Footprints of worldwide adaptation in structured populations ofD. melanogasterthrough the expanded DEST 2.0 genomic resource
Authors: Nunez Joaquin C. B. , Coronado-Zamora Marta , Gautier Mathieu , Kapun Martin , Steindl Sonja , Ometto Lino , Hoedjes Katja M. , Beets Julia , Wiberg R. Axel W. , Mazzeo Giovanni R. , Bass David J. , Radionov Denys , Kozeretska Iryna , Zinchenko Mariia , Protsenko Oleksandra , Serga Svitlana , Amor-Jimenez Cristina , Casillas Sònia , Sanchez-Gracia Alejandro , Patenkovic Aleksandra , Glaser-Schmitt Amanda , Barbadilla Antonio , Buendia-Ruiz Antonio J. , Bertelli Astra Clelia , Kiss Balázs , Önder Banu Sebnem , Matrín Bélen Roldán , Wertheim Bregje , Deschamps Candice , Arboleda-Bustos Carlos E. , Tinedo Carlos , Feller Christian , Schlötterer Christian , Lawler Clancy , Fricke Claudia , Vieira Cristina P. , Vieira Cristina , Obbard Darren J. , Orengo Dorcas , Vela Doris , Amat Eduardo , Loreto Elgion , Kerdaffrec Envel , Mitchell Esra Durmaz , Puerma Eva , Staubach Fabian , Camus Florencia , Colinet Hervé , Hrcek Jan , Sørensen Jesper G. , Abbott Jessica , Torro Joan , Parsch John , Vieira Jorge , Olmo Jose Luis , Khfif Khalid , Wojciechowski Krzysztof , Madi-Ravazzi Lilian , Kankare Maaria , Schou Mads F. , Ladoukakis Manolis , Gomez-Julian Maria Josefa , Espinosa-Jimenez Maria Luisa , Garcia Guerreiro Maria Pilar , Parakatselaki Maria-Eleni , Veselinovic Marija Savic , Tanaskovic Marija , Stamenkovic-Radak Marina , Paris Margot , Pascual Marta , Ritchie Michael G. , Rera Michel , Jelić Mihailo , Ansari Mina Hojat , Rakic Mina , Merenciano Miriam , Hernandes Natalia , Gora Nazar , Rode Nicolas , Rota-Stabelli Omar , Sepulveda Paloma , Gibert Patricia , Carazo Pau , Kohlmeier Pinar , Erickson Priscilla A. , Vitalis Renaud , Torres Roberto , Guirao-Rico Sara , Ramos-Onsins Sebastian E. , Castillo Silvana , Paulo Tânia F. , Tyukmaeva Venera , Alonso Zahara , Alatortsev Vladimir , Pasyukova Elena , Mukha Dmitry , Petrov Dmitri , Schmidt Paul , Flatt Thomas , Bergland Alan O. , Gonzalez Josefa 
Published: November 2024

AbstractLarge scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit flyDrosophila melanogaster, we present an expanded release of the community-generated population genomics resourceDrosophila 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.