Monophyly of some North American species of<i>Ramalina</i>and inferred polyketide synthase gene function
Bibliographic record
Abstract
Ramalina thrausta (Ach.) Nyl., Ramalina roesleri (Hochst. Ex Schaerer) Hue, and Ramalina dilacerata (Hoffm.) Hoffm. are three common North American species that have not been placed in a phylogeny and are sympatric in their distribution leading to uncertainty about monophyly. Species characters include secondary metabolites (polyketides) in Ramalina that may be both hereditary and influenced by environmental conditions, but little is known about the function of polyketide synthase (PKS) genes. The main goal of this study was to examine the monophyly among some of the more common species in northern North America and secondarily to compare potential PKS gene function with the phylogeny. Nucleotide sequences of two genes, the internal transcribed spacer 1 of ribosomal DNA and the mitochondrial small subunit, were used to infer a phylogeny. Gene function was inferred from three PKS genes by the ratio of nonsynonymous to synonymous substitutions (d N :d S ) ratios. Although seven species of Ramalina are highly supported in monophyletic clades, two other species form clusters with low support: Ramalina americana Hale is paraphyletic, and Ramalina pollinaria (Westr.) Ach. is polyphyletic. Three PKS genes were inferred to be functional but were not present in all samples. Functional PKS genes could enable adaptation to new habitats and facilitate species diversification.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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) | 0.000 | 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 teacher head, 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".