supporting its use as a therapeutic option. Further study in double-blinded trials is needed.
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Affiliation(s)
- Veda D. Khadka
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Felix M. Key
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Carolina Romo-González
- Experimental Bacteriology Laboratory, National Institute of Pediatrics, Mexico City, Mexico
| | | | | | | | - Tucker C. Lynn
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Rafael Coria-Jiménez
- Experimental Bacteriology Laboratory, National Institute of Pediatrics, Mexico City, Mexico
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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4
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Wu X, Ning C, Key FM, Andrades Valtueña A, Lankapalli AK, Gao S, Yang X, Zhang F, Liu L, Nie Z, Ma J, Krause J, Herbig A, Cui Y. A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road. PLoS Pathog 2021; 17:e1009886. [PMID: 34547027 PMCID: PMC8486138 DOI: 10.1371/journal.ppat.1009886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 10/01/2021] [Accepted: 08/11/2021] [Indexed: 01/03/2023] Open
Abstract
Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis-the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.
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Affiliation(s)
- Xiyan Wu
- School of Life Sciences, Jilin University, Changchun, China
- School of History and Culture, Henan University, Kaifeng, China
| | - Chao Ning
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Felix M. Key
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aida Andrades Valtueña
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Shizhu Gao
- College of Pharmacia Sciences, Jilin University, Changchun, China
| | - Xuan Yang
- School of Life Sciences, Jilin University, Changchun, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Linlin Liu
- Department of Radiation Oncology, The Second Hospital of Jilin University, Changchun, China
| | - Zhongzhi Nie
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
| | - Jian Ma
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, China
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
- Key Laboratory for Evolution of Past Life and Environment in Northeast Asia (Jilin University), Ministry of Education, Changchun, China
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5
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Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, Bos KI, Forrest S, Hernández-Zaragoza DI, Sauter J, Solloch U, Schmidt AH, Schuenemann VJ, Reiter E, Kairies MS, Weiß R, Arnold S, Wahl J, Hollenbach JA, Kohlbacher O, Herbig A, Norman PJ, Krause J. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol 2021; 38:4059-4076. [PMID: 34002224 PMCID: PMC8476174 DOI: 10.1093/molbev/msab147] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggests that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.
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Affiliation(s)
- Alexander Immel
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Rodrigo Barquera
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Madeline K Robinson
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - William H Palmer
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Stephen Forrest
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Diana I Hernández-Zaragoza
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | | | | | | | - Verena J Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madita S Kairies
- Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Rainer Weiß
- State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Susanne Arnold
- State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Joachim Wahl
- Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Jill A Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, USA
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.,Translational Bioinformatics, University Hospital Tübingen, Sand 14, 72076 Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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6
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Key FM, Posth C, Esquivel-Gomez LR, Hübler R, Spyrou MA, Neumann GU, Furtwängler A, Sabin S, Burri M, Wissgott A, Lankapalli AK, Vågene ÅJ, Meyer M, Nagel S, Tukhbatova R, Khokhlov A, Chizhevsky A, Hansen S, Belinsky AB, Kalmykov A, Kantorovich AR, Maslov VE, Stockhammer PW, Vai S, Zavattaro M, Riga A, Caramelli D, Skeates R, Beckett J, Gradoli MG, Steuri N, Hafner A, Ramstein M, Siebke I, Lösch S, Erdal YS, Alikhan NF, Zhou Z, Achtman M, Bos K, Reinhold S, Haak W, Kühnert D, Herbig A, Krause J. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat Ecol Evol 2020; 4:324-333. [PMID: 32094538 PMCID: PMC7186082 DOI: 10.1038/s41559-020-1106-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022]
Abstract
It has been hypothesized that the Neolithic transition towards an
agricultural and pastoralist economy facilitated the emergence of human adapted
pathogens. Here, we recovered eight Salmonella enterica subsp.
enterica genomes from human skeletons of transitional
foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to
6,500 years old. Despite the high genetic diversity of S.
enterica all ancient bacterial genomes clustered in a single
previously uncharacterized branch that contains S. enterica
adapted to multiple mammalian species. All ancient bacterial genomes from
prehistoric (agro-)pastoralists fall within a part of this branch that also
includes the human-specific S. enterica Paratyphi C,
illustrating the evolution of a human pathogen over a period of five thousand
years. Bacterial genomic comparisons suggest that the earlier ancient strains
were not host specific, differed in pathogenic potential, and experienced
convergent pseudogenization that accompanied their downstream host adaptation.
These observations support the concept that the emergence of human adapted
S. enterica is linked to human cultural
transformations.
