Footprints of Worldwide Adaptation in Structured Populations of <i>Drosophila melanogaster</i> Through the Expanded DEST 2.0 Genomic Resource

Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

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Publication Details

Journal
Molecular Biology and Evolution
Published
2025-07-30
DOI
https://doi.org/10.1093/molbev/msaf132
Citations
9
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
16.36

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article

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Tânia F. Paulo, Patricia Gibert, Emmanuel D. Ladoukakis, Dorcas J. Orengo et al.
9 citations
Molecular Biology and Evolution
Genetic diversity and population structure
16.36
article

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Tânia F. Paulo, Patricia Gibert, Emmanuel D. Ladoukakis, Dorcas J. Orengo, Thomas Flatt, Miriam Merenciano, Hervé Colinet, Margot Paris, Sònia Casillas, Mihailo Jelić, Khalid Khfif, Banu Şebnem Önder, Д. В. Муха, Lílian Madi-Ravazzi, Marta Coronado‐Zamora, Christian Feller, Jorge Vieira, O. V. Protsenko, Eva Puerma, Antonio Barbadilla, Iryna Kozeretska, Claudia Fricke, Marta Pascual, Pau Carazo, Renaud Vitalis, Omar Rota‐Stabelli, Candice Deschamps, Maria Zinchenko, Amanda Glaser‐Schmitt, Marija Savić Veselinović, Silvia Castillo, Eduardo Amat, Mads F. Schou, Darren J. Obbard, Martin Kapun, Katja M. Hoedjes, Maria Pilar García Guerreiro, Denys Radionov, Jan Hrček, Alejandro Sánchez‐Gracia, Bregje Wertheim, Jesper Givskov Sørensen, Nazar Gora, Natalia Hernandes, Christian Schlötterer, Sebastián E. Ramos‐Onsins, Balázs Kiss, M. Florencia Camus, Mina Rakić, José Olmo, Maria-Eleni Parakatselaki, Sonja Steindl, Alan O. Bergland, Doris Vela, Maria Luisa Espinosa-Jimenez, Nicolas O. Rode, R. Axel W. Wiberg, E. G. Pasyukova, Marina Stamenković‐Radak, В. Е. Алаторцев, John Parsch, Antonio J. Buendía-Ruíz, Priscilla A. Erickson, Sara Guirao‐Rico, Lino Ometto, Joaquin C. B. Nunez, Cristina Vieira, Svitlana Serga, Michael G. Ritchie, Marija Tanasković, Maaria Kankare, Mathieu Gautier, Fabian Staubach, Maria Josefa Gómez-Julián, Mina Ansari, Dmitri A. Petrov, Cristina P. Vieira, Élgion L. S. Loreto, Esra Durmaz Mitchell, Venera Tyukmaeva, David J. Bass, Aleksandra Patenković, Jessica K. Abbott, Envel Kerdaffrec, Josefa González, Paul Schmidt, Clancy Lawler, Giovanni R Mazzeo, Carlos Bustos, Michaël Rera, Jorge Roberto Torres, A. Bertelli, Paulina Sepúlveda, Pinar Güler Kohlmeier, Cristina Amor‐Jimenez, Bélen Roldán Matrín, Carlos Tinedo, Joan Torro, Krzysztof Wojciechowski, Julia Beets, Zahara Alonso
article en
9 citations

Abstract

Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Molecular Biology and EvolutionVol. 42(8)
Université Claude Bernard Lyon 1 (FR), Andrews University (US), St. Andrews University (US), University of Vermont (US), Hebron University (PS), Universitat Autònoma de Barcelona (ES), Landscape Institute (GB), Natural History Museum Vienna (AT), Centre National de la Recherche Scientifique (FR), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR), Institut National de la Recherche Agronomique (MA), University of Crete (GR), Johns Hopkins University (US), University of Liverpool (GB), Lawrence Berkeley National Laboratory (US), University of Veterinary Medicine Vienna (AT), University of Fribourg (CH), University of Richmond (US), University of Freiburg (DE), Stockholm University (SE), The University of Melbourne (AU), University of St Andrews (GB), University of Groningen (NL), Odesa I. I. Mechnikov National University (UA), Lund University (SE), Taras Shevchenko National University of Kyiv (UA), University of Trento (IT), Université de Montpellier (FR), Aarhus University (DK), Instituto Benjamin Constant (BR), Institut Agro Montpellier (FR), University of Pavia (IT), Johns Hopkins Medicine (US), Luther University (KR), Parc Científic de la Universitat de València (ES), Aarhus University Hospital (DK), Lesya Ukrainka Volyn National University (UA), Université Rennes 2 (FR), Ensenada Institute of Technology (MX), National University Odesa Law Academy (UA), Universidade Federal de Santa Maria (BR), Universidad Nacional de Colombia (CO), Pontificia Universidad Católica del Ecuador (EC), University of Belgrade (RS), Ecosystèmes, Biodiversité, Evolution (FR), State Institution National Antarctic Scientific Center (UA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Departament de Salut (ES), Antioquia Institute of Technology (CO), Institut Botànic de Barcelona (ES), Chan Zuckerberg Biohub San Francisco (US), Vall d'Hebron Institut de Recerca (ES), Exact Sciences (United States) (US), Hospital General de Tomelloso (ES), Institut Jacques Monod (FR), Hospital General Universitario de Ciudad Real (ES), Institute of Entomology (CZ), Centro de Investigación y Tecnología Agroalimentaria de Aragón (ES), Vall d'Hebron Hospital Universitari (ES), Institute of Molecular Genetics (RU), Institut de Ciència de Materials de Barcelona (ES), Institut de Biologia Evolutiva (ES), Laboratoire de Biométrie et Biologie Evolutive (FR), Protestant University of Applied Sciences Freiburg (DE), Centre de Biologie pour la Gestion des Populations (FR), Vavilov Institute of General Genetics (RU), AgriBio (AU), Institute of Physics Belgrade (RS), Landesmuseum Kärnten (AT), Plant Protection Institute (HU), i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto (PT), Center for Research in Agricultural Genomics (ES), Institut de Recherche pour le Développement (FR), University College London (GB), Instituto Gulbenkian de Ciência (PT), University of Virginia (US), Université de Rennes (FR), Hacettepe University (TR), Martin Luther University Halle-Wittenberg (DE), Universitat de Barcelona (ES), University of Pennsylvania (US), Ludwig-Maximilians-Universität München (DE), Vrije Universiteit Amsterdam (NL), University of Toledo (US), University of Jyväskylä (FI), Stanford University (US), University of Edinburgh (GB)
Jane Coffin Childs Memorial Fund for Medical Research, University of Vermont, Deutsche Forschungsgemeinschaft, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Academy of Finland, Austrian Science Fund, EMBO, Ministerio de Economía y Competitividad, Ministerio de Ciencia e Innovación, Fondation Bettencourt Schueller, Ministry of Science and Technology, Government of the People’s Republic of Bangladesh, Pontificia Universidad Católica del Ecuador, Association Neurofibromatoses et Recklinghause, National Institutes of Health, Biotechnology and Biological Sciences Research Council, Natural Environment Research Council, Australian Research Council, Comissió Interdepartamental de Recerca i Innovació Tecnològica, European Regional Development Fund
Openalex Percentile: Top 1%
Genetic diversity and population structure
16.36
DOIOpen Access PDFOpenAlex
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