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

Joaquin C. B. Nunez, Marta Coronado-Zamora, Mathieu Gautier, Martin Kapun, Sonja Steindl, Lino Ometto, Katja M. Hoedjes, Julia Beets, R. Axel W. Wiberg, Giovanni R. Mazzeo, David J. Bass, Denys Radionov, Iryna Kozeretska, Mariia Zinchenko, Oleksandra Protsenko, Svitlana Serga, Cristina Amor-Jimenez, Sònia Casillas, Alejandro Sanchez-Gracia, Aleksandra PatenkovicAmanda Glaser-Schmitt, Antonio Barbadilla, Antonio J. Buendia-Ruiz, Astra Clelia Bertelli, Balázs Kiss, Banu Sebnem Önder, Bélen Roldán Matrin, Bregje Wertheim, Candice Deschamps, Carlos E. Arboleda-Bustos, Carlos Tinedo, Christian Feller, Christian Schlötterer, Clancy Lawler, Claudia Fricke, Cristina P. Vieira, Cristina Vieira, Darren J. Obbard, Dorcas Orengo, Doris Vela, Eduardo Amat, Elgion Loreto, Envel Kerdaffrec, Esra Durmaz Mitchell, Eva Puerma, Fabian Staubach, Florencia Camus, Hervé Colinet, Jan Hrcek, Jesper G. Sørensen, Jessica Abbott, Joan Torro, John Parsch, Jorge Vieira, Jose Luis Olmo, Khalid Khfif, Krzysztof Wojciechowski, Lilian Madi-Ravazzi, Maaria Kankare, Mads F. Schou, Manolis Ladoukakis, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Maria Pilar Garcia-Guerreiro, Maria-Eleni Parakatselaki, Marija Savic Veselinovic, Marija Tanaskovic, Marina Stamenkovic-Radak, Margot Paris, Marta Pascual, Michael G. Ritchie, Michel Rera, Mihailo Jelić, Mina Hojat Ansari, Mina Rakic, Miriam Merenciano, Natalia Hernandes, Nazar Gora, Nicolas Rode, Omar Rota-Stabelli, Paloma Sepulveda, Patricia Gibert, Pau Carazo, Pinar Kohlmeier, Priscilla A. Erickson, Renaud Vitalis, Roberto Torres, Sara Guirao-Rico, Sebastian E. Ramos-Onsins, Silvana Castillo, Tânia F. Paulo, Venera Tyukmaeva, Zahara Alonso, Vladimir Alatortsev, Elena Pasyukova, Dmitry Mukha, Dmitri Petrov, Paul Schmidt, Thomas Flatt, Alan O. Bergland, Josefa Gonzalez

Research output: Working paperPreprint

Abstract

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.Competing Interest StatementThe authors have declared no competing interest.
Original languageEnglish
Number of pages59
DOIs
Publication statusPublished - 11 Nov 2024

Publication series

NamebioRxiv
PublisherCold Spring Harbor Laboratory Press

Fingerprint

Dive into the research topics of 'Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource'. Together they form a unique fingerprint.

Cite this