Footprints of Worldwide Adaptation in Structured Populations of <i>Drosophila melanogaster</i> 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, Maria Zinchenko, O. V. Protsenko, Svitlana Serga, Cristina Amor‐Jimenez, Sònia Casillas, Alejandro Sánchez‐Gracia, Aleksandra Patenković, Amanda Glaser‐Schmitt, Antonio Barbadilla, Antonio J. Buendía-Ruíz, Astra Clelia Bertelli, Balázs Kiss, Banu Şebnem Önder, Bélen Roldán Matrín, Bregje Wertheim, Candice Deschamps, Carlos Bustos, Carlos Tinedo, Christian Feller, Christian Schlötterer, Clancy Lawler, Claudia Fricke, Cristina P. Vieira, Cristina Vieira, Darren J. Obbard, Dorcas J. Orengo, Doris Vela, Eduardo Amat, Élgion L. S. Loreto, Envel Kerdaffrec, Esra Durmaz Mitchell, Eva Puerma, Fabian Staubach, M. Florencia Camus, Hervé Colinet, Jan Hrček, Jesper Givskov Sørensen, Jessica K. Abbott, Joan Torro, John Parsch, Jorge Vieira, José Olmo, Khalid Khfif, Krzysztof Wojciechowski, Lílian Madi-Ravazzi, Maaria Kankare, Mads F. Schou, Emmanuel D. Ladoukakis, Maria Josefa Gómez-Julián, Maria Luisa Espinosa-Jimenez, Maria Pilar García Guerreiro, Maria-Eleni Parakatselaki, Marija Savić Veselinović, Marija Tanasković, Marina Stamenković‐Radak, Margot Paris, Marta Pascual, Michael G. Ritchie, Michaël Rera, Mihailo Jelić, Mina Ansari, Mina Rakić, Miriam Merenciano, Natalia Hernandes, Nazar Gora, Nicolas O. Rode, Omar Rota‐Stabelli, Paloma Sepulveda, Patricia Gibert, Pau Carazo, Pinar Güler Kohlmeier, Priscilla A. Erickson, Renaud Vitalis, Jorge Roberto Torres, Sara Guirao‐Rico, Sebastián E. Ramos‐Onsins, Silvia Castillo, Tânia F. Paulo, Venera Tyukmaeva, Zahara Alonso, В. Е. Алаторцев, E. G. Pasyukova, Д. В. Муха, Dmitri A. Petrov, Paul Schmidt, Thomas Flatt, Alan O. Bergland
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 to 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. For example, we showed 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 spatiotemporal patterns of genetic variation in this classic model system.