Conflicting phylogenetic signals obscure the taxonomic position of <i>Ferula heuffelii</i> (Apiaceae), a rare Southeast European endemic
Bibliographic record
Abstract
ABSTRACT Ferula heuffelii (Apiaceae) is a rare endemic species of the Balkan Peninsula, with herbarium specimens collected from a few localities, often during the 19th and early 20th centuries. To determine the phylogenetic position of this species within the genus, we extracted DNA from a few fruits collected in the late 19th century and assembled nearly the entire plastid genome and the complete nrDNA cistron from sequence data obtained through genome skimming. These newly acquired markers were integrated into two previously published datasets: the first comprised three plastid and two nuclear markers, while the second included complete plastid genomes. Using maximum likelihood and Bayesian methods, we found that according to the nuclear data, F. heuffelii clustered with a clade containing species with proliferating compound umbels. This modification, also shared by F. heuffelii, involves a new compound umbel developing in place of a central umbellet, thus forming a pseudoverticillate inflorescence and continuing its monopodial growth. However, this relationship was obscured by incongruence between plastid and nuclear datasets, attributed to poor phylogenetic signal and hybridization. Furthermore, the analysis of complete plastid genomes revealed discrepancies between phylogenetic trees constructed from different parts of the plastid genome. Considering these results, along with additional challenges such as unclear species boundaries and misidentifications, we discuss the difficulties in reconstructing the phylogeny of the genus Ferula.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 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".