ArticleMolecular biology and evolution2025
Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource.
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15 citing papers in PubMed.
- ProteoCast: a web server to predict, validate, and interpret missense variant effects.Journal of molecular biology · 2026Article
- Dissecting Fluctuating Selection: A Unified Population and Quantitative Genetics Framework.Genome biology and evolution · 2026Article
- The Inversion in(2L)t Impacts Complex, Temperature-Sensitive Behaviors inEcology and evolution · 2026Article
- Climate predictsbioRxiv : the preprint server for biology · 2026Article
- Proteome-wide prediction of the functional impact of missense variants with ProteoCast.Nature communications · 2026Article
- Body size, wing area, and wing loading follow a pattern of trait conservatism inbioRxiv : the preprint server for biology · 2026Article
- Early life-stage thermal resilience is determined by climate-linked regulatory variation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Predicting the functional impact of single nucleotide variants in Drosophila melanogaster with FlyCADD.Genetics · 2026Article
- Cosmopolitan inversions have a major impact on trait variation and the power of different GWAS approaches to identify associations.PLoS genetics · 2026Article
- Beneficial reversal of dominance maintains a large-effect resistance polymorphism under fluctuating insecticide selection.Nature ecology & evolution · 2025Article
- The ongoing invasion of the endogenous retrovirusbioRxiv : the preprint server for biology · 2025Article
- Gene and transposable element expression in response to stress in temperate and tropical populations of Drosophila.Mobile DNA · 2025Article
- Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models.bioRxiv : the preprint server for biology · 2025Article
- The inversion In(2L)t impacts complex, environmentally sensitive behaviors inbioRxiv : the preprint server for biology · 2025Article
- Cosmopolitan inversions have a major impact on trait variation and the power of different GWAS approaches to identify associations.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
101 authors.
Joaquin C B NunezDepartment of Biology, University of Vermont, Burlington, VT, USA.ORCID 0000-0002-3171-8918
Marta Coronado-ZamoraInstitut Botànic de Barcelona (IBB) CSIC-CMCNB, Barcelona, Spain.ORCID 0000-0001-9779-9661
Mathieu GautierCBGP, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.ORCID 0000-0001-7257-5880
Martin KapunNatural History Museum, Vienna, Austria.ORCID 0000-0002-3810-0504
Sonja SteindlNatural History Museum, Vienna, Austria.ORCID 0009-0007-5354-1950
Lino OmettoDepartment of Biology and Biotechnology, University of Pavia, Pavia, Italy.ORCID 0000-0002-2679-625X
Katja HoedjesAmsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.ORCID 0000-0001-6090-232X
Julia BeetsAmsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.ORCID 0009-0005-8375-9884
R Axel W WibergDepartment of Zoology, Stockholm University, Stockholm, Sweden.ORCID 0000-0002-8074-8670
Giovanni R MazzeoDepartment of Biology, University of Virginia, Charlottesville, VA, USA.ORCID 0009-0008-0898-2041
David J BassDepartment of Biology, University of Virginia, Charlottesville, VA, USA.ORCID 0000-0001-7414-2747
Denys RadionovDepartment of Zoology, Hydrobiology and General Ecology, Odesa I.I. Mechnikov National University, Odesa, Ukraine.ORCID 0000-0003-0138-1303
Iryna KozeretskaNational Antarctic Scientific Center of Ukraine, Kyiv, Ukraine.ORCID 0000-0002-6485-1408
Mariia ZinchenkoFaculty of Biology and Forestry, Lesya Ukrainka Volyn National University, Lutsk, Ukraine.ORCID 0000-0001-6485-3668
Oleksandra ProtsenkoNational Antarctic Scientific Center of Ukraine, Kyiv, Ukraine.ORCID 0000-0002-6019-9731
Svitlana V SergaCBGP, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.ORCID 0000-0003-1875-3185
Cristina Amor-JimenezDepartment of Genetics and Microbiology, Facultat de Biociencies, Universitat Autònoma de Barcelona, Barcelona, Spain.ORCID 0009-0009-7822-8199
Sònia CasillasDepartment of Genetics and Microbiology, Facultat de Biociencies, Universitat Autònoma de Barcelona, Barcelona, Spain.ORCID 0000-0001-8191-0062
Alejandro Sánchez-GraciaDepartament de Genetica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.ORCID 0000-0003-4543-4577
Aleksandra PatenkovicInstitute for Biological Research, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.ORCID 0000-0001-5763-6294
Amanda Glaser-SchmittDivision of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.ORCID 0000-0002-1322-1000
Antonio BarbadillaDepartment of Genetics and Microbiology, Facultat de Biociencies, Universitat Autònoma de Barcelona, Barcelona, Spain.ORCID 0000-0002-0374-1475
Antonio J Buendia-RuízInstituto de Enseñanza Secundaria Eladio Cabañero, Tomelloso, Spain.
