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

Martin Kapun (1) , Maite G Barrón (2) , Fabian Staubach (3) , Darren J 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 A. 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 O 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 G Ritchie (5) , Bas J Zwaan (29) , Eran Tauber (30) , Dorcas J Orengo (14) , Eva Puerma (14) , Montserrat Aguadé (14) , Paul S Schmidt (31) , John Parsch (23) , Andrea J 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
16 GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
17 ERABLE - Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale
18 EGCE - Evolution, génomes, comportement et écologie
19 Lund University [Lund]
20 Génétique et évolution des interactions hôtes-parasites
21 Department of Animal and Plant Sciences [Sheffield]
22 Georg-August-University = 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 - Université de Lausanne = University of Lausanne

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.

Domains: Environmental Sciences; Biodiversity and Ecology; Life Sciences [q-bio]; Biodiversity; Populations and Evolution [q-bio.PE]; Life Sciences [q-bio]; Genetics; Populations and Evolution [q-bio.PE]; Life Sciences [q-bio]; Ecology, environment; Symbiosis

Martin Kapun, Maite G Barrón, Fabian Staubach, Darren J 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, 2020, 37 (9), pp.2661-2678. ⟨10.1093/molbev/msaa120⟩. ⟨hal-03014405⟩