Longitudinal sequencing reveals polygenic and epistatic nature of genomic response to selection
How adaptations are built genetically depends on if and how genes interact with one another. To investigate this question, we tracked genetic changes over 100 generations in fruit flies adapting to high-sugar diets, showing that adaptation is not only highly polygenic but also shaped by interactions between genes (epistasis). Our longitudinal approach reveals that natural selection favors specific gene combinations, as seen in coordinated genetic shifts and unexpected patterns of genetic variation. These findings provide a framework for identifying the genomic footprint of epistasis in evolving populations and offer insights into the complex genetic architecture that underlies adaptation to environmental challenges.