Astra Clelia BertelliNatural History Museum, Vienna, Austria.ORCID 0009-0002-3595-0498
Balázs KissHUN-REN Plant Protection Institute, Centre for Agricultural Research, Budapest, Hungary.ORCID 0000-0003-2511-9094
Banu Sebnem ÖnderGenetic Variation and Adaptation Laboratory, Department of Biology, Hacettepe University, Ankara, Turkey.ORCID 0000-0002-3003-248X
Bélen Roldán MatrínInstituto de Enseñanza Secundaria Alonso de Ercilla, Toledo, Spain.
Bregje WertheimGroningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.ORCID 0000-0001-8555-1925
Candice DeschampsCBGP, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.ORCID 0000-0002-5167-5433
Carlos E Arboleda-BustosNeuroscience Group, Genetics Institute, Universidad Nacional de Colombia, Bogotá, Colombia.ORCID 0000-0002-1783-3063
Carlos TinedoDepartament de Genetica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.ORCID 0009-0004-8038-9817
Christian FellerLandesgymnasium Sankt Afra zu Meißen, Meißen, Germany.
Christian SchlöttererInstitute of Population Genetics, Vetmeduni Austria, Vienna, Austria.ORCID 0000-0003-4710-6526
Clancy LawlerDepartment of Biosciences, The University of Melbourne, Victoria, Australia.ORCID 0009-0007-1867-4969
Claudia FrickeInstitute for Zoology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany.ORCID 0000-0002-0691-6779
Cristina P VieiraInstituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.ORCID 0000-0002-7139-2107
Cristina VieiraLaboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France.ORCID 0000-0003-3414-3993
Darren J ObbardInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.ORCID 0000-0001-5392-8142
Dorcas Juana OrengoDepartament de Genetica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.ORCID 0000-0001-7911-3224
Doris VelaFaculty of Exact, Natural and Environmental Sciences, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.ORCID 0000-0001-7690-7758
Eduardo AmatBioforense Research Group, Faculty of Law and Forensic Sciences, Tecnológico de Antioquia, Medellin, Colombia.ORCID 0000-0002-0962-777X
Elgion LoretoDepartment of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil.ORCID 0000-0002-7586-8168
Envel KerdaffrecDepartment of Biology, University of Fribourg, Fribourg, Switzerland.ORCID 0000-0001-8667-6850
Esra Durmaz MitchellDepartment of Biology, University of Fribourg, Fribourg, Switzerland.ORCID 0000-0002-4345-2264
Eva PuermaVall d'Hebron Institute of Oncology, Barcelona, Spain.ORCID 0000-0001-7261-187X
Fabian StaubachDepartment of Evolution and Ecology, University of Freiburg, Freiburg, Germany.ORCID 0000-0002-8097-2349
M Florencia CamusResearch Department of Genetics, Evolution & Environment, University College London, London, UK.ORCID 0000-0003-0626-6865
Hervé ColinetUniversity of Rennes, CNRS, ECOBIO, Rennes, France.ORCID 0000-0002-8806-3107
Jan HrcekBiology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.ORCID 0000-0003-0711-6447
Jesper Givskov SørensenDepartment of Biology, Aarhus University, Aarhus, Denmark.ORCID 0000-0002-9149-3626
Jessica AbbottDepartment of Biology, Lund University, Lund, Sweden.ORCID 0000-0002-8743-2089
Joan TorroInstituto de Enseñanza Secundaria Benjamín Jarnés, Zaragoza, Spain.
John ParschDivision of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.ORCID 0000-0001-9068-5549
Jorge VieiraInstituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.ORCID 0000-0001-7032-5220
Jose Luis OlmoInstituto de Enseñanza Secundaria Azuer, Ciudad Real, Spain.
