Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource
Kapun, Martin (University of Zurich)
Nunez, Joaquin C B (University of Virginia. Department of Biology)
Bogaerts-Márquez, María (Universitat Pompeu Fabra)
Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Paris, Margot (University of Fribourg. Department of Biology)
Outten, Joseph (University of Virginia. Department of Biology)
Coronado-Zamora, Marta (Universitat Pompeu Fabra)
Tern, Courtney (University of Virginia. Department of Biology)
Rota-Stabelli, Omar (University of Trento)
García Guerreiro, María Pilar (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Orengo, Dorcas J. (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Puerma, Eva (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
Kankare, Maaria (University of Jyväskylä. Department of Biological and Environmental Science)
Ometto, Lino (University of Pavia. Department of Biology and Biotechnology)
Loeschcke, Volker (Aarhus University. Department of Biology)
Onder, Banu S. (Hacettepe University. Department of Biology)
Abbott, Jessica (Lund University. Department of Biology)
Schaeffer, Stephen W. (The Pennsylvania State University. Department of Biology)
Rajpurohit, Subhash (Ahmedabad University)
Behrman, Emily L (Janelia Research Campus)
Schou, Mads F. (Lund University. Department of Biology)
Merritt, Thomas J.S. (Laurentian University. Department of Chemistry & Biochemistry)
Lazzaro, Brian P. (Cornell University. Department of Entomology)
Glaser-Schmitt, Amanda (Ludwig-Maximilians-Universität München)
Argyridou, Eliza (Ludwig-Maximilians-Universität München)
Staubach, Fabian (Department of Evolution and Ecology, University of Freiburg)
Wang, Yun (University of Freiburg. Department of Evolution and Ecology)
Tauber, Eran (University of Haifa. Department of Evolutionary and Environmental Biology)
Serga, Svitlana V. (State Institution National Antarctic Scientific Center (Ukraine))
Fabian, Daniel K. (University of Cambridge. Department of Genetics)
Dyer, Kelly A. (University of Georgia. Department of Genetics)
Wheat, Christopher W. (Stockholm University. Department of Zoology)
Parsch, John (Ludwig-Maximilians-Universität München)
Grath, Sonja (Ludwig-Maximilians-Universität München)
Veselinovic, Marija Savic (University of Belgrade)
Stamenkovic-Radak, Marina (University of Belgrade)
Jelic, Mihailo (University of Belgrade)
Buendía-Ruíz, Antonio J. (IES Eladio Cabañero)
Gómez-Julián, Maria Josefa (IES Eladio Cabañero)
Espinosa-Jimenez, Maria Luisa (IES Eladio Cabañero)
Gallardo-Jiménez, Francisco D. (IES Jose de Mora)
Patenkovic, Aleksandra (University of Belgrade)
Eric, Katarina (Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade)
Tanaskovic, Marija (University of Belgrade)
Ullastres, Anna (Institut de Biologia Evolutiva (Barcelona))
Guio, Lain (Institut de Biologia Evolutiva (Barcelona))
Merenciano, Miriam (Institut de Biologia Evolutiva (Barcelona))
Guirao-Rico, Sara (Institut de Biologia Evolutiva (Barcelona))
Horváth, Vivien (Institut de Biologia Evolutiva (Barcelona))
Obbard, Darren (University of Edinburgh)
Pasyukova, Elena (Institute of Molecular Genetics of the National Research Centre "Kurchatov Institute")
Alatortsev, Vladimir E. (Institute of Molecular Genetics of the National Research Centre "Kurchatov Institute")
Vieira, Cristina (Universidade do Porto)
Vieira, Jorge (Universidade do Porto)
Torres, Jorge Roberto (La ciència al teu món)
Kozeretska, Iryna (State Taras Shevchenko National University of Kyiv. Department of General and Medical Genetics)
Maistrenko, Oleksandr M. (State Taras Shevchenko National University of Kyiv. Department of General and Medical Genetics)
Montchamp-Moreau, Catherine (Université Paris-Saclay)
Mukha, Dmitry V. (Russian Academy of Sciences)
Machado, Heather E. (Stanford University. Department of Biology)
Lamb, Keric (University of Virginia. Department of Biology)
Paulo, Tânia (Instituto Gulbenkian de Ciência)
Yusuf, Leeban (University of St. Andrews)
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Petrov, Dmitri (Stanford University. Department of Biology)
Schmidt, Paul (The Pennsylvania State University. Department of Biology)
Gonzalez, Josefa (Institut de Biologia Evolutiva (Barcelona))
Flatt, Thomas (University of Fribourg. Department of Biology)
Bergland, Alan O. (University of Virginia. Department of Biology)

Data:	2021
Resum:	Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. 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 >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.
Ajuts:	European Commission 647900 Ministerio de Ciencia e Innovación BFU-2011-24397
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Drosophila melanogaster ; Population genomics ; SNPs ; Evolution ; Adaptation ; Demography
Publicat a:	Molecular biology and evolution, Vol. 38, Issue 12 (December 2021) , p. 5782-5805, ISSN 1537-1719

DOI: 10.1093/molbev/msab259
PMID: 34469576

24 p, 4.3 MB

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