Combining small and large subunit ribosomal DNA genes to resolve relationships among orders of the Rhodymeniophycidae (Rhodophyta): recognition of the Acrosymphytales ord. nov. and Sebdeniales ord. nov.
Bibliographic record
Abstract
Published phylogenies based on nuclear small-subunit (SSU) ribosomal DNA have largely failed to resolve ordinal relationships within the Rhodymeniophycidae. Of the nine orders currently recognized, SSU analyses only consistently resolved an association between the Halymeniales and Rhodymeniales. This situation was confounded by an unexpected association between the Rhodymeniales and Gracilariales shown in published combined SSU + LSU (large subunit ribosomal DNA) phylogenies. To investigate this conundrum further, nuclear SSU and LSU sequences were determined to produce a comprehensive combined data set of 61 ingroup taxa, representing 22 families within the Rhodymeniophycidae, emphasizing disparate lineages of the Gigartinales sensu lato. Molecular phylogenies were constructed from individual gene and combined data sets in an effort to achieve increased ordinal resolution. The new analyses realized little increased resolution among the orders, but they did resolve the conflicting taxonomic affinities of the Rhodymeniales indicating that they ally with the Halymeniales and not the Gracilariales. The latter order was affiliated to the Nemastomatales in all SSU-only analyses, as well as for SSU + LSU combined Bayesian results with the covarion option invoked. In addition, the resulting phylogenetic hypotheses have shed light on the taxonomic associations of a few rogue families of the Gigartinales sensu lato. Notably, the Acrosymphytaceae failed to join other families of the Gigartinales and we therefore propose the Acrosymphytales ord. nov. to accommodate this family. The Sebdeniaceae was generally weakly allied as sister to the Rhodymeniales rather than with the Halymeniales where it is currently placed. Owing to its consistently equivocal placement in contemporary molecular analyses, as well as a suite of anatomical characters intermediate between the Halymeniales sensu stricto and Rhodymeniales, we here propose the Sebdeniales ord. nov.
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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 | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| 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 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".