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

Martin Kapun; Maite G. Barron; Fabian Staubach; Darren J. Obbard; Axel W. Wiberg; Jorge Vieira; Clement Goubert; Omar Rota-Stabelli; Maaria Kankare; Maria Bogaerts-Marquez; Annabelle Haudry; Lena Waidele; Iryna Kozeretska; Elena G. Pasyukova; Volker Loeschcke; Marta Pascual; Cristina P. Vieira; Svitlana Serga; Catherine Montchamp-Moreau; Jessica Abbott; Patricia Gibert; Damiano Porcelli; Nico Posnien; Alejandro Sanchez-Gracia; Sonja Grath; Elio Sucena; Alan O. Bergland; Maria Pilar Garcia Guerreiro; Banu Sebnem Onder; Eliza Argyridou; Lain Guio; Mads Fristrup Schou; Bart Deplancke; Cristina Vieira; Michael G. Ritchie; Bas J. Zwaan; Eran Tauber; Dorcas J. Orengo; Eva Puerma; Montserrat Aguade; Paul Schmidt; John Parsch; Andrea J. Betancourt; Thomas Flatt; Josefa Gonzalez

doi:10.1093/molbev/msaa120

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

Martin Kapun^*, Maite G. Barron, Fabian Staubach, Darren J. Obbard, Axel W. Wiberg, Jorge Vieira, Clement Goubert, Omar Rota-Stabelli, Maaria Kankare, Maria Bogaerts-Marquez, Annabelle Haudry, Lena Waidele, Iryna Kozeretska, Elena G. Pasyukova, Volker Loeschcke, Marta Pascual, Cristina P. Vieira, Svitlana Serga, Catherine Montchamp-Moreau, Jessica AbbottPatricia Gibert, Damiano Porcelli, Nico Posnien, Alejandro Sanchez-Gracia, Sonja Grath, Elio Sucena, Alan O. Bergland, Maria Pilar Garcia Guerreiro, Banu Sebnem Onder, Eliza Argyridou, Lain Guio, Mads Fristrup Schou, Bart Deplancke, Cristina Vieira, Michael G. Ritchie, Bas J. Zwaan, Eran Tauber, Dorcas J. Orengo, Eva Puerma, Montserrat Aguade, Paul Schmidt, John Parsch, Andrea J. Betancourt, Thomas Flatt^*, Josefa Gonzalez^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

92 Citations (Scopus)

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.

Original language	English
Pages (from-to)	2661-2678
Number of pages	18
Journal	Molecular Biology and Evolution
Volume	37
Issue number	9
DOIs	https://doi.org/10.1093/molbev/msaa120
Publication status	Published - 1 Sept 2020

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 13 Climate Action

Keywords

Adaptation
Clines
Demography
Population genomics
Selection
SNPs
Structural variants

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10.1093/molbev/msaa120Licence: CC BY-NC

https://edepot.wur.nl/538240Licence: CC BY-NC

Cite this

Kapun, M., Barron, M. G., Staubach, F., Obbard, D. J., Wiberg, A. W., Vieira, J., Goubert, C., Rota-Stabelli, O., Kankare, M., Bogaerts-Marquez, M., Haudry, A., Waidele, L., Kozeretska, I., Pasyukova, E. G., Loeschcke, V., Pascual, M., Vieira, C. P., Serga, S., Montchamp-Moreau, C., ... Gonzalez, J. (2020). Genomic analysis of european drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses. Molecular Biology and Evolution, 37(9), 2661-2678. https://doi.org/10.1093/molbev/msaa120

@article{7f7933b647c842ffb35887e36c020fed,

title = "Genomic analysis of european drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses",

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.",

keywords = "Adaptation, Clines, Demography, Population genomics, Selection, SNPs, Structural variants",

author = "Martin Kapun and Barron, \{Maite G.\} and Fabian Staubach and Obbard, \{Darren J.\} and Wiberg, \{Axel W.\} and Jorge Vieira and Clement Goubert and Omar Rota-Stabelli and Maaria Kankare and Maria Bogaerts-Marquez and Annabelle Haudry and Lena Waidele and Iryna Kozeretska and Pasyukova, \{Elena G.\} and Volker Loeschcke and Marta Pascual and Vieira, \{Cristina P.\} and Svitlana Serga and Catherine Montchamp-Moreau and Jessica Abbott and Patricia Gibert and Damiano Porcelli and Nico Posnien and Alejandro Sanchez-Gracia and Sonja Grath and Elio Sucena and Bergland, \{Alan O.\} and Guerreiro, \{Maria Pilar Garcia\} and Onder, \{Banu Sebnem\} and Eliza Argyridou and Lain Guio and Schou, \{Mads Fristrup\} and Bart Deplancke and Cristina Vieira and Ritchie, \{Michael G.\} and Zwaan, \{Bas J.\} and Eran Tauber and Orengo, \{Dorcas J.\} and Eva Puerma and Montserrat Aguade and Paul Schmidt and John Parsch and Betancourt, \{Andrea J.\} and Thomas Flatt and Josefa Gonzalez",

