A phylogeny of the genus <i>Agaricus</i> based on mitochondrial <i>atp</i> 6 sequences
Bibliographic record
Abstract
The genus Agaricus includes the most economically-important, commercially-cultivated mushroom in the world, A. bisporus. Effective efforts to improve A. bisporus through breeding will require a greater understanding of the evolutionary relationships between A. bisporus and other Agaricus species. We present here the complete mitochondrial atp6 gene of A. bitorquis and amplified homologues from 9 other species of Agaricus, including 6 different isolates of A. bisporus. Unexpectedly, only 2 variants of atp6 were found among the 6 isolates of A. bisporus, which had been chosen to represent mitochondrial types thought to be highly divergent based on RFLP data. Although interspecific variation was high, parsimony and maximum likelihood analyses resulted in identical phylogenetic trees for the genus: A. bisporus, A. subfloccosus and A. subperonatus were tightly clustered as a single subgroup, whereas the remaining species were highly divergent. The species representatives with the closest proximity to the A. bisporus cluster were A. bitorquis and A. campestris, which is in agreement with published phylogenies derived from nuclear sequence data. Incongruency between this mitochondrial gene-based phylogeny and a phylogeny of linear mitochondrial plasmids found in these same species indicates separate evolutionary histories for the plasmids and their host mitochondria.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".