Co‐phylogenetic constraints on host breadth within an emerging fungal pathogen complex of global concern
Bibliographic record
Abstract
Abstract Emerging fungal infectious diseases constitute the largest pathogen threat to plants. However, the factors influencing fungal‐plant interactions, host shifts, and the emergence of pathogens on a novel host are still not well understood. Evolutionary relationships among hosts appear to be important, with closely related hosts often sharing pathogens and pests, but we typically lack information on the evolutionary history of the pathogens. Here, we gather over 27,000 sequences to construct a comprehensive phylogenetic tree for Botryosphaeriaceae, a fungal family including many emerging pathogens of global concern, and explore the evolutionary conservatism in fungal‐plant associations across host and pathogen phylogenies. We reveal a significant influence of both phylogenies in constraining fungal‐plant associations. However, we also show that most fungal pathogens are generalists, able to infect multiple hosts, and demonstrate an evolutionary trend toward increased generalism, contrary to theory that suggests that pathogens should evolve toward increased host specialization. We suggest that the anthropogenic movement of plant species and agricultural practices might have allowed some Botryosphaeriaceae to escape phylogenetic constraints on host range via increasing the ecological opportunities for host shifts. Understanding the factors influencing fungal‐plant interaction and host breadth of pathogenic fungi could help identify emerging threats, prevent spillover onto naïve plants, and reduce the risk of further host range expansion.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 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".