<i>Pleospora</i>species with<i>Stemphylium</i>anamorphs: a four locus phylogeny resolves new lineages yet does not distinguish among species in the<i>Pleospora herbarum</i>clade
Bibliographic record
Abstract
Stemphylium is a genus of plant pathogens and saprobes in the Pleosporaceae (Pleosporales, Dothideomycetes, Ascomycetes). The teleomorphs of Stemphylium, where known, are in Pleospora, with Pleospora herbarum as the type. The goal of this study was to present a rigorous phylogenetic analysis of the relationships among Stemphylium isolates with particular emphasis on species delimitation in the P. herbarum clade, on possible new species and on the relationship of clades to cultures from type specimens. Our taxon sampling comprised 110 Stemphylium strains collected worldwide from various hosts and DNA sequences from four loci, from the ITS, the protein encoding GPD and EF-1 alpha genes and the intergenic spacer between vmaA and vpsA. A large EF-1 alpha intron delimited by noncanonical splice sites and encoding putative proteins was present in three unrelated isolates and was excluded from analyses. Isolates comprised 23 representatives derived from type strains, compared to type strains or otherwise connected to type material, 40 unnamed strains morphologically similar to the type P. herbarum, four strains from an outbreak of Stemphylium leaf blight of cotton in Brazil and eight strains collected in British Columbia mainly from nonagricultural hosts. Our findings provided strong support for the main groupings of Stemphylium obtained earlier and also revealed six possible new species. Other variation within morphological species might point to additional cryptic species. On the other hand, even with four loci, cultures ex-type of five species including P. herbarum were inseparable. We speculate that being self-fertile the clade including P. herbarum might represent a group of highly inbred, morphologically distinct lineages that have yet to accumulate detectable species-specific sequence variation. The lack of variation in P. herbarum clade contrasts with many other a priori defined morphological species where multigene phylogenetic analyses revealed new cryptic species.
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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 | 0.000 |
| 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 | 0.000 |
| 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".