Genomic adaptation to a century of environmental change in zooplankton from the Canadian Shield
Bibliographic record
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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".