Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource - INRA - Institut national de la recherche agronomique
Pré-Publication, Document De Travail Année : 2024

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

Joaquin C. B. Nunez (1, 2) , Marta Coronado-Zamora (3, 4) , Mathieu Gautier (5) , Martin Kapun (6) , Sonja Steindl (6) , Lino Ometto (7) , Katja M. Hoedjes (8, 9) , Julia Beets (8, 9) , R. Axel W. Wiberg (10) , Giovanni R. Mazzeo (2) , David J. Bass (2, 11) , Denys Radionov (12) , Iryna Kozeretska (13) , Mariia Zinchenko (14) , Oleksandra Protsenko (13, 15) , Svitlana Serga (5, 13) , Cristina Amor-Jimenez (16, 17) , Sònia Casillas (16, 17) , Alejandro Sanchez-Gracia (18) , Aleksandra Patenkovic (19) , Amanda Glaser-Schmitt (20, 21) , Antonio Barbadilla (16, 17) , Antonio J. Buendia-Ruiz (22) , Astra Clelia Bertelli (7) , Balázs Kiss (23, 24) , Banu Sebnem Önder (25) , Bélen Roldán Matrín (26) , Bregje Wertheim (27) , Candice Deschamps (5) , Carlos E. Arboleda-Bustos (28) , Carlos Tinedo (29, 30) , Christian Feller (31) , Christian Schlötterer (32, 33) , Clancy Lawler (34) , Claudia Fricke (35) , Cristina P. Vieira (36) , Cristina Vieira (37) , Darren J. Obbard (38) , Dorcas Orengo (18, 30) , Doris Vela (39) , Eduardo Amat (40) , Elgion Loreto (41) , Envel Kerdaffrec (42) , Esra Durmaz Mitchell (42) , Eva Puerma (43) , Fabian Staubach (44) , Florencia Camus (45, 46) , Hervé Colinet (47) , Jan Hrcek (48) , Jesper G. Sørensen (49) , Jessica Abbott (50) , Joan Torro (51) , John Parsch (20, 21) , Jorge Vieira (36) , Jose Luis Olmo (52) , Khalid Khfif (53) , Krzysztof Wojciechowski (54) , Lilian Madi-Ravazzi (55) , Maaria Kankare (56) , Mads F. Schou (49) , Manolis Ladoukakis (57) , Maria Josefa Gomez-Julian (22) , Maria Luisa Espinosa-Jimenez (22) , Maria Pilar Garcia-Guerreiro (16) , Maria-Eleni Parakatselaki (57) , Marija Savic Veselinovic (58) , Marija Tanaskovic (19) , Marina Stamenkovic-Radak (58) , Margot Paris (42) , Marta Pascual (18, 30) , Michael G. Ritchie (59) , Michael Rera (60) , Mihailo Jelić (58) , Mina Hojat Ansari (44) , Mina Rakic (58) , Miriam Merenciano (61, 3) , Natalia Hernandes (34) , Nazar Gora (62, 63) , Nicolas Rode (5) , Omar Rota-Stabelli (64, 65) , Paloma Sepulveda (66) , Patricia Gibert (37) , Pau Carazo (67) , Pinar Kohlmeier (27) , Priscilla A. Erickson (2, 68) , Renaud Vitalis (5) , Roberto Torres (69) , Sara Guirao-Rico (18, 30) , Sebastian E. Ramos-Onsins (70) , Silvana Castillo (71) , Tânia F. Paulo (72) , Venera Tyukmaeva (73) , Zahara Alonso (74) , Vladimir Alatortsev (75) , Elena Pasyukova (75) , Dmitry Mukha (76, 77) , Dmitri Petrov (78, 79) , Paul Schmidt (80) , Thomas Flatt (42) , Alan O. Bergland (2) , Josefa Gonzalez (81, 3)
1 University of Vermont [Burlington]
2 University of Virginia
3 Institute of Evolutionary Biology
4 Botanical Institute of Barcelona
5 UMR CBGP - Centre de Biologie pour la Gestion des Populations
6 NHM - Naturhistorisches Museum Wien = Natural History Museum Vienna
7 DBB UNIPV - Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani" = Department of Biology and Biotechnology [Univ di Pavia]
8 VU - Vrije Universiteit Amsterdam [Amsterdam]
9 Amsterdam Institute for Life and Environment
10 Department of Zoology [Stockholm]
11 JHU - Johns Hopkins University
12 Odesa I. I. Mechnikov National University
13 National Antarctic Scientific Center of Ukraine
14 Lesya Ukrainka Volyn National University
15 Taras Shevchenko National University of Kyiv
16 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
17 Institut de Biotecnologia i Biomedicina
18 IRBio UB - Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain]
19 IBISS - Institute for Biological Research Sinisa Stankovic [Belgrade]
20 LMU - Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München
21 Division of Evolutionary Biology
22 Instituto de Enseñanza Secundaria Eladio Cabañero
23 ATK NOVI - Plant Protection Institute [Budapest]
24 HUN-REN - Hungarian Research Network
25 Hacettepe University = Hacettepe Üniversitesi
