Systematics of the <i>Phialophora verrucosa</i> complex: new insights from analyses of β-tubulin, large subunit nuclear rDNA and ITS sequencesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Bibliographic record
Abstract
Phialophora Medlar, as defined currently, is a genus encompassing melanized, anamorphic Ascomycota that produce one-celled conidia from phialides with distinct, darkened collarettes. The type species, Phialophora verrucosa Medlar, is closely related to Phialophora americana (Nannf.) S. Hughes, the anamorph of Capronia semiimmersa (Candoussau & Sulmont) Untereiner & Naveau (Herpotrichiellaceae, Chaetothyriales). To confirm that P. americana and P. verrucosa are distinct taxa, and to examine their phylogenetic relationships to species of Capronia and other representatives of the Chaetothyriales, we sequenced portions of the β-tubulin gene and nuclear ribosomal RNA cistron (ITS and LSU rDNA). We also compared isolates of P. americana grown on a number of media. Isolates of C. semiimmersa, Capronia svrcekiana Réblová, and P. americana produced phialides bearing deep, vase-shaped collarettes and formed a strongly supported clade that did not include P. verrucosa in a phylogeny inferred from the combined β-tubulin–ITS–LSU dataset. Capronia svrcekiana was found to be conspecific with C. semiimmersa based on the comparison of cultural, micromorphological, and molecular characters. In the LSU phylogeny, three recently described species of Phialophora ( Phialophora europaea de Hoog et al., Phialophora reptans de Hoog, and Phialophora sessilis de Hoog) were grouped outside of the clade containing sampled members of the Herpotrichiellaceae. While the position of these species in the Chaetothyriales remained unresolved, it was evident that P. europaea, P. reptans, and P. sessilis are not members of the P. verrucosa complex.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".