Phylogeny of <i>Opuntia</i> s.s. (Cactaceae): Clade delineation, geographic origins, and reticulate evolution
Bibliographic record
Abstract
PREMISE OF THE STUDY: The opuntias (nopales, prickly pears) are not only culturally, ecologically, economically, and medicinally important, but are renowned for their taxonomic difficulty due to interspecific hybridization, polyploidy, and morphological variability. Evolutionary relationships in these stem succulents have been insufficiently studied; thus, delimitation of Opuntia s.s. and major subclades, as well as the biogeographic history of this enigmatic group, remain unresolved. METHODS: We sequenced the plastid intergenic spacers atpB-rbcL, ndhF-rpl32, psbJ-petA, and trnL-trnF, the plastid genes matK and ycf1, the nuclear gene ppc, and ITS to reconstruct the phylogeny of tribe Opuntieae, including Opuntia s.s. We used phylogenetic hypotheses to infer the biogeographic history, divergence times, and potential reticulate evolution of Opuntieae. KEY RESULTS: Within Opuntieae, a clade of Tacinga, Opuntia lilae, Brasiliopuntia, and O. schickendantzii is sister to a well-supported Opuntia s.s., which includes Nopalea. Opuntia s.s. originated in southwestern South America (SA) and then expanded to the Central Andean Valleys and the desert region of western North America (NA). Two major clades evolved in NA, which subsequently diversified into eight subclades. These expanded north to Canada and south to Central America and the Caribbean, eventually returning back to SA primarily via allopolyploid taxa. Dating approaches suggest that most of the major subclades in Opuntia s.s. originated during the Pliocene. CONCLUSIONS: Opuntia s.s. is a well-supported clade that includes Nopalea. The clade originated in southwestern SA, but the NA radiation was the most extensive, resulting in broad morphological diversity and frequent species formation through reticulate evolution and polyploidy.
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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 | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| 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".