A phylogenetic analysis of <i>Bromus</i> (Poaceae: Pooideae: Bromeae) based on nuclear ribosomal and plastid data, with a focus on <i>Bromus</i> sect. <i>Bromus</i>
Bibliographic record
Abstract
To investigate phylogenetic relationships among and within major lineages of Bromus , with focus on Bromus sect. Bromus , we analyzed DNA sequences from two nuclear ribosomal (ITS, ETS) and two plastid ( rpl32-trnL UAG , matK ) regions. We sampled 103 ingroup accessions representing 26 taxa of B . section Bromus and 15 species of other Bromus sections. Our analyses confirm the monophyly of Bromus s.l. and identify incongruence between nuclear ribosomal and plastid data partitions for relationships within and among major Bromus lineages. Results support classification of B. pumilio and B. gracillimus within B . sect. Boissiera and B . sect. Nevskiella , respectively. These species are sister groups and are closely related to B. densus ( B . sect. Mexibromus ) in nrDNA trees and Bromus sect. Ceratochloa in plastid trees. Bromus sect. Bromopsis is paraphyletic. In nrDNA trees, species of Bromus sects. Bromopsis , Ceratochloa , Neobromus , and Genea plus B. rechingeri of B . sect. Bromus form a clade, in which B. tomentellus is sister to a B . sect. Genea – B. rechingeri clade. In the plastid trees, by contrast, B . sect. Bromopsis species except B. tomentosus form a clade, and B. tomentosus is sister to a clade comprising B . sect. Bromus and B . sect. Genea species. Affinities of B. gedrosianus , B. pulchellus , and B. rechingeri (members of the B. pectinatus complex), as well as B. oxyodon and B. sewerzowii , are discordant between nrDNA and plastid trees. We infer these species may have obtained their plastomes via chloroplast capture from species of B . sect. Bromus and B . sect. Genea . Within B . sect. Bromus , B. alopecuros subsp. caroli-henrici , a clade comprising B. hordeaceus and B. interruptus , and B. scoparius are successive sister groups to the rest of the section in the nrDNA phylogeny. Most relationships among the remaining species of B . sect. Bromus are unresolved in the nrDNA and plastid trees. Given these results, we infer that most B . sect. Bromus species likely diversified relatively recently. None of the subdivisional taxa proposed for Bromus sect. Bromus over the last century correspond to natural groups identified in our phylogenetic analyses except for a group including B. hordeaceus and B. interruptus .
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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 | 0.000 |
| 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".