Phylogenetics of Helotiales and Rhytismatales based on partial small subunit nuclear ribosomal DNA sequences
Bibliographic record
Abstract
The evolutionary sequence leading to the differentiation of ascomatal and ascal types in the Euascomycetes remains poorly understood. To investigate the placement of the inoperculate discomycetes in the phylogeny of Euascomycetes, partial small subunit ribosomal DNA sequences for 36 species placed in Helotiales and Rhytismatales were combined with those of 54 additional species representing the major ascomycete lineages, and two basidiomycetes as outgroups. The apothecial orders Helotiales, Rhytismatales, Pezizales, Caliciales, Lecanorales, and Peltigerales were represented by multiple genera. Maximum parsimony recovered over 100 000 equally most parsimonious trees, with the strict consensus tree collapsing many inoperculate discomycetes into a large Euascomycete polytomy. Weighted parsimony resolved a paraphyletic clade composed of Rhytismatales and Helotiales. Families grouping consistently in the Helotiales/Rhytismatales clade included Bulgariaceae, Helotiaceae, Hemiphacidiaceae, Leotiaceae, Loramycetaceae, Phacidiaceae, Rhytismataceae, Rutstroemiaceae, Sclerotiniaceae, and Thelebolaceae. Orbiliaceae did not group with Helotiales. The small subunit data matrix was more useful for familial relationships in Helotiales and Rhytismatales. Of families represented by multiple taxa, Sclerotiniaceae and Hemiphacidiaceae were monophyletic, Rhytismataceae was paraphyletic, and Helotiaceae and Phacidiaceae were polyphyletic. The placement of several inoperculate discomycete genera with historically problematic ordinal or familial placement based on morphological and developmental features remained equivocal in the small subunit phylogeny. These genera include Cyclaneusma, Darkera, Gremmeniella, Naemacyclus, Phacidium, and Piceomphale. Although further studies are needed, we use the small subunit phylogeny as a framework for discussing the evolution of the ascoma and ascus, the delimitation between Helotiales and Rhytismatales, and certain family concepts within the inoperculate discomycetes.
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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 | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| 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".