26 Instituto de Enseñanza Secundaria Alonso de Ercilla
27 GELIFES - Groningen Institute for Evolutionary Life Sciences [Groningen]
28 UNAL - Universidad Nacional de Colombia [Bogotà]
29 UB - Universitat de Barcelona
30 Departament de Genètica, Microbiologia i Estadística [Barcelona]
31 Justus-von-Liebig-Schule
32 Vetmeduni - University of Veterinary Medicine [Vienna]
33 Institute of Population Genetics
34 University of Melbourne
35 Martin-Luther-University Halle-Wittenberg
36 I3S - Instituto de Investigação e Inovação em Saúde
37 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
38 Edin. - University of Edinburgh
39 Pontificia Universidad Católica del Ecuador
40 Tecnológico de Antioquia
41 UFSM - Universidade Federal de Santa Maria = Federal University of Santa Maria [Santa Maria, RS, Brazil]
42 UNIFR - Université de Fribourg = University of Fribourg
43 VHIO - Vall d'Hebron Institute of Oncology [Barcelone]
44 Albert-Ludwigs-Universität Freiburg = University of Freiburg
45 UCL - University College of London [London]
46 Department of Genetics, Evolution & Environment
47 ECOBIO - Ecosystèmes, biodiversité, évolution [Rennes]
48 BIOLOGY CENTRE CAS - Biology Centre of the Czech Academy of Sciences
49 Aarhus University [Aarhus]
50 Lund University
51 Instituto de Enseñanza Secundaria Benjamín Jarnés
52 Instituto de Enseñanza Secundaria Azuer
53 INRA Maroc - Institut national de la recherche agronomique [Maroc]
54 Regional Landscape Parks of Lublin
55 UNESP - Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University
56 JYU - University of Jyväskylä
57 UOC - University of Crete [Heraklion]
58 University of Belgrade [Belgrade]
59 University of St Andrews [Scotland]
60 IJM (UMR_7592) - Institut Jacques Monod
61 UPF - Universitat Pompeu Fabra [Barcelona]
62 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
63 Molecular Biophysics and Integrated Bioimaging Division [Berkeley, CA, USA]
64 UNITN - Università degli Studi di Trento = University of Trento
65 C3A - Centro Agricoltura Alimenti Ambiente [San Michele All'adige] = Center Agriculture Food Environment [San Michele All'adige]
66 Instituto de Enseñanza Secundaria Carpetania
67 Instituto Cavanilles de Biodiversidad y Biologia Evolutiva
68 University of Richmond
69 La Ciència Al Teu Món
70 CRAG - Centre for Research in Agricultural Genomics
71 Instituto de Enseñanza Secundaria Jose de Mora
72 IGC - Instituto Gulbenkian de Ciência [Oeiras]
73 University of Liverpool
74 Centro de Educación Infantil y Primaria Ramón y Cajal
75 Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia]
76 RAS - Russian Academy of Sciences [Moscow]
77 Vavilov Institute of General Genetics
78 Stanford University
79 CZ Biohub
80 University of Pennsylvania
81 IBB - Institut Botànic de Barcelona
Joaquin C. B. Nunez
University of Vermont [Burlington]
University of Virginia
Marta Coronado-Zamora
Institute of Evolutionary Biology
Botanical Institute of Barcelona
Mathieu Gautier
Centre de Biologie pour la Gestion des Populations
Martin Kapun
Naturhistorisches Museum Wien = Natural History Museum Vienna
Sonja Steindl
Naturhistorisches Museum Wien = Natural History Museum Vienna
Lino Ometto
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani" = Department of Biology and Biotechnology [Univ di Pavia]
Katja M. Hoedjes
Vrije Universiteit Amsterdam [Amsterdam]
Amsterdam Institute for Life and Environment
Julia Beets
Vrije Universiteit Amsterdam [Amsterdam]
Amsterdam Institute for Life and Environment
R. Axel W. Wiberg
Department of Zoology [Stockholm]
Giovanni R. Mazzeo
University of Virginia
David J. Bass
University of Virginia
Johns Hopkins University
Denys Radionov
Odesa I. I. Mechnikov National University
Iryna Kozeretska
National Antarctic Scientific Center of Ukraine
Mariia Zinchenko
Lesya Ukrainka Volyn National University
Oleksandra Protsenko
National Antarctic Scientific Center of Ukraine
Taras Shevchenko National University of Kyiv
Svitlana Serga
