Exploring criteria for constructing suprageneric classifications of fungi in the genomic era: a case study of suborders Agaricineae, Pluteineae, and Tricholomatineae (Agaricales)
Bibliographic record
Abstract
The burgeoning accumulation of genomic data in recent years has revolutionized our understanding of fungal phylogenies and classifications. However, the genomic era also brings new challenges, as phylogenetic incongruences make the appearance of monophyly in some phylogenetic trees questionable. Existing criteria for constructing taxonomic systems, such as diagnostic characters and divergence time, become insufficient to address this challenge. Through order-level analyses of genomic data of the Subkingdom Dikarya within the Kingdom Fungi , we introduce the extended quadripartition internode certainty (EQP-IC) value as a novel criterion for constructing high-level fungal classifications, with a recommended threshold of 0.1 for each taxonomic rank. Suprageneric taxa with an EQP-IC value exceeding 0.1 exhibit reduced topological variation, suggesting a stronger correspondence with natural taxonomic category. This new criterion was also put into practice to investigate the derived suborders of mushroom-forming Agaricales , including three suborders, Agaricineae , Pluteineae , and Tricholomatineae (APT), that had been long-standing problems in phylogenetic analyses. In total, 142 genomes, including 64 newly generated ones, were utilized to reconstruct the phylogenetic relationships and delve into the phylogenetic incongruencies and evolutionary histories of APT. Our data suggested widespread and high-level incomplete lineage sorting (ILS) and introgression/hybridization (IH) present among suborders within the APT. Therefore, a dichotomous phylogenetic tree may not reflect the real relationships among the clades within the APT. Instead, their natural relationships may be reticulate. Three newly named suborders, Amanitineae , Macrocystidiineae , and Omphalinineae are added to the clade including APT. The new combination Baisuzhenia humphreyi , new genus Baisuzhenia , new family Baisuzheniaceae , and new suborder Baisuzheniineae are proposed to accommodate Stereopsis humphreyi , which shows an independent, but close relationship, with the clade formed by the six above-mentioned derived suborders of Agaricales .
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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 | 0.002 | 0.007 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.003 | 0.003 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".