<i>Cortinarius</i> species diversity in British Columbia and molecular phylogenetic comparison with European specimen sequences
Bibliographic record
Abstract
Throughout the world, the diversity of fungi remains poorly characterized and Cortinarius is a classical example of a difficult, species-rich, and under-researched mushroom genus. Here, we sequenced and analyzed ribosomal internal transcribed spacer (ITS) sequence barcodes from herbarium specimens to improve understanding of Cortinarius species diversity in British Columbia (B.C.), Canada. Starting with 962 specimen sequences, 617 from B.C. herbaria, we present a maximum likelihood tree showing 179 putative Cortinarius species in British Columbia. As a working definition, we considered a “species” to be a monophyletic clade that included a reliably identified reference sequence, with a maximum of 3% ITS sequence variation. If no reference sequence was available, “species” were groups sharing 97% or more sequence identity. By these criteria, 110 putative B.C. species matched European species and 12 B.C. species matched species exclusively found in the Americas. Of the 56 B.C. species that did not match an identified reference sequence, some may be new to science, while others likely represent described species without available sequences. By depositing sequences from B.C. specimens into GenBank and BOLD, and by providing our alignment to TreeBASE, we have supplied the resources necessary to improve accuracy in identifications of Cortinarius in future systematic and ecological studies.
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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 | 0.004 | 0.005 |
| 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) | 0.002 | 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".