Phylogenetic relationships of Echeveria (Crassulaceae) and related genera from Mexico, based on three DNA barcoding loci
Bibliographic record
Abstract
Mexico is considered as diversification and endemism center of the genus Echeveria. Previous tree inference studies have shown the genus to be non-monophyletic in relation to other genera, but sampling for Echeveria has been poor, and has not allowed to understand the relationships within the genus. In this work, Bayesian and maximum likelihood phylogenetic analysis were performed, using a combined standard DNA barcoding loci matrix (rbcL, matK and ITS2) and GenBank ITS2 accessions for Graptopetalum, some Sedum and few Echeveria taxa. The selection of taxa encompasses all current infrageneric categories of the genus Echeveria, as well as species from genera previously associated with it. The inferred consensus trees suggested that Echeveria is paraphyletic. Instead, four main clades were retrieved within the “Echeveria group”: Clade I includes exclusively Pachyphytum species. Clade II is formed by the majority of series Urbiniae; Clade III encompasses series Chloranthae, Ciliatae, Echeveria, Mucronatae, Nudae, Racemosae, Thyrsiflorae, Pachyphytum cuicatecananum and Thompsonella; Clade IV contains series Angulatae, Gibbiflorae, Occidentales, Pruinosae, Secundae, some Urbiniae species, Valvatae. genera Cremnophila, Graptopetalum and Reidmorania. Pachyphytum and Thompsonella were retrieved as monophyletic groups, but the first outside Echeveria while the latter inside. Results of our study suggest that Echeveria and the Echeveria Group require a redefinition.
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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 | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".