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Affiliation(s)
- Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Luis R Esquivel-Gomez
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tuebingen, Tuebingen, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Åshild J Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rezeda Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russian Federation
| | - Andrey Chizhevsky
- Institute of Archaeology named after A.Kh. Khalikov of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russian Federation
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | | | - Alexey Kalmykov
- 'Nasledie' Cultural Heritage Unit, Stavropol, Russian Federation
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence, Italy
| | - Alessandro Riga
- Department of Biology, University of Florence, Florence, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | | | | | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | | | - Inga Siebke
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | | | | | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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7
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Hübler R, Key FM, Warinner C, Bos KI, Krause J, Herbig A. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol 2019; 20:280. [PMID: 31842945 PMCID: PMC6913047 DOI: 10.1186/s13059-019-1903-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 11/27/2019] [Indexed: 01/28/2023] Open
Abstract
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.
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Affiliation(s)
- Ron Hübler
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | | | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany.
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8
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Spyrou MA, Keller M, Tukhbatova RI, Scheib CL, Nelson EA, Andrades Valtueña A, Neumann GU, Walker D, Alterauge A, Carty N, Cessford C, Fetz H, Gourvennec M, Hartle R, Henderson M, von Heyking K, Inskip SA, Kacki S, Key FM, Knox EL, Later C, Maheshwari-Aplin P, Peters J, Robb JE, Schreiber J, Kivisild T, Castex D, Lösch S, Harbeck M, Herbig A, Bos KI, Krause J. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat Commun 2019; 10:4470. [PMID: 31578321 PMCID: PMC6775055 DOI: 10.1038/s41467-019-12154-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14th and 18th centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes. Our data support an initial entry of the bacterium through eastern Europe, the absence of genetic diversity during the Black Death, and low within-outbreak diversity thereafter. Analysis of post-Black Death genomes shows the diversification of a Y. pestis lineage into multiple genetically distinct clades that may have given rise to more than one disease reservoir in, or close to, Europe. In addition, we show the loss of a genomic region that includes virulence-related genes in strains associated with late stages of the pandemic. The deletion was also identified in genomes connected with the first plague pandemic (541-750 AD), suggesting a comparable evolutionary trajectory of Y. pestis during both events.
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Affiliation(s)
- Maria A Spyrou
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany.
| | - Marcel Keller
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation, 420008
| | | | - Elizabeth A Nelson
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany
| | | | - Gunnar U Neumann
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Don Walker
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | - Amelie Alterauge
- Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland
| | - Niamh Carty
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | - Craig Cessford
- Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | - Hermann Fetz
- Archaeological Service, State Archive Nidwalden, 6371, Nidwalden, Switzerland
| | - Michaël Gourvennec
- Archeodunum SAS, Agency Toulouse, 8 allée Michel de Montaigne, 31770, Colomiers, France
| | - Robert Hartle
- MOLA (Museum of London Archaeology), London, N1 7ED, UK
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | - Sacha Kacki
- PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France
- Department of Archaeology, Durham University, South Rd, Durham, DH1 3LE, UK
| | - Felix M Key
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Christian Later
- Bavarian State Department of Monuments and Sites, 80539, Munich, Germany
| | | | - Joris Peters
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, Kaulbachstr. 37/III, 80539, Munich, Germany
| | - John E Robb
- Department of Archaeology, University of Cambridge, Downing St, Cambridge, CB2 3ER, UK
| | | | - Toomas Kivisild
- Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Dominique Castex
- PACEA, CNRS Institute, Université de Bordeaux, 33615, Pessac, France
| | - Sandra Lösch
- Department of Physical Anthropology, Institute for Forensic Medicine, University of Bern, 3007, Bern, Switzerland
| | - Michaela Harbeck
- SNSB, State Collection for Anthropology and Palaeoanatomy Munich, 80333, Munich, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, 72070, Tübingen, Germany.
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9
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Abstract
Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups, and at different time points on the Neandertal lineage, with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC). We find that the two Neandertals and a Denisovan have similar gene diversity, all significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared with the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.
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Affiliation(s)
- David Reher
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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10
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Krause-Kyora B, Susat J, Key FM, Kühnert D, Bosse E, Immel A, Rinne C, Kornell SC, Yepes D, Franzenburg S, Heyne HO, Meier T, Lösch S, Meller H, Friederich S, Nicklisch N, Alt KW, Schreiber S, Tholey A, Herbig A, Nebel A, Krause J. Neolithic and medieval virus genomes reveal complex evolution of hepatitis B. eLife 2018; 7:36666. [PMID: 29745896 PMCID: PMC6008052 DOI: 10.7554/elife.36666] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022] Open
Abstract
The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.
