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Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses
Journal article

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

  • Kapun, Martin ORCID Department of Biology, University of Fribourg, Fribourg, Switzerland
  • Barrón, Maite G Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
  • Staubach, Fabian Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
  • Obbard, Darren J Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
  • Wiberg, R Axel W ORCID Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
  • Vieira, Jorge Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
  • Goubert, Clément Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
  • Rota-Stabelli, Omar Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
  • Kankare, Maaria ORCID Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
  • Bogaerts-Márquez, María Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
  • Haudry, Annabelle Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
  • Waidele, Lena Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
  • Kozeretska, Iryna State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
  • Pasyukova, Elena G Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
  • Loeschcke, Volker Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
  • Pascual, Marta Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
  • Vieira, Cristina P Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
  • Serga, Svitlana General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
  • Montchamp-Moreau, Catherine Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
  • Abbott, Jessica Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
  • Gibert, Patricia Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
  • Porcelli, Damiano Department of Animal and Plant Sciences, Sheffield, United Kingdom
  • Posnien, Nico ORCID Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
  • Sánchez-Gracia, Alejandro Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
  • Grath, Sonja Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
  • Sucena, Élio Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
  • Bergland, Alan O Department of Biology, University of Virginia, Charlottesville, VA
  • Guerreiro, Maria Pilar Garcia Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
  • Onder, Banu Sebnem Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
  • Argyridou, Eliza Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
  • Guio, Lain Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
  • Schou, Mads Fristrup Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
  • Deplancke, Bart Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
  • Vieira, Cristina Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
  • Ritchie, Michael G ORCID Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
  • Zwaan, Bas J ORCID Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
  • Tauber, Eran Institute of Evolution, University of Haifa, Haifa, Israel
  • Orengo, Dorcas J Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
  • Puerma, Eva Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
  • Aguadé, Montserrat Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
  • Schmidt, Paul ORCID Department of Biology, University of Pennsylvania, Philadelphia, PA
  • Parsch, John Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
  • Betancourt, Andrea J Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
  • Flatt, Thomas ORCID Department of Biology, University of Fribourg, Fribourg, Switzerland
  • González, Josefa Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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  • 2020-5-15
Published in:
  • Molecular Biology and Evolution. - Oxford University Press (OUP). - 2020, vol. 37, no. 9, p. 2661-2678
Genetics
Ecology, Evolution, Behavior and Systematics
Molecular Biology
English Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
Language
  • English
Open access status
hybrid
Identifiers
Persistent URL
https://sonar.ch/global/documents/215806
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