Khalid KhfifEntomology Laboratory, URTNEQ, INRA, Tangier, Morocco.ORCID 0000-0002-3874-8845
Krzysztof WojciechowskiAdministration of Regional Landscape Parks of Lublin, Voivodeship, Chelm, Poland.
Lilian Madi-RavazziInstitute of Biosciences, Humanities, and Exact Sciences, Sao Paulo State University, Sao José do Rio Preto, Brazil.ORCID 0000-0002-6250-0794
Maaria KankareDepartment of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland.ORCID 0000-0003-1541-9050
Mads F SchouDepartment of Biology, Aarhus University, Aarhus, Denmark.ORCID 0000-0001-5521-5269
Emmanuel D LadoukakisDepartment of Biology, University of Crete, Heraklion, Greece.ORCID 0000-0002-1123-5396
M Josefa Gómez-JuliánInstituto de Enseñanza Secundaria Eladio Cabañero, Tomelloso, Spain.
M Luisa Espinosa-JimenezInstituto de Enseñanza Secundaria Eladio Cabañero, Tomelloso, Spain.
Maria Pilar Garcia GuerreiroDepartment of Genetics and Microbiology, Facultat de Biociencies, Universitat Autònoma de Barcelona, Barcelona, Spain.ORCID 0000-0001-9951-1879
Maria-Eleni ParakatselakiDepartment of Biology, University of Crete, Heraklion, Greece.ORCID 0000-0003-0150-6153
Marija Savic VeselinovicFaculty of Biology, University of Belgrade, Belgrade, Serbia.ORCID 0000-0001-8461-4373
Marija TanaskovicInstitute for Biological Research, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.ORCID 0000-0003-1440-2257
Marina Stamenkovic-RadakFaculty of Biology, University of Belgrade, Belgrade, Serbia.ORCID 0000-0002-6937-7282
Margot ParisDepartment of Biology, University of Fribourg, Fribourg, Switzerland.ORCID 0000-0001-7328-3820
Marta PascualDepartament de Genetica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.ORCID 0000-0002-6189-0612
Michael G RitchieSchool of Biology, University of St Andrews, St Andrews, UK.ORCID 0000-0001-7913-8675
Michel ReraInstitut Jacques Monod, Paris, France.ORCID 0000-0002-6574-6511
Mihailo JelićFaculty of Biology, University of Belgrade, Belgrade, Serbia.ORCID 0000-0002-1637-0933
Mina Hojat AnsariDepartment of Evolution and Ecology, University of Freiburg, Freiburg, Germany.ORCID 0000-0002-3602-7884
Mina RakicFaculty of Biology, University of Belgrade, Belgrade, Serbia.ORCID 0000-0002-6069-3369
Miriam MerencianoInstitute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain.ORCID 0000-0001-8592-949X
Natalia HernandesDepartment of Biosciences, The University of Melbourne, Victoria, Australia.ORCID 0000-0001-5644-6974
Nazar GoraMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, USA.ORCID 0000-0003-0589-8799
Nicolas RodeCBGP, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.ORCID 0000-0002-1121-4202
Omar Rota-StabelliCenter Agriculture Food Environment (C3A), University of Trento, Trento, Italy.ORCID 0000-0002-0030-7788
Paloma SepulvedaInstituto de Enseñanza Secundaria Carpetania, Toledo, Spain.
Patricia GibertLaboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France.ORCID 0000-0002-9461-6820
Pau CarazoCavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain.ORCID 0000-0002-1525-6522
Pinar KohlmeierGroningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.ORCID 0009-0001-2404-3625
Priscilla A EricksonDepartment of Biology, University of Virginia, Charlottesville, VA, USA.ORCID 0000-0001-8420-995X
Renaud VitalisCBGP, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.ORCID 0000-0001-7096-3089
Jorge Roberto TorresLa Ciència Al Teu Món, Barcelona, Spain.
Sara Guirao-RicoDepartament de Genetica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.ORCID 0000-0001-9896-4665
Sebastian E Ramos-OnsinsCentre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain.ORCID 0000-0002-1776-140X
Silvana CastilloInstituto de Enseñanza Secundaria Jose de Mora, Granada, Spain.
