Phylogeny, ecology and taxonomy of systemic pathogens and their relatives in Ajellomycetaceae (Onygenales): Blastomyces, Emergomyces, Emmonsia, Emmonsiellopsis
Why this work is in the frame
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Bibliographic record
Abstract
The family Ajellomycetaceae (Onygenales) includes mammal-associated pathogens within the genera Blastomyces, Emmonsia, Histoplasma and Paracoccidioides, as well as the recently described genera, Emergomyces that causes disease in immunocompromised hosts, and Emmonsiellopsis, known only from soil. To further assess the phylogenetic relationships among and between members of these genera and several previously undescribed species, we sequenced and analyzed the DNA-directed RNA polymerase II (rPB2), translation elongation factor 3-α (TEF3), β-tubulin (TUB2), 28S large subunit rDNA (LSU) and the internal transcribed spacer regions (ITS) in 68 strains, in addition to morphological and physiological investigations. To better understand the thermal dimorphism among these fungi, the dynamic process of transformation from mycelial to yeast-like or adiaspore-like forms was also assessed over a range of temperatures (6–42 °C). Molecular data resolved the relationships and recognized five major well-supported lineages that correspond largely to the genus level. Emmonsia, typified by Emmonsia parva, is a synonym of Blastomyces that also accommodates Blastomyces helicus (formerly Emmonsia helica). Emmonsia crescens is phylogenetically distinct, and found closely related to a single strain from soil without known etiology. Blastomyces silverae, Emergomyces canadensis, Emergomyces europaeus and Emmonsia sola are newly described. Almost all of the taxa are associated with human and animal disease. Emmonsia crescens, B. dermatitidis and B. parvus are prevalently associated with pulmonary disease in humans or animals. Blastomyces helicus, B. percursus, Emergomyces africanus, Es. canadensis, Es. europaeus, Es. orientalis and Es. pasteurianus (formerly Emmonsia pasteuriana) are predominantly found in human hosts with immune disorders; no animal hosts are known for these species except B. helicus.
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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 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| 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