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Drosophila Evolution over Space and Time (DEST) - a new population genomics resource

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Kapun_2021_Drosophilia_evolution_MBE_msab259_CCBY_NC.pdf (4.547Mb)
Date
01/09/2021
Author
Kapun, Martin
Nunez, Joaquin C B
Bogaerts-Márquez, María
Murga-Moreno, Jesús
Paris, Margot
Outten, Joseph
Coronado-Zamora, Marta
Tern, Courtney
Rota-Stabelli, Omar
García Guerreiro, Maria P
Casillas, Sònia
Orengo, Dorcas J
Puerma, Eva
Kankare, Maaria
Ometto, Lino
Loeschcke, Volker
Onder, Banu S
Abbott, Jessica K
Schaeffer, Stephen W
Rajpurohit, Subhash
Behrman, Emily L
Schou, Mads F
Merritt, Thomas J S
Lazzaro, Brian P
Glaser-Schmitt, Amanda
Argyridou, Eliza
Staubach, Fabian
Wang, Yun
Tauber, Eran
Serga, Svitlana V
Fabian, Daniel K
Dyer, Kelly A
Wheat, Christopher W
Parsch, John
Grath, Sonja
Veselinovic, Marija Savic
Stamenkovic-Radak, Marina
Jelic, Mihailo
Buendía-Ruíz, Antonio J
Gómez-Julián, M Josefa
Espinosa-Jimenez, M Luisa
Gallardo-Jiménez, Francisco D
Patenkovic, Aleksandra
Eric, Katarina
Tanaskovic, Marija
Ullastres, Anna
Guio, Lain
Merenciano, Miriam
Guirao-Rico, Sara
Horváth, Vivien
Obbard, Darren J
Pasyukova, Elena
Alatortsev, Vladimir E
Vieira, Cristina P
Vieira, Jorge
Torres, J Roberto
Kozeretska, Iryna
Maistrenko, Oleksandr M
Montchamp-Moreau, Catherine
Mukha, Dmitry V
Machado, Heather E
Lamb, Keric
Paulo, Tânia
Yusuf, Leeban
Barbadilla, Antonio
Petrov, Dmitri
Schmidt, Paul
Gonzalez, Josefa
Flatt, Thomas
Bergland, Alan O
Keywords
Demography
Population genomics
Drosophila melanogaster
SNPs
Evolution
Adaptation
QH301 Biology
QH426 Genetics
3rd-DAS
NIS
MCP
Metadata
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Abstract
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, 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 dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. 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 dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
Citation
Kapun , M , Nunez , J C B , Bogaerts-Márquez , M , Murga-Moreno , J , Paris , M , Outten , J , Coronado-Zamora , M , Tern , C , Rota-Stabelli , O , García Guerreiro , M P , Casillas , S , Orengo , D J , Puerma , E , Kankare , M , Ometto , L , Loeschcke , V , Onder , B S , Abbott , J K , Schaeffer , S W , Rajpurohit , S , Behrman , E L , Schou , M F , Merritt , T J S , Lazzaro , B P , Glaser-Schmitt , A , Argyridou , E , Staubach , F , Wang , Y , Tauber , E , Serga , S V , Fabian , D K , Dyer , K A , Wheat , C W , Parsch , J , Grath , S , Veselinovic , M S , Stamenkovic-Radak , M , Jelic , M , Buendía-Ruíz , A J , Gómez-Julián , M J , Espinosa-Jimenez , M L , Gallardo-Jiménez , F D , Patenkovic , A , Eric , K , Tanaskovic , M , Ullastres , A , Guio , L , Merenciano , M , Guirao-Rico , S , Horváth , V , Obbard , D J , Pasyukova , E , Alatortsev , V E , Vieira , C P , Vieira , J , Torres , J R , Kozeretska , I , Maistrenko , O M , Montchamp-Moreau , C , Mukha , D V , Machado , H E , Lamb , K , Paulo , T , Yusuf , L , Barbadilla , A , Petrov , D , Schmidt , P , Gonzalez , J , Flatt , T & Bergland , A O 2021 , ' Drosophila Evolution over Space and Time (DEST) - a new population genomics resource ' , Molecular Biology and Evolution , vol. Advance Article , msab259 . https://doi.org/10.1093/molbev/msab259
Publication
Molecular Biology and Evolution
Status
Peer reviewed
DOI
https://doi.org/10.1093/molbev/msab259
ISSN
0737-4038
Type
Journal article
Rights
Copyright © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Description
Funding: We are grateful to the members of the DrosEU and DrosRTEC consortia for their long-standing support, collaboration, and for discussion. DrosEU was funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). M.K. was supported by the Austrian Science Foundation (grant no. FWF P32275); J.G. by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020- ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); T.F. by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of Mu ̈nster; AOB by the National Institutes of Health (R35 GM119686); M.K. by Academy of Finland grant 322980; V.L. by Danish Natural Science Research Council (FNU) (grant no. 4002-00113B); FS Deutsche Forschungsgemeinschaft (DFG) (grant no. STA1154/4-1), Project 408908608; J.P. by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; A.U. by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) (grant no. 1737/17); M.S.V., M.S.R. and M.J. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); A.P., K.E. and M.T. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451- 03-68/2020-14/200007); and TM NSERC grant RGPIN-2018- 05551.
Collections
  • University of St Andrews Research
URI
http://hdl.handle.net/10023/24403

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