Candida albicans phylogenetics: historical context and recent advances
Bibliographic record
Abstract
Candida albicans is a prevalent opportunistic fungal pathogen that typically resides as a commensal in multiple niches in the human body. C. albicans exhibits substantial phenotypic and genotypic diversity, driven by standard mutational events and genomic mechanisms such as loss of heterozygosity, aneuploidy, and a parasexual cycle. For the past 60 years, efforts have been made to characterize intrapopulation diversity to identify C. albicans relatedness groups. The methods used for strain delineation have transitioned from low-resolution phenotypic typing methods to more robust sequence-based approaches, including multilocus sequence typing (MLST) and, more recently, whole-genome sequencing (WGS). MLST provided the first widely adopted framework for phylogenetic classification, distinguishing genetically distinct clusters among C. albicans isolates. However, in recent years, WGS has offered improved resolution, revealing evidence of gene flow and recombination. These methodological advances have also enhanced our understanding of population structure and associated traits, including antifungal resistance and virulence. This review traces the development of methods used to characterize genetic phenotypic and diversity in C. albicans , outlines current common practices in describing its population structure, and highlights opportunities for greater consistency in how phylogenetic clusters are named and defined.
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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 | 0.004 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.006 | 0.009 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".