Umbilicaria phaea var. coccinea: conservation status, variety rank, and secondary chemistry
Bibliographic record
Abstract
Originally described from a single collection in northern California, Umbilicaria phaea var. coccinea has since been reported from additional sites in California, Oregon and Washington. Although relatively rare in all three states, there is currently no conservation status for U. phaea var. coccinea in California. Developing conservation strategies and status ranks requires a sound understanding of distribution, frequency, habitat requirements and taxonomic placement. Therefore, we evaluated distributions and constructed climate envelope models for both varieties of U. phaea. Umbilicaria phaea var. coccinea appears to be restricted to relatively small habitats within the range of U. phaea var. phaea and is only locally common in portions of the Klamath River watershed. To assess evolutionary relationships between the varieties, we evaluated four molecular loci: ITS2, LSU, Mcm7, and mtSSU. A combined phylogeny using maximum-likelihood and Bayesian inference indicated that U. phaea is monophyletic. Within the U. phaea clade, var. coccinea and var. phaea do not form mutually exclusive, monophyletic clades; instead, individuals are intermixed. Based on variation in pigment production, morphology, and geographic distribution, we recommend continued designation of U. phaea var. coccinea as a variety. To better understand the chemical diversity within U. phaea, we compared qualitative differences between secondary metabolite profiles of U. phaea var. phaea and U. phaea var. coccinea acetone extracts using ultraperformance-liquid chromatography high resolution tandem mass spectrometry in negative ion mode. UV spectroscopy, thin-layer chromatography and chemical spot testing were used to further characterize the compounds present. Overall, ten compounds were detected in extracts of U. phaea var. phaea and U. phaea var. coccinea. Five previously known chemical substances were identified in both U. phaea varieties including: orsellinic acid, lecanoric acid, hiascic acid, gyrophoric acid, and orsellinylgyrophorate, along with four unknown metabolites. One additional unknown substance whose chemical properties are consistent with a polyhydroxylated anthraquinone pigment was detected only in U. phaea var. coccinea. Given its rarity, chemical uniqueness, and distinct ecological association, U. phaea var. coccinea warrants a protected status throughout its range.
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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 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".