Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA<i>psbI</i>–<i>5′trnK</i><sup>(UUU)</sup>sequences, with emphasis on the North American Endemics clade
Bibliographic record
Abstract
Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU)and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU)and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU)intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.
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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".