Towards a phylogenetic nomenclature of <i>Tracheophyta</i>
Bibliographic record
Abstract
Phylogenetic definitions are provided for the names of 53 clades of vascular plants. Emphasis has been placed on well‐supported clades that are widely known to non‐specialists and/or have a deep origin within Tracheophyta or Angiospermae . These treatments follow the draft PhyloCode and illustrate the application of phylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy‐based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of the PhyloCode ) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named “ Pan‐X ”, where “ X ” is the name of the crown (e.g., Pan‐Spermatophyta for the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name “ X ” that is based etymologically on an apomorphy is applied to the crown, the name “ Apo‐X ” is applied to the clade for which this trait is synapomorphic (e.g., Apo‐Spermatophyta for the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node‐based and branch‐modified node‐based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of the PhyloCode on real definitions rather than simplified hypothetical ones.
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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 | 0.008 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.006 |
| Science and technology studies | 0.003 | 0.005 |
| Scholarly communication | 0.007 | 0.008 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.002 | 0.009 |
| Insufficient payload (model declined to judge) | 0.008 | 0.009 |
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".