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A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in &amp;gt;20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.<\/jats:p>","DOI":"10.1093\/molbev\/msab259","type":"journal-article","created":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T13:46:57Z","timestamp":1630504017000},"page":"5782-5805","source":"Crossref","is-referenced-by-count":79,"title":["<i>Drosophila<\/i>\n                    Evolution over Space and Time (DEST): A New Population Genomics Resource"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3810-0504","authenticated-orcid":false,"given":"Martin","family":"Kapun","sequence":"first","affiliation":[{"name":"Department of Evolutionary Biology and Environmental Studies, University of Z\u00fcrich, Switzerland"},{"name":"Department of Cell & Developmental Biology, Center of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria"}]},{"given":"Joaquin C B","family":"Nunez","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Virginia, Charlottesville, VA, USA"}]},{"given":"Mar\u00eda","family":"Bogaerts-M\u00e1rquez","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"given":"Jes\u00fas","family":"Murga-Moreno","sequence":"additional","affiliation":[{"name":"Department of Genetics and Microbiology, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"},{"name":"Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}]},{"given":"Margot","family":"Paris","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Fribourg, Fribourg, Switzerland"}]},{"given":"Joseph","family":"Outten","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Virginia, Charlottesville, VA, USA"}]},{"given":"Marta","family":"Coronado-Zamora","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"given":"Courtney","family":"Tern","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Virginia, Charlottesville, VA, USA"}]},{"given":"Omar","family":"Rota-Stabelli","sequence":"additional","affiliation":[{"name":"Center Agriculture Food Environment, University of Trento, San Michele all' Adige, Italy"}]},{"given":"Maria P Garc\u00eda","family":"Guerreiro","sequence":"additional","affiliation":[{"name":"Department of Genetics and Microbiology, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8191-0062","authenticated-orcid":false,"given":"S\u00f2nia","family":"Casillas","sequence":"additional","affiliation":[{"name":"Department of Genetics and Microbiology, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"},{"name":"Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}]},{"given":"Dorcas J","family":"Orengo","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica, Microbiologia i Estad\u00edstica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain"},{"name":"Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain"}]},{"given":"Eva","family":"Puerma","sequence":"additional","affiliation":[{"name":"Departament de Gen\u00e8tica, Microbiologia i Estad\u00edstica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain"},{"name":"Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain"}]},{"given":"Maaria","family":"Kankare","sequence":"additional","affiliation":[{"name":"Department of Biological and Environmental Science, University of Jyv\u00e4skyl\u00e4, Jyv\u00e4skyl\u00e4, Finland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2679-625X","authenticated-orcid":false,"given":"Lino","family":"Ometto","sequence":"additional","affiliation":[{"name":"Department of Biology and Biotechnology, University of Pavia, Pavia, Italy"}]},{"given":"Volker","family":"Loeschcke","sequence":"additional","affiliation":[{"name":"Department of Biology, Aarhus University, Aarhus, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3003-248X","authenticated-orcid":false,"given":"Banu S","family":"Onder","sequence":"additional","affiliation":[{"name":"Department of Biology, Hacettepe University, Ankara, Turkey"}]},{"given":"Jessica K","family":"Abbott","sequence":"additional","affiliation":[{"name":"Department of Biology, Lund University, Lund, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2070-5342","authenticated-orcid":false,"given":"Stephen W","family":"Schaeffer","sequence":"additional","affiliation":[{"name":"Department of Biology, The Pennsylvania State University, University Park, PA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9149-391X","authenticated-orcid":false,"given":"Subhash","family":"Rajpurohit","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India"}]},{"given":"Emily L","family":"Behrman","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"Janelia