Tânia F PauloInstituto Gulbenkian de Ciência, Oeiras, Portugal.ORCID 0000-0002-8815-2636
Venera TyukmaevaInstitute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, UK.ORCID 0000-0002-1864-5101
Zahara AlonsoCentro de Educación Infantil y Primaria Ramón y Cajal, Zaragoza, Spain.
Vladimir E AlatortsevInstitute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia.ORCID 0000-0003-4713-6610
Elena PasyukovaInstitute of Molecular Genetics of Russian Academy of Sciences, Moscow, Russia.ORCID 0000-0002-6491-8561
Dmitry V MukhaVavilov Institute of General Genetics of Russian Academy of Sciences, Moscow, Russia.ORCID 0000-0002-7380-0776
Dmitri A PetrovDepartment of Biology, Stanford University, Stanford, CA, USA.ORCID 0000-0002-3664-9130
Paul SchmidtDepartment of Biology, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0002-8076-6705
Thomas FlattDepartment of Biology, University of Fribourg, Fribourg, Switzerland.ORCID 0000-0002-5990-1503
Alan O BerglandDepartment of Biology, University of Virginia, Charlottesville, VA, USA.ORCID 0000-0001-7145-7575
Josefa GonzalezInstitut Botànic de Barcelona (IBB) CSIC-CMCNB, Barcelona, Spain.ORCID 0000-0001-9824-027X
Funding
Genomics of rapid adaptation in the lab and in the wildR35GM118165 · NIGMS · STANFORD UNIVERSITY · PI Dmitri Petrov · 2016 to 2026
$8.3MThe genetic and physiological architecture of rapid and cyclic adaptationR35GM119686 · NIGMS · UNIVERSITY OF VIRGINIA · PI BERGLAND, ALAN OLAV · 2016 to 2020
$1.9MAcademy of Finland project 322980Academy of Finland project 451-03-47/2023-01/200178Academy of Finland project 451-03-65/2024-03/ 200178ANR ANR-20-CE02-011-01Australian Research Council DP190102512Austrian Science Funds 10.55776/P32935Austrian Science Funds 10.55776/P33734Bettencourt Schueller Foundation #61-1673Biotechnology and Biological Sciences Research Council BB/T007516/1Comissió Interdepartamental de Recerca I Innovació Tecnològica 2021SGR00279CRI Core Research FellowshipDepartament de Recerca i UniversitatsDeutsche Forschungsgemeinschaft 255619725Deutsche Forschungsgemeinschaft 503272152EMBO ALT 248-02018European Regional Development FundGerman Science Foundation FR2973/11-1Horizon Europe project FAIRiCUBE 101059238Horizon Europe project FAIRiCUBE 2R35GM11816506Jane Coffin Childs Memorial Fund for Medical Research PID2020-119255GB-I00Ministerio de Ciencia e Innovación of Spain MCIN/AEI/10.13039/501100011033Ministerio de Ciencia e Innovación of Spain PID2020-113168GB-I00Ministry of Economy and Competitiveness CEX2019-000917Ministry of Economy and Competitiveness SEV-2015-0533Ministry of Science 451-03-66/2024-03/200007Ministry of Science PID2021-127107NB-I00NERC NE/V001566/1NIGMS NIH HHS R35 GM118165NIH HHS 2021 SGR 00417NIH HHS 2145688NIH HHS MICIU/AEI /10.13039/501100011033NIH HHS MICIU/AEI/10.13039/501100011033NIH HHS PID2020-115874GB-I00NIH HHS PID2023-148838NB-I00NIH HHS R35 GM119686Pontificia Universidad Católica del Ecuador QINV0196-IINV529010100Pontificia Universidad Católica del Ecuador VR-2015-04680Pontificia Universidad Católica del Ecuador VR-2020-05412Swiss National Science Foundation 310030_219283Swiss National Science Foundation 31003A-182262Swiss National Science Foundation FZEB-0-214654University of Vermont
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.
Indexed as
Adaptation, BiologicalAdaptation, PhysiologicalDrosophila melanogasterAnimalsGenetics, PopulationGenetic VariationGenome, InsectGenomicsdatasetDrosophila melanogasterecological genomicslocal adaptationpopulation structureseasonal selection
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