Genomic adaptation to a century of environmental change in zooplankton from the Canadian Shield

Abstract

Understanding how keystone organisms respond to environmental change, including the introduction of invasive species, is necessary to predict how global change will affect vulnerable ecosystems and how we can best manage and protect nature into the future. My Ph.D. investigates the adaptation of a zooplankton grazer (Daphnia pulicaria) in the wild by integrating population genetics with palaeoecology and exploiting a ‘’natural experiment’’ of 12 environmentally similar lakes exposed to different environmental stressors. This thesis specifically focuses on the introduction of the spiny water flea (Bythotrephes longimanus) in the Canadian Shield and its impacts on Daphnia pulicaria genomics across time and space. Chapter 1 provides an overview of key concepts in limnology and paleoecology, presents the commonly accepted timeline of Bythotrephes invasion of North America, and reviews current knowledge about the genomics and adaptation potential of Daphnia. Chapter 2 applies standard palaeoecological methods, such as high-resolution 210Pb dating and extraction of organic material from lake sediment cores, combined with recently developed whole genome sequencing protocols for individual Daphnia resting embryos. It addresses questions about the predictability and repeatability of native prey responses to novel predation pressure on a phenotypic and genetic level. Chapter 3 re-examines the introduction and spread of Bythotrephes in the Canadian Shield and presents new evidence from microfossils, sediment DNA, and radiocarbon dating to suggest an earlier presence in the continent and raises new questions about the detection of invasive species. Chapter 4 expands on the ecological and genomic datasets generated in previous chapters, in search of common explanatory variables of temporal genomic variation across five lakes. Further, it compares the impact of ‘bottom-up’ (nutrient availability) versus ‘top down’ (predation) effects on the genetic architecture of Daphnia populations during a century of major environmental stress. Chapter 5 discusses the main thesis findings, their ecological significance and implications for conservation, ending with suggestions for further research.