year = "2020",

month = sep,

day = "1",

doi = "10.1093/molbev/msaa120",

language = "English",

volume = "37",

pages = "2661--2678",

journal = "Molecular Biology and Evolution",

issn = "0737-4038",

publisher = "Oxford University Press",

number = "9",

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Kapun, M, Barron, MG, Staubach, F, Obbard, DJ, Wiberg, AW, Vieira, J, Goubert, C, Rota-Stabelli, O, Kankare, M, Bogaerts-Marquez, M, Haudry, A, Waidele, L, Kozeretska, I, Pasyukova, EG, Loeschcke, V, Pascual, M, Vieira, CP, Serga, S, Montchamp-Moreau, C, Abbott, J, Gibert, P, Porcelli, D, Posnien, N, Sanchez-Gracia, A, Grath, S, Sucena, E, Bergland, AO, Guerreiro, MPG, Onder, BS, Argyridou, E, Guio, L, Schou, MF, Deplancke, B, Vieira, C, Ritchie, MG, Zwaan, BJ, Tauber, E, Orengo, DJ, Puerma, E, Aguade, M, Schmidt, P, Parsch, J, Betancourt, AJ, Flatt, T & Gonzalez, J 2020, 'Genomic analysis of european drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses', Molecular Biology and Evolution, vol. 37, no. 9, pp. 2661-2678. https://doi.org/10.1093/molbev/msaa120

Genomic analysis of european drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses. / Kapun, Martin; Barron, Maite G.; Staubach, Fabian et al.
In: Molecular Biology and Evolution, Vol. 37, No. 9, 01.09.2020, p. 2661-2678.

Research output: Contribution to journal › Article › Academic › peer-review

TY - JOUR

T1 - Genomic analysis of european drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

AU - Kapun, Martin

AU - Barron, Maite G.

AU - Staubach, Fabian

AU - Obbard, Darren J.

AU - Wiberg, Axel W.

AU - Vieira, Jorge

AU - Goubert, Clement

AU - Rota-Stabelli, Omar

AU - Kankare, Maaria

AU - Bogaerts-Marquez, Maria

AU - Haudry, Annabelle

AU - Waidele, Lena

AU - Kozeretska, Iryna

AU - Pasyukova, Elena G.

AU - Loeschcke, Volker

AU - Pascual, Marta

AU - Vieira, Cristina P.

AU - Serga, Svitlana

AU - Montchamp-Moreau, Catherine

AU - Abbott, Jessica

AU - Gibert, Patricia

AU - Porcelli, Damiano

AU - Posnien, Nico

AU - Sanchez-Gracia, Alejandro

AU - Grath, Sonja

AU - Sucena, Elio

AU - Bergland, Alan O.

AU - Guerreiro, Maria Pilar Garcia

AU - Onder, Banu Sebnem

AU - Argyridou, Eliza

AU - Guio, Lain

AU - Schou, Mads Fristrup

AU - Deplancke, Bart

AU - Vieira, Cristina

AU - Ritchie, Michael G.

AU - Zwaan, Bas J.

AU - Tauber, Eran

AU - Orengo, Dorcas J.

AU - Puerma, Eva

AU - Aguade, Montserrat

AU - Schmidt, Paul

AU - Parsch, John

AU - Betancourt, Andrea J.

AU - Flatt, Thomas

AU - Gonzalez, Josefa

PY - 2020/9/1

Y1 - 2020/9/1

N2 - 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.

AB - 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.

KW - Adaptation

KW - Clines

KW - Demography

KW - Population genomics

KW - Selection

KW - SNPs

KW - Structural variants

U2 - 10.1093/molbev/msaa120

DO - 10.1093/molbev/msaa120

M3 - Article

C2 - 32413142

AN - SCOPUS:85090025034

SN - 0737-4038

VL - 37

SP - 2661

EP - 2678

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

IS - 9

ER -

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

Abstract

UN SDGs

Keywords

Access to Document

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