Fungal phylogenies based on mitogenomes and a study of novel introns in the cob and cox3 genes of Ophiostoma ips
Bibliographic record
Abstract
Fungi are a diverse group of organisms with complex mitochondrial genomes and poorly resolved taxonomic schemes. This study examined the utility of concatenated mitochondrial amino acid sequences for inferring fungal phylogenies. Phylogenetic trees generated, supported existing taxonomic proposals based on the analysis of nuclear genes. This study also examined complex introns within Ophiostoma ips strains embedded in the cob and cox3 genes. Fifty-six strains were examined and 11 were selected for sequence analysis. The O. ips cob-490 intron was noted to be composed of three components, two group I intron are situated side by side and one group II intron is nested within the first group I intron. The cox3-640 intron was noted to be a side-by-side twintron composed of two group I introns located next to each other. These introns in part demonstrate why fungal mtDNAs are variable in size and complex in their architecture.
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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 | 0.000 | 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".