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
(2)
,
María Bogaerts-Márquez
(2)
,
Annabelle Haudry
(8)
,
Lena Waidele
(3)
,
Iryna Kozeretska
(10)
,
Elena G Pasyukova
(11)
,
Volker Loeschcke
(12)
,
Marta Pascual
(13)
,
Cristina P Vieira
(14)
,
Svitlana Serga
(10)
,
Catherine Montchamp-Moreau
(15)
,
Jessica Abbott
(16)
,
Patricia Gibert
(8)
,
Damiano Porcelli
(17)
,
Nico Posnien
(18)
,
Alejandro Sánchez-Gracia
(13)
,
Sonja Grath
(19)
,
Élio Sucena
(20)
,
Alan O Bergland
(21)
,
Maria Pilar Garcia Guerreiro
(22)
,
Banu Sebnem Onder
(23)
,
Eliza Argyridou
(19)
,
Lain Guio
(2)
,
Mads Fristrup Schou
(16)
,
Bart Deplancke
(24)
,
Cristina Vieira
(8)
,
Michael G Ritchie
(5)
,
Bas J Zwaan
(25)
,
Eran Tauber
(26)
,
Dorcas J Orengo
(13)
,
Eva Puerma
(13)
,
Montserrat Aguadé
(13)
,
Paul Schmidt
(27)
,
John Parsch
(19)
,
Andrea J Betancourt
(28)
,
Thomas Flatt
(1)
,
Josefa González
(2)
1
UNIL -
Université de Lausanne = University of Lausanne
2 UPF - Universitat Pompeu Fabra [Barcelona]
3 Albert-Ludwigs-Universität Freiburg = University of Freiburg
4 Edin. - University of Edinburgh
5 University of St Andrews [Scotland]
6 Unibas - Université de Bâle = University of Basel = Basel Universität
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 UKMA - National University of Kyiv-Mohyla Academy
11 Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia]
12 Aarhus University [Aarhus]
13 UB - Universitat de Barcelona
14 Universidade do Porto = University of Porto
15 EGCE - Evolution, génomes, comportement et écologie
16 Skane University Hospital [Lund]
17 Department of Animal and Plant Sciences [Sheffield]
18 Georg-August-University = Georg-August-Universität Göttingen
19 LMU - Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München
20 IGC - Instituto Gulbenkian de Ciência [Oeiras]
21 University of Virginia
22 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
23 Hacettepe University = Hacettepe Üniversitesi
24 School of Life Sciences [Lausanne]
25 WUR - Wageningen University and Research [Wageningen]
26 University of Haifa [Haifa]
27 University of Pennsylvania
28 University of Liverpool
2 UPF - Universitat Pompeu Fabra [Barcelona]
3 Albert-Ludwigs-Universität Freiburg = University of Freiburg
4 Edin. - University of Edinburgh
5 University of St Andrews [Scotland]
6 Unibas - Université de Bâle = University of Basel = Basel Universität
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 UKMA - National University of Kyiv-Mohyla Academy
11 Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia]
12 Aarhus University [Aarhus]
13 UB - Universitat de Barcelona
14 Universidade do Porto = University of Porto
15 EGCE - Evolution, génomes, comportement et écologie
16 Skane University Hospital [Lund]
17 Department of Animal and Plant Sciences [Sheffield]
18 Georg-August-University = Georg-August-Universität Göttingen
19 LMU - Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München
20 IGC - Instituto Gulbenkian de Ciência [Oeiras]
21 University of Virginia
22 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
23 Hacettepe University = Hacettepe Üniversitesi
24 School of Life Sciences [Lausanne]
25 WUR - Wageningen University and Research [Wageningen]
26 University of Haifa [Haifa]
27 University of Pennsylvania
28 University of Liverpool
Martin Kapun
- Fonction : Auteur
- PersonId : 1315782
- ORCID : 0000-0002-3810-0504
R Axel W Wiberg
- Fonction : Auteur
- PersonId : 1393281
- ORCID : 0000-0001-5392-8142
Clément Goubert
- Fonction : Auteur
- PersonId : 775598
- ORCID : 0000-0001-8034-5559
- IdRef : 16819256X
Maaria Kankare
- Fonction : Auteur
- PersonId : 1393282
- ORCID : 0000-0003-1541-9050
Annabelle Haudry
- Fonction : Auteur
- PersonId : 169546
- IdHAL : annabelle-haudry
- ORCID : 0000-0001-6088-0909
- IdRef : 083544887
Catherine Montchamp-Moreau
- Fonction : Auteur
- PersonId : 1304445
- ORCID : 0000-0002-5044-9709
Patricia Gibert
- Fonction : Auteur
- PersonId : 21690
- IdHAL : patricia-gibert
- ORCID : 0000-0002-9461-6820
- IdRef : 175383537
Nico Posnien
- Fonction : Auteur
- PersonId : 1393283
- ORCID : 0000-0003-0700-5595
Cristina Vieira
- Fonction : Auteur
- PersonId : 21934
- IdHAL : cristina-vieira
- ORCID : 0000-0003-3414-3993
- IdRef : 121157318
Michael G Ritchie
- Fonction : Auteur
- PersonId : 1393284
- ORCID : 0000-0001-7913-8675
Bas J Zwaan
- Fonction : Auteur
- PersonId : 1393285
- ORCID : 0000-0002-8221-4998
Paul Schmidt
- Fonction : Auteur
- PersonId : 1393286
- ORCID : 0000-0002-8076-6705
Thomas Flatt
- Fonction : Auteur
- PersonId : 1001436
- ORCID : 0000-0002-5990-1503
Josefa González
- Fonction : Auteur
- PersonId : 1099403
- ORCID : 0000-0001-9824-027X
- IdRef : 203070569
Résumé
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.
Domaines
Evolution [q-bio.PE]| Origine | Publication financée par une institution |
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