The molecular phylogeny of the order Acipenseriformes revisited
Bibliographic record
Abstract
As evolutionary relationships within the order Acipenseriformes are not well understood and some classifications are currently controversial, the study of evolutionary relationships, especially based on genetic data, has received much recent attention. In this reanalysis we present a nearly complete proposed phylogeny of the order, including 25 species, based on the maximum likelihood analysis of combined DNA sequence data (4406 base pairs) from five mitochondrial genes sequenced in our laboratories (cytochrome b, 12S rRNA, cytochrome c oxidase subunit II, tRNAAsp and tRNAPhe) and three mitochondrial gene regions sequenced by Birstein et al. (2002) (16S rRNA, NADH5 and control region). Examination of the molecular phylogeny using either maximum likelihood, Bayesian analysis, maximum parsimony or neighbor-joining leads to the following conclusions: (i) the two species of paddlefish do form a clade; (ii) the most basal position within the Acipenseridae remains unresolved, held either by the genus Scaphirhynchus or by the clade containing Acipenser oxyrinchus and A. sturio; (iii) Huso is not monophyletic, with the two species of Huso found embedded separately within the genus Acipenser; (iv) A. sinensis and A. dabryanus are confirmed as closely related; (v) the previously described Atlantic-Pacific subdivision within the Acipenser/Huso complex is supported and (vi) the unexpected placement of Pseudoscaphirhynchus kaufmanni within Acipenser is supported by this analysis. These results offer further evidence that some revision of acipenseriform classification may be needed to accurately inform conservation efforts and that future phylogenetic studies of this group should focus on the analysis of nuclear genes.
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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 | 0.001 |
| 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 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| 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".