Centre de Biologie pour la Gestion des Populations
National Antarctic Scientific Center of Ukraine
Cristina Amor-Jimenez
Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
Institut de Biotecnologia i Biomedicina
Sònia Casillas
Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
Institut de Biotecnologia i Biomedicina
Alejandro Sanchez-Gracia
Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain]
Aleksandra Patenkovic
Institute for Biological Research Sinisa Stankovic [Belgrade]
Amanda Glaser-Schmitt
Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München
Division of Evolutionary Biology
Antonio Barbadilla
Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
Institut de Biotecnologia i Biomedicina
Antonio J. Buendia-Ruiz
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Eladio Cabañero
Astra Clelia Bertelli
Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani" = Department of Biology and Biotechnology [Univ di Pavia]
Balázs Kiss
Plant Protection Institute [Budapest]
Hungarian Research Network
Banu Sebnem Önder
Hacettepe University = Hacettepe Üniversitesi
Bélen Roldán Matrín
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Alonso de Ercilla
Bregje Wertheim
Groningen Institute for Evolutionary Life Sciences [Groningen]
Candice Deschamps
Centre de Biologie pour la Gestion des Populations
Carlos E. Arboleda-Bustos
Universidad Nacional de Colombia [Bogotà]
Carlos Tinedo
  • Fonction : Auteur
Universitat de Barcelona
Departament de Genètica, Microbiologia i Estadística [Barcelona]
Christian Feller
  • Fonction : Auteur
Justus-von-Liebig-Schule
Christian Schlötterer
University of Veterinary Medicine [Vienna]
Institute of Population Genetics
Clancy Lawler
University of Melbourne
Claudia Fricke
Martin-Luther-University Halle-Wittenberg
Cristina P. Vieira
Instituto de Investigação e Inovação em Saúde
Cristina Vieira
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
CV
Darren J. Obbard
University of Edinburgh
Dorcas Orengo
Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain]
Departament de Genètica, Microbiologia i Estadística [Barcelona]
Doris Vela
Pontificia Universidad Católica del Ecuador
Eduardo Amat
Tecnológico de Antioquia
Elgion Loreto
Universidade Federal de Santa Maria = Federal University of Santa Maria [Santa Maria, RS, Brazil]
Envel Kerdaffrec
  • Fonction : Auteur
Université de Fribourg = University of Fribourg
Esra Durmaz Mitchell
Université de Fribourg = University of Fribourg
Eva Puerma
Vall d'Hebron Institute of Oncology [Barcelone]
Fabian Staubach
  • Fonction : Auteur
Albert-Ludwigs-Universität Freiburg = University of Freiburg
Florencia Camus
University College of London [London]
Department of Genetics, Evolution & Environment
Hervé Colinet
Ecosystèmes, biodiversité, évolution [Rennes]
CV
Jan Hrcek
Biology Centre of the Czech Academy of Sciences
Jesper G. Sørensen
Aarhus University [Aarhus]
Jessica Abbott
Lund University
Joan Torro
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Benjamín Jarnés
John Parsch
Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München
Division of Evolutionary Biology
Jorge Vieira
Instituto de Investigação e Inovação em Saúde
Jose Luis Olmo
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Azuer
Khalid Khfif
Institut national de la recherche agronomique [Maroc]
Krzysztof Wojciechowski
  • Fonction : Auteur
Regional Landscape Parks of Lublin
Lilian Madi-Ravazzi
Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University
Maaria Kankare
University of Jyväskylä
Mads F. Schou
Aarhus University [Aarhus]
Manolis Ladoukakis
University of Crete [Heraklion]
Maria Josefa Gomez-Julian
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Eladio Cabañero
Maria Luisa Espinosa-Jimenez
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Eladio Cabañero
Maria Pilar Garcia-Guerreiro
Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
Maria-Eleni Parakatselaki
  • Fonction : Auteur
University of Crete [Heraklion]
Marija Savic Veselinovic
  • Fonction : Auteur
University of Belgrade [Belgrade]
