Testing generic limits in Cercidoideae (Leguminosae): Insights from plastid and duplicated nuclear gene sequences
Bibliographic record
Abstract
Abstract Reconstructing the phylogenetic history of species in large taxonomic groups remains a challenge despite ever increasing access to molecular data. In subfamily Cercidoideae (Leguminosae), the large pantropicalBauhinias.l. (~380 spp.) is never supported as monophyletic, but the generic boundaries and the number of genera that should be recognised remains a challenging taxonomic and phylogenetic question. Here we reconstruct the phylogeny ofBauhinias.l. and related genera in the subfamily using sequences obtained from five loci (matK,trnL‐F,Leafy, and two previously undetected duplicate copies ofLegcyc), which we analyse individually and in a concatenated matrix (excludingLeafy). The individual and concatenated analyses generally support two distinct lineages inBauhinias.l.: (1) the Bauhinia clade, containingBauhinias.str.,Brenierea, andPiliostigma; and (2) the Phanera clade, containingBarklya,Cheniella,Gigasiphon,Lasiobema,Lysiphyllum,Phaneras.str.,Schnella, andTylosema. Based on our analyses, we recognise 14 genera in Cercidoideae. We resurrect the genusTournayafromGigasiphon, and synonymise the Asian segregate genusLasiobemaback intoPhaneras.str. Our analyses reveal a clear gene duplication event inCYCLOIDEAthat is shared by all Cercidoideae excluding the sister lineage to the subfamily,Cercis, supporting recent hypotheses for a whole genome duplication in all Cercidoideae except this genus.
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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 | 0.001 | 0.004 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".