A Taxonomic and Phylogenetic Investigation of Conifer Endophytes of Eastern Canada
Bibliographic record
Abstract
Research interest in endophytic fungi has increased substantially, yet is the current research paradigm capable of addressing fundamental taxonomic questions?More than half of the ca.30,000 endophyte sequences accessioned into GenBank are unidentified to the family rank and this disparity grows every year.The problems with identifying endophytes are a lack of taxonomically informative morphological characters in vitro and a paucity of relevant DNA reference sequences.A study involving ca.2,600 Picea endophyte cultures from the Acadian Forest Region in Eastern Canada sought to address these taxonomic issues with a combined approach involving molecular methods, classical taxonomy, and field work.It was hypothesized that foliar endophytes have complex life histories involving saprotrophic reproductive stages associated with the host foliage, alternative host substrates, or alternate hosts.Based on inferences from phylogenetic data, new field collections or herbarium specimens were sought to connect unidentifiable endophytes with identifiable material.Approximately 40 endophytes were connected with identifiable material, which resulted in the description of four novel genera and 21 novel species and substantial progress in endophyte taxonomy.Endophytes were connected with saprotrophs and exhibited reproductive stages on non-foliar tissues or different hosts.These results provide support for the foraging ascomycete hypothesis, postulating that for some fungi endophytism is a secondary life history strategy that facilitates persistence and dispersal in the absence of a primary host.This thesis provides an alternate approach to identifying endophytes by considering the whole fungus interacting within its natural habitat.iii
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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 | 0.003 | 0.004 |
| Science and technology studies | 0.005 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 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".