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Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

Martin Kapun 1 Maite Barrón 2 Fabian Staubach 3 Darren Obbard 4 R Axel W. Wiberg 5, 6 Jorge Vieira 7 Clément Goubert 8 Omar Rota-Stabelli 9 Maaria Kankare 10 María Bogaerts-Márquez 2 Annabelle Haudry 8 Lena Waidele 3 Iryna Kozeretska 11 Elena G Pasyukov 12 Volker Loeschcke 13 Marta Pascual 14 Cristina P Vieira 15, 16, 17, 8 Svitlana Serga 11 Catherine Montchamp-Moreau 18 Jessica Abbott 19 Patricia Gibert 20, 8 Damiano Porcelli 21 Nico Posnien 22 Alejandro Sánchez-Gracia 14 Sonja Grath 23 Élio Sucena 24 Alan Bergland 25 Maria Pilar Garcia Guerreiro 26 Banu Sebnem Onder 27 Eliza Argyridou 23 Lain Guio 2 Fristrup Schou 19 Bart Deplancke 28 Cristina Vieira 8 Michael Ritchie 5 Bas Zwaan 29 Eran Tauber 30 Dorcas Orengo 14 Eva Puerma 14 Montserrat Aguadé 14 Paul Schmidt 31 John Parsch 23 Andrea Betancourt 32 Thomas Flatt 33 Josefa González 2
1 University of Fribourg
2 UPF - Universitat Pompeu Fabra [Barcelona]
3 University of Freiburg [Freiburg]
4 University of Edinburgh
5 University of St Andrews [Scotland]
6 Unibas - University of Basel
7 IBMC - Instituto de Biologia Molecular e Celular - institute for molecular and cell biology [Porto, Portugal]
8 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
9 Fondazione Edmund Mach [San Michele all'Adige]
10 JYU - University of Jyväskylä
11 UKMA - National University of Kyiv-Mohyla Academy
12 Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia]
13 Aarhus University [Aarhus]
14 UB - Universitat de Barcelona
15 Eléments transposables, évolution, populations
GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
16 GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
17 ERABLE - Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale
Inria Grenoble - Rhône-Alpes
18 EGCE - Evolution, génomes, comportement et écologie
19 Lund University [Lund]
20 Génétique et évolution des interactions hôtes-parasites
GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
21 Department of Animal and Plant Sciences [Sheffield]
22 University of Göttingen - Georg-August-Universität Göttingen
23 LMU - Ludwig-Maximilians-Universität München
24 IGC - Instituto Gulbenkian de Ciência [Oeiras]
25 University of Virginia [Charlottesville]
26 UAB - Universitat Autònoma de Barcelona
27 Hacettepe University = Hacettepe Üniversitesi
28 School of Life Sciences [Lausanne]
29 WUR - Wageningen University and Research [Wageningen]
30 University of Haifa [Haifa]
31 University of Pennsylvania [Philadelphia]
32 University of Liverpool
33 UNIL - University of Lausanne
Abstract : Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Submitted on : Thursday, November 19, 2020 - 6:05:10 PM
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Martin Kapun, Maite Barrón, Fabian Staubach, Darren Obbard, R Axel W. Wiberg, et al.. Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses. Molecular Biology and Evolution, Oxford University Press (OUP), 2020, 37 (9), pp.2661-2678. ⟨10.1093/molbev/msaa120⟩. ⟨hal-03014405⟩

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