Unrooted Maximum Likelihood phylogenetic analysis of the concatenated SCAR-MLST dataset.
Bibliographic record
Abstract
<p>The STs corresponding to haplotypes H17, H24, H27 and H28, being the ancestral lineages in the coalescence gene genealogy analysis, were found to be the most basal lineages when rooted with <i>C. gattii</i> AFLP4. Populations are indicated as AFR (Africa), AUS (Australasia), EUR (Europe), NA (North America) and SA (South America), followed by symbols indicating clinical (), environmental (♣) and/or veterinary (•) strains within the given ST. The most ancestral lineage H17 is indicated by a tree to highlight its environmental origin from a tree in pristine Amazon rainforest in Northern Brazil. STs that fell into H01 as the major genotype AFLP6A/VGIIa Vancouver Island outbreak lineage, H02 as the case cluster of <i>C. gattii</i> infections among psittacine birds in Brazil, H03 the minor genotype Vancouver Island outbreak lineage (ST4 and ST5), and the recently emerged genotype AFLP6C/VGIIc outbreak in the Pacific Northwest (ST39) are indicated with symbols referring to their respective origin (e.g. human referring to human infections, cat representing veterinary cases, dolphin representing infections among sea animals) (Fig. 1; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone-0071148-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071148#pone.0071148.s009" target="_blank">S3</a>). Bootstrap values are given for branches that are highly supported (≥75).</p>
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.460 | 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".