A Multigene Phylogeny for Oecomys (Rodentia: Cricetidae: Sigmodontinae) with Descriptions of New and Revalidated Taxa and a Partial Species-Group Classification
Bibliographic record
Abstract
We report phylogenetic analyses of a multigene dataset for 24 species of the Neotropical cricetid genus Oecomys, including one new species from western Amazonia (O. hiceae) and a revalidated trans-Andean species (O. trabeatus). In addition, we analyze sequence data from four species that have not previously been included in any molecular analysis (O. flavicans, O. phaeotis, O. speciosus, and O. trinitatis sensu stricto) and from historical specimens of O. concolor (a species represented in previous analyses by sequences of problematic homology). Our results provide strong support for a monophyletic Rutilus Group (including O. hiceae, O. rutilus, O. trabeatus), a Bicolor Group (O. bicolor, O. cleberi, O. nanus, O. jamari, O. phaeotis), and a Mamorae Group (O. franciscorum, O. mamorae). We tentatively recognize two other clades that are less strongly supported by our analytic results but that seem to merit heuristic recognition: a Concolor Group (O. concolor, O. speciosus) and a Trinitatis Group (O. catherinae, O. flavicans, O. matogrossensis, O. rex, O. trinitatis). Future taxonomic progress will require sequence data from additional genes, revisionary studies of still problematic species (e.g., O. bicolor, O. trinitatis), and fresh collections from hitherto poorly surveyed regions.
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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 | 0.003 | 0.002 |
| 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) | 0.003 | 0.001 |
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".