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Affiliation(s)
- Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, Jena, Germany.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Esther Bosse
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | | | - Diego Yepes
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Henrike O Heyne
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, United States.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, United States.,Program in Medical and Population Genetics, Broad Institute of MIT & Harvard, Cambridge, United States
| | - Thomas Meier
- Institute for Pre- and Protohistory and Near Eastern Archaeology, Heidelberg University, Heidelberg, Germany.,Heidelberg Center for the Environment, Heidelberg University, Heidelberg, Germany
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany
| | - Nicole Nicklisch
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany.,Danube Private University, Krems, Austria
| | - Kurt W Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany.,Danube Private University, Krems, Austria.,Department of Biomedical Engineering, University Hospital Basel, University of Basel, Basel, Switzerland.,Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.,Clinic for Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
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11
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Key FM, Abdul-Aziz MA, Mundry R, Peter BM, Sekar A, D'Amato M, Dennis MY, Schmidt JM, Andrés AM. Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. PLoS Genet 2018; 14:e1007298. [PMID: 29723195 PMCID: PMC5933706 DOI: 10.1371/journal.pgen.1007298] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/07/2018] [Indexed: 01/22/2023] Open
Abstract
Ambient temperature is a critical environmental factor for all living organisms. It was likely an important selective force as modern humans recently colonized temperate and cold Eurasian environments. Nevertheless, as of yet we have limited evidence of local adaptation to ambient temperature in populations from those environments. To shed light on this question, we exploit the fact that humans are a cosmopolitan species that inhabit territories under a wide range of temperatures. Focusing on cold perception-which is central to thermoregulation and survival in cold environments-we show evidence of recent local adaptation on TRPM8. This gene encodes for a cation channel that is, to date, the only temperature receptor known to mediate an endogenous response to moderate cold. The upstream variant rs10166942 shows extreme population differentiation, with frequencies that range from 5% in Nigeria to 88% in Finland (placing this SNP in the 0.02% tail of the FST empirical distribution). When all populations are jointly analyzed, allele frequencies correlate with latitude and temperature beyond what can be explained by shared ancestry and population substructure. Using a Bayesian approach, we infer that the allele originated and evolved neutrally in Africa, while positive selection raised its frequency to different degrees in Eurasian populations, resulting in allele frequencies that follow a latitudinal cline. We infer strong positive selection, in agreement with ancient DNA showing high frequency of the allele in Europe 3,000 to 8,000 years ago. rs10166942 is important phenotypically because its ancestral allele is protective of migraine. This debilitating disorder varies in prevalence across human populations, with highest prevalence in individuals of European descent-precisely the population with the highest frequency of rs10166942 derived allele. We thus hypothesize that local adaptation on previously neutral standing variation may have contributed to the genetic differences that exist in the prevalence of migraine among human populations today.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Muslihudeen A Abdul-Aziz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roger Mundry
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, California, United States of America
| | - Mauro D'Amato
- BioDonostia Health Research Institute and IKERBASQUE, Basque Foundation for Science, San Sebastian, Spain
| | - Megan Y Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, California, United States of America
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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12
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Andrades Valtueña A, Mittnik A, Key FM, Haak W, Allmäe R, Belinskij A, Daubaras M, Feldman M, Jankauskas R, Janković I, Massy K, Novak M, Pfrengle S, Reinhold S, Šlaus M, Spyrou MA, Szécsényi-Nagy A, Tõrv M, Hansen S, Bos KI, Stockhammer PW, Herbig A, Krause J. The Stone Age Plague and Its Persistence in Eurasia. Curr Biol 2017; 27:3683-3691.e8. [PMID: 29174893 DOI: 10.1016/j.cub.2017.10.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/31/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6th century AD, which persisted until the 8th century [1]; the renowned Black Death of the 14th century [2, 3], with recurrent outbreaks until the 18th century [4]; and the most recent 19th century pandemic, in which Y. pestis spread worldwide [5] and became endemic in several regions [6]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [7]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA; 4,800 to 3,700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross-European networks of contact and exchange [8, 9]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations.
