Phylogenetic position of a Pacific Northwest North American endemic cyanolichen, <b><i>Nephroma occultum</i></b> (Ascomycota, <b><i>Peltigerales</i></b>)
Why this work is in the frame
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Bibliographic record
Abstract
Nephroma occultum is a COSEWIC listed cyanolichen of “Special Concern”. It is endemic to old-growth cedar-hemlock forests in western North America. This is the first study to place N. occultum into a phylogenetic framework using nucleotide sequence and secondary structure data. It also addresses the phylogenetic relationship between N. occultum and N. arcticum . Analysis of fungal Internal Transcribed Spacer (ITS) ribosomal DNA (rDNA) produced four major clades. The cyanobacterial transfer RNA Leu intron (tRNA Leu ) from N. occultum was separated from that of N. isidiosum and fell between the Eurasian and North American epiphytic taxa. Examination of length and complexity of the folded secondary structures revealed different trends in the ITS1 and ITS2 rRNA regions. Even though N. occultum is endemic to North America, it seems more closely related to South American temperate rainforest species than to the sympatric N. arcticum . Nephroma occultum is alone among the studied species of Peltigerales in having an exceptionally long ITS1 region, and a different tRNA Leu intron DNA sequence of the photobiont suggesting association with a unique genotype of Nostoc . It may be argued that the fitness of N. occultum may be influenced by the complex ITS1 RNA structure, a unique photobiont genotype undergoing a genetic bottleneck, no sexual reproduction to generate variation, and the inability to associate with different photobionts to adapt to changing habitats.
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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) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 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 it