Research Campus, Ashburn, VA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5521-5269","authenticated-orcid":false,"given":"Mads F","family":"Schou","sequence":"additional","affiliation":[{"name":"Department of Biology, Aarhus University, Aarhus, Denmark"},{"name":"Department of Biology, Lund University, Lund, Sweden"}]},{"given":"Thomas J S","family":"Merritt","sequence":"additional","affiliation":[{"name":"Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON, Canada"}]},{"given":"Brian P","family":"Lazzaro","sequence":"additional","affiliation":[{"name":"Department of Entomology, Cornell University, Ithaca, NY, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1322-1000","authenticated-orcid":false,"given":"Amanda","family":"Glaser-Schmitt","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"}]},{"given":"Eliza","family":"Argyridou","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8097-2349","authenticated-orcid":false,"given":"Fabian","family":"Staubach","sequence":"additional","affiliation":[{"name":"Department of Evolution and Ecology, University of Freiburg, Freiburg, 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A","family":"Dyer","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of Georgia, Athens, GA, USA"}]},{"given":"Christopher W","family":"Wheat","sequence":"additional","affiliation":[{"name":"Department of Zoology, Stockholm University, Stockholm, Sweden"}]},{"given":"John","family":"Parsch","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3621-736X","authenticated-orcid":false,"given":"Sonja","family":"Grath","sequence":"additional","affiliation":[{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany"}]},{"given":"Marija Savic","family":"Veselinovic","sequence":"additional","affiliation":[{"name":"Faculty of Biology, University of Belgrade, Belgrade, Serbia"}]},{"given":"Marina","family":"Stamenkovic-Radak","sequence":"additional","affiliation":[{"name":"Faculty of Biology, University of Belgrade, Belgrade, Serbia"}]},{"given":"Mihailo","family":"Jelic","sequence":"additional","affiliation":[{"name":"Faculty of Biology, University of Belgrade, Belgrade, Serbia"}]},{"given":"Antonio J","family":"Buend\u00eda-Ru\u00edz","sequence":"additional","affiliation":[{"name":"IES Eladio Caba\u00f1ero, Tomelloso, Spain"}]},{"given":"Maria Josefa","family":"G\u00f3mez-Juli\u00e1n","sequence":"additional","affiliation":[{"name":"IES Eladio Caba\u00f1ero, Tomelloso, Spain"}]},{"given":"Maria Luisa","family":"Espinosa-Jimenez","sequence":"additional","affiliation":[{"name":"IES Eladio Caba\u00f1ero, Tomelloso, Spain"}]},{"given":"Francisco D","family":"Gallardo-Jim\u00e9nez","sequence":"additional","affiliation":[{"name":"IES Jose de Mora, Baza, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5763-6294","authenticated-orcid":false,"given":"Aleksandra","family":"Patenkovic","sequence":"additional","affiliation":[{"name":"Institute for Biological Research \u201cSini\u0161a Stankovi\u0107\u201d, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia"}]},{"given":"Katarina","family":"Eric","sequence":"additional","affiliation":[{"name":"Institute for Biological Research \u201cSini\u0161a Stankovi\u0107\u201d, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia"}]},{"given":"Marija","family":"Tanaskovic","sequence":"additional","affiliation":[{"name":"Institute for Biological Research \u201cSini\u0161a Stankovi\u0107\u201d, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia"}]},{"given":"Anna","family":"Ullastres","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"given":"Lain","family":"Guio","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"given":"Miriam","family":"Merenciano","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"given":"Sara","family":"Guirao-Rico","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"given":"Vivien","family":"Horv\u00e1th","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5392-8142","authenticated-orcid":false,"given":"Darren J","family":"Obbard","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom"}]},{"given":"Elena","family":"Pasyukova","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics of the National Research Centre \u201cKurchatov Institute\u201d, Moscow, Russia"}]},{"given":"Vladimir E","family":"Alatortsev","sequence":"additional","affiliation":[{"name":"Institute of Molecular Genetics of the National Research Centre \u201cKurchatov Institute\u201d, Moscow, Russia"}]},{"given":"Cristina