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Affiliation(s)
| | - Alissa Mittnik
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany; School of Biological Sciences, The University of Adelaide, Adelaide SA 5005, South Australia, Australia
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Mantas Daubaras
- Department of Archaeology, Lithuanian Institute of History, Vilnius, Lithuania
| | - Michal Feldman
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Rimantas Jankauskas
- Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius, Lithuania
| | - Ivor Janković
- Institute for Anthropological Research, Zagreb, Croatia; Department of Anthropology, University of Wyoming, Laramie, WY, USA
| | - Ken Massy
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany; Heidelberg Academy of Sciences, Heidelberg, Germany
| | - Mario Novak
- Institute for Anthropological Research, Zagreb, Croatia
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Anna Szécsényi-Nagy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Mari Tõrv
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Philipp W Stockhammer
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
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13
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Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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14
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Key FM, Posth C, Krause J, Herbig A, Bos KI. Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication. Trends Genet 2017; 33:508-520. [PMID: 28688671 DOI: 10.1016/j.tig.2017.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 12/21/2022]
Abstract
While a comparatively young area of research, investigations relying on ancient DNA data have been highly valuable in revealing snapshots of genetic variation in both the recent and the not-so-recent past. Born out of a tradition of single-locus PCR-based approaches that often target individual species, stringent criteria for both data acquisition and analysis were introduced early to establish high standards of data quality. Today, the immense volume of data made available through next-generation sequencing has significantly increased the analytical resolution offered by processing ancient tissues and permits parallel analyses of host and microbial communities. The adoption of this new approach to data acquisition, however, requires an accompanying update on methods of DNA authentication, especially given that ancient molecules are expected to exist in low proportions in archaeological material, where an environmental signal is likely to dominate. In this review, we provide a summary of recent data authentication approaches that have been successfully used to distinguish between endogenous and nonendogenous DNA sequences in metagenomic data sets. While our discussion mostly centers on the detection of ancient human and ancient bacterial pathogen DNA, their applicability is far wider.
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Affiliation(s)
- Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany.
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15
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Key FM, Fu Q, Romagné F, Lachmann M, Andrés AM. Human adaptation and population differentiation in the light of ancient genomes. Nat Commun 2016; 7:10775. [PMID: 26988143 PMCID: PMC4802047 DOI: 10.1038/ncomms10775] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 01/24/2023] Open
Abstract
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. Detecting the targets of positive selection in the human genome is challenging. Here, the authors combine modern and ancient genomes to show that alleles strongly differentiated between Africans and Europeans mediated local adaptation in European populations, and were mostly contributed by ancient hunter-gatherers.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,Department of Genetics, Harvard Medical School, Boston 02115, Massachusetts, USA
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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16
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de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A, Parra G, Green ED, Andrés AM. Recent Selection Changes in Human Genes under Long-Term Balancing Selection. Mol Biol Evol 2016; 33:1435-47. [PMID: 26831942 DOI: 10.1093/molbev/msw023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Balancing selection is an important evolutionary force that maintains genetic and phenotypic diversity in populations. Most studies in humans have focused on long-standing balancing selection, which persists over long periods of time and is generally shared across populations. But balanced polymorphisms can also promote fast adaptation, especially when the environment changes. To better understand the role of previously balanced alleles in novel adaptations, we analyzed in detail four loci as case examples of this mechanism. These loci show hallmark signatures of long-term balancing selection in African populations, but not in Eurasian populations. The disparity between populations is due to changes in allele frequencies, with intermediate frequency alleles in Africans (likely due to balancing selection) segregating instead at low- or high-derived allele frequency in Eurasia. We explicitly tested the support for different evolutionary models with an approximate Bayesian computation approach and show that the patterns in PKDREJ, SDR39U1, and ZNF473 are best explained by recent changes in selective pressure in certain populations. Specifically, we infer that alleles previously under long-term balancing selection, or alleles linked to them, were recently targeted by positive selection in Eurasian populations. Balancing selection thus likely served as a source of functional alleles that mediated subsequent adaptations to novel environments.
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Affiliation(s)
- Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Juan R Meneu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Genís Parra
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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17
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Key FM, Teixeira JC, de Filippo C, Andrés AM. Advantageous diversity maintained by balancing selection in humans. Curr Opin Genet Dev 2014; 29:45-51. [PMID: 25173959 DOI: 10.1016/j.gde.2014.08.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/30/2014] [Accepted: 08/02/2014] [Indexed: 11/16/2022]
Abstract
Most human polymorphisms are neutral or slightly deleterious, but some genetic variation is advantageous and maintained in populations by balancing selection. Considered a rarity and overlooked for years, balanced polymorphisms have recently received renewed attention with several lines of evidence showing their relevance in human evolution. From theoretical work on its role in adaptation to empirical studies that identify its targets, recent developments have showed that balancing selection is more prevalent than previously thought. Here we review these developments and discuss their implications in our understanding of the influence of balancing selection in human evolution. We also review existing evidence on the biological functions that benefit most from advantageous diversity, and the functional consequences of these variants. Overall, we argue that balancing selection must be considered an important selective force in human evolution.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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18
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Key FM, Mendel EB. Bilateral choanal atresia. A newborn emergency. Obstet Gynecol 1968; 32:58-9. [PMID: 5742090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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