The Relationships of Major Lineages within Peromyscine Rodents: A Molecular Phylogenetic Hypothesis and Systematic Reappraisal
Bibliographic record
Abstract
Peromyscine mice of the cricetid subfamily Neotominae comprise the most common