P","family":"Vieira","sequence":"additional","affiliation":[{"name":"Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal"},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Porto, Portugal"}]},{"given":"Jorge","family":"Vieira","sequence":"additional","affiliation":[{"name":"Instituto de Biologia Molecular e Celular (IBMC), Porto, Portugal"},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Porto, Portugal"}]},{"given":"Jorge Roberto","family":"Torres","sequence":"additional","affiliation":[{"name":"La ci\u00e8ncia al teu m\u00f3n, Barcelona, Spain"}]},{"given":"Iryna","family":"Kozeretska","sequence":"additional","affiliation":[{"name":"Department of General and Medical Genetics, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine"},{"name":"State Institution National Antarctic Scientific Center, Ministry of Education and Science of Ukraine, Kyiv, Ukraine"}]},{"given":"Oleksandr M","family":"Maistrenko","sequence":"additional","affiliation":[{"name":"Department of General and Medical Genetics, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine"},{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany"}]},{"given":"Catherine","family":"Montchamp-Moreau","sequence":"additional","affiliation":[{"name":"UMR \u00c9volution, G\u00e9nomes, Comportement et \u00c9cologie, Universit\u00e9 Paris-Saclay, CNRS, Gif-sur-Yvette, France"}]},{"given":"Dmitry V","family":"Mukha","sequence":"additional","affiliation":[{"name":"Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia"}]},{"given":"Heather E","family":"Machado","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, CA, USA"},{"name":"Wellcome Trust Sanger Institute, Hinxton, United Kingdom"}]},{"given":"Keric","family":"Lamb","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Virginia, Charlottesville, VA, USA"}]},{"given":"T\u00e2nia","family":"Paulo","sequence":"additional","affiliation":[{"name":"Departamento de Biologia Animal, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal"}]},{"given":"Leeban","family":"Yusuf","sequence":"additional","affiliation":[{"name":"Center for Biological Diversity, University of St. Andrews, St Andrews, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0374-1475","authenticated-orcid":false,"given":"Antonio","family":"Barbadilla","sequence":"additional","affiliation":[{"name":"Department of Genetics and Microbiology, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"},{"name":"Institute of Biotechnology and Biomedicine, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}]},{"given":"Dmitri","family":"Petrov","sequence":"additional","affiliation":[{"name":"Department of Biology, Stanford University, Stanford, CA, USA"}]},{"given":"Paul","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Department of Biology, The Pennsylvania State University, University Park, PA, USA"}]},{"given":"Josefa","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5990-1503","authenticated-orcid":false,"given":"Thomas","family":"Flatt","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Fribourg, Fribourg, Switzerland"}]},{"given":"Alan O","family":"Bergland","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Virginia, Charlottesville, VA, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,9,1]]},"reference":[{"key":"2021121011112490600_msab259-B1","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1126\/science.287.5461.2185","article-title":"The genome sequence of Drosophila melanogaster","volume":"287","author":"Adams","year":"2000","journal-title":"Science"},{"issue":"3","key":"2021121011112490600_msab259-B3","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1093\/gbe\/evz022","article-title":"Demographic history of the human commensal Drosophila melanogaster","volume":"11","author":"Arguello","year":"2019","journal-title":"Genome Biol Evol"},{"issue":"12","key":"2021121011112490600_msab259-B4","doi-asserted-by":"crossref","first-page":"1988","DOI":"10.1101\/gr.219956.116","article-title":"Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations","volume":"27","author":"Assaf","year":"2017","journal-title":"Genome Res"},{"issue":"6","key":"2021121011112490600_msab259-B5","doi-asserted-by":"crossref","first-page":"e1003534","DOI":"10.1371\/journal.pgen.1003534","article-title":"A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster","volume":"9","author":"Bastide","year":"2013","journal-title":"PLoS Genet"},{"issue":"1","key":"2021121011112490600_msab259-B6","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1534\/genetics.120.303143","article-title":"Space is the place: effects of continuous spatial structure on 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