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Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource
dc.creator | Kapun, Martin | |
dc.creator | Nunez, Joaquin C B | |
dc.creator | Bogaerts-Márquez, María | |
dc.creator | Murga-Moreno, Jesús | |
dc.creator | Paris, Margot | |
dc.creator | Outten, Joseph | |
dc.creator | Coronado-Zamora, Marta | |
dc.creator | Tern, Courtney | |
dc.creator | Rota-Stabelli, Omar | |
dc.creator | Guerreiro, Maria P García | |
dc.creator | Casillas, Sònia | |
dc.creator | Orengo, Dorcas J | |
dc.creator | Puerma, Eva | |
dc.creator | Kankare, Maaria | |
dc.creator | Ometto, Lino | |
dc.creator | Loeschcke, Volker | |
dc.creator | Onder, Banu S | |
dc.creator | Abbott, Jessica K | |
dc.creator | Schaeffer, Stephen W | |
dc.creator | Rajpurohit, Subhash | |
dc.creator | Behrman, Emily L | |
dc.creator | Schou, Mads F | |
dc.creator | Merritt, Thomas J S | |
dc.creator | Lazzaro, Brian P | |
dc.creator | Glaser-Schmitt, Amanda | |
dc.creator | Argyridou, Eliza | |
dc.creator | Staubach, Fabian | |
dc.creator | Wang, Yun | |
dc.creator | Tauber, Eran | |
dc.creator | Serga, Svitlana V | |
dc.creator | Fabian, Daniel K | |
dc.creator | Dyer, Kelly A | |
dc.creator | Wheat, Christopher W | |
dc.creator | Parsch, John | |
dc.creator | Grath, Sonja | |
dc.creator | Savić Veselinović, Marija | |
dc.creator | Stamenković-Radak, Marina | |
dc.creator | Jelić, Mihailo | |
dc.creator | Buendía-Ruíz, Antonio J | |
dc.creator | Gómez-Julián, Maria Josefa | |
dc.creator | Espinosa-Jimenez, Maria Luisa | |
dc.creator | Gallardo-Jiménez, Francisco D | |
dc.creator | Patenković, Aleksandra | |
dc.creator | Erić, Katarina | |
dc.creator | Tanasković, Marija | |
dc.creator | Ullastres, Anna | |
dc.creator | Guio, Lain | |
dc.creator | Merenciano, Miriam | |
dc.creator | Guirao-Rico, Sara | |
dc.creator | Horváth, Vivien | |
dc.creator | Obbard, Darren J | |
dc.creator | Pasyukova, Elena | |
dc.creator | Alatortsev, Vladimir E | |
dc.creator | Vieira, Cristina P | |
dc.creator | Vieira, Jorge | |
dc.creator | Torres, Jorge Roberto | |
dc.creator | Kozeretska, Iryna | |
dc.creator | Maistrenko, Oleksandr M | |
dc.creator | Montchamp-Moreau, Catherine | |
dc.creator | Mukha, Dmitry V | |
dc.creator | Machado, Heather E | |
dc.creator | Lamb, Keric | |
dc.creator | Paulo, Tânia | |
dc.creator | Yusuf, Leeban | |
dc.creator | Barbadilla, Antonio | |
dc.creator | Petrov, Dmitri | |
dc.creator | Schmidt, Paul | |
dc.creator | Gonzalez, Josefa | |
dc.creator | Flatt, Thomas | |
dc.creator | Bergland, Alan O | |
dc.creator | Nielsen, Rasmus | |
dc.date.accessioned | 2022-01-26T11:29:07Z | |
dc.date.available | 2022-01-26T11:29:07Z | |
dc.date.issued | 2021 | |
dc.identifier.issn | 0737-4038 | |
dc.identifier.uri | https://academic.oup.com/mbe/article/38/12/5782/6361628 | |
dc.identifier.uri | http://radar.ibiss.bg.ac.rs/handle/123456789/4765 | |
dc.description.abstract | 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. | |
dc.publisher | Oxford: Oxford University Press | |
dc.relation | info:eu-repo/grantAgreement/MESTD/inst-2020/200007/RS// | |
dc.relation | info:eu-repo/grantAgreement/MESTD/inst-2020/200178/RS// | |
dc.relation | Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB) | |
dc.relation | Austrian Science Fund (FWF) | |
dc.relation | European Research Council (ERC) | |
dc.relation | Spanish Government | |
dc.relation | Swiss National Science Foundation (SNSF) | |
dc.relation | German Research Foundation (DFG) | |
dc.relation | Danish Natural Science Research Council | |
dc.relation | United States Department of Health & Human Services National Institutes of Health (NIH) - USA | |
dc.relation | Israel Science Foundation | |
dc.relation | Natural Sciences and Engineering Research Council of Canada (NSERC) | |
dc.rights | openAccess | |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0/ | |
dc.source | Molecular Biology and Evolution | |
dc.subject | Drosophila melanogaster | |
dc.subject | Population genomics | |
dc.subject | SNPs | |
dc.subject | Evolution | |
dc.subject | Adaptation | |
dc.subject | Demography | |
dc.title | Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource | |
dc.type | article | en |
dc.rights.license | BY-NC-ND | |
dc.rights.holder | © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. | |
dc.citation.issue | 12 | |
dc.citation.volume | 38 | |
dc.identifier.doi | 10.1093/molbev/msab259 | |
dc.identifier.pmid | 34469576 | |
dc.identifier.wos | 000741368600039 | |
dc.citation.apa | Kapun, M., Nunez, J. C. B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., et al. (2021). Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Molecular Biology and Evolution, 38(12), 5782–5805. | |
dc.citation.vancouver | Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga S V, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha D V, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. Nielsen R, editor. Mol Biol Evol. 2021;38(12):5782–805. | |
dc.citation.spage | 5782 | |
dc.citation.epage | 5805 | |
dc.type.version | publishedVersion | |
dc.identifier.fulltext | https://radar.ibiss.bg.ac.rs/bitstream/id/9889/msab259.pdf | |
dc.citation.rank | aM21 |