Marija Tanaskovic
Institute for Biological Research Sinisa Stankovic [Belgrade]
Marina Stamenkovic-Radak
University of Belgrade [Belgrade]
Margot Paris
Université de Fribourg = University of Fribourg
Marta Pascual
Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain]
Departament de Genètica, Microbiologia i Estadística [Barcelona]
Michael G. Ritchie
University of St Andrews [Scotland]
Michael Rera
Institut Jacques Monod
CV
Mihailo Jelić
University of Belgrade [Belgrade]
Mina Hojat Ansari
Albert-Ludwigs-Universität Freiburg = University of Freiburg
Mina Rakic
University of Belgrade [Belgrade]
Miriam Merenciano
Universitat Pompeu Fabra [Barcelona]
Institute of Evolutionary Biology
Natalia Hernandes
University of Melbourne
Nazar Gora
Lawrence Berkeley National Laboratory [Berkeley]
Molecular Biophysics and Integrated Bioimaging Division [Berkeley, CA, USA]
Nicolas Rode
Centre de Biologie pour la Gestion des Populations
Omar Rota-Stabelli
Università degli Studi di Trento = University of Trento
Centro Agricoltura Alimenti Ambiente [San Michele All'adige] = Center Agriculture Food Environment [San Michele All'adige]
Paloma Sepulveda
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Carpetania
Patricia Gibert
  • Fonction : Auteur
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Pau Carazo
Instituto Cavanilles de Biodiversidad y Biologia Evolutiva
Pinar Kohlmeier
  • Fonction : Auteur
Groningen Institute for Evolutionary Life Sciences [Groningen]
Priscilla A. Erickson
University of Virginia
University of Richmond
Renaud Vitalis
Centre de Biologie pour la Gestion des Populations
CV
Roberto Torres
  • Fonction : Auteur
La Ciència Al Teu Món
Sara Guirao-Rico
Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain]
Departament de Genètica, Microbiologia i Estadística [Barcelona]
Sebastian E. Ramos-Onsins
Centre for Research in Agricultural Genomics
Silvana Castillo
  • Fonction : Auteur
Instituto de Enseñanza Secundaria Jose de Mora
Tânia F. Paulo
Instituto Gulbenkian de Ciência [Oeiras]
Venera Tyukmaeva
University of Liverpool
Zahara Alonso
  • Fonction : Auteur
Centro de Educación Infantil y Primaria Ramón y Cajal
Vladimir Alatortsev
Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia]
Elena Pasyukova
Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia]
Dmitry Mukha
Russian Academy of Sciences [Moscow]
Vavilov Institute of General Genetics
Dmitri Petrov
Stanford University
CZ Biohub
Paul Schmidt
University of Pennsylvania
Thomas Flatt
Université de Fribourg = University of Fribourg
Alan O. Bergland
University of Virginia
Josefa Gonzalez
Institut Botànic de Barcelona
Institute of Evolutionary Biology

Résumé

Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster , we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009-2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. We showed that patterns of secondary contact, originally characterized in North America, are replicated in South America and Australia. We also found that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatio-temporal patterns of genetic variation in this classic model system.

Domaines

Génétique des populations [q-bio.PE] Base de données [cs.DB] Zoologie des invertébrés Génomique, Transcriptomique et Protéomique [q-bio.GN] Evolution [q-bio.PE]
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https://hal.science/hal-04779897

Soumis le : vendredi 15 novembre 2024-12:15:56

Dernière modification le : mardi 19 novembre 2024-14:42:03

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hal-04779897 , version 1 (15-11-2024)

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Paternité - Pas d'utilisation commerciale - Pas de modification

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Joaquin C. B. Nunez, Marta Coronado-Zamora, Mathieu Gautier, Martin Kapun, Sonja Steindl, et al.. Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource. 2024. ⟨hal-04779897⟩

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