Adaptation in a keystone grazer under novel predation pressure

Understanding how species adapt to environmental change is necessary to protect biodiversity and ecosystem services. Growing evidence suggests species can adapt rapidly to novel selection pressures like predation from invasive species, but the repeatability and predictability of selection remain poorly understood in wild populations. We tested how a keystone aquatic herbivore, Daphnia pulicaria, evolved in response to predation pressure by the introduced zooplanktivore Bythotrephes longimanus. Using high-resolution ²¹⁰Pb-dated sediment cores from 12 lakes in Ontario (Canada), which primarily differed in invasion status by Bythotrephes, we compared Daphnia population genetic structure over time using whole-genome sequencing of individual resting embryos. We found strong genetic differentiation between populations approximately 70 years before versus 30 years after reported Bythotrephes invasion, with no difference over this period in uninvaded lakes. Compared with uninvaded lakes, we identified, on average, 64 times more loci were putatively under selection in the invaded lakes. Differentiated loci were mainly associated with known reproductive and stress responses, and mean body size consistently increased by 14.1% over time in invaded lakes. These results suggest Daphnia populations were repeatedly acquiring heritable genetic adaptations to escape gape-limited predation. More generally, our results suggest some aspects of environmental change predictably shape genome evolution.