Revisiting phylogenetic relationships in Phoradendreae (Viscaceae): utility of the <i>trnL-F</i> region of chloroplast DNA and presence of a homoplasious inversion in the intergenic spacer
Bibliographic record
Abstract
The utility of the trnL-F region of the chloroplast DNA for inferring relationships in 26 taxa in the mistletoe tribe Phoradendreae (Viscaceae) was compared with that of sequences from three regions of the nuclear ribosomal DNA (nrDNA). Chloroplast- and nuclear-inferred phylogenies generally were congruent based on maximum parsimony analysis of nucleotide substitution data. Results suggested that the intron and intergenic spacer of the chloroplast partition were not sufficiently variable to resolve phylogenetic relationships among either close relatives or more distantly related species. The distribution of insertions and deletions generally supported the phylogeny inferred from nucleotide substitution data. However, presence or absence of a 59-nucleotide inversion in the trnL-F intergenic spacer of eight Phoradendron species showed no agreement with the topology inferred from molecular and morphological data. Combined analyses of the nuclear partitions and the chloroplast region (with the homoplasious inversion inserted in reverse orientation) provided strong support for P. californicum as sister to a clade uniting North American species and not as sister to a clade comprising more tropical species. Consistent with results from previous studies using nrDNA, a lineage in the Phoradendron leucarpum complex (comprising subsp. leucarpum and macrophyllum) was strongly supported, but subspecies tomentosum was not confidently placed.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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) | 0.000 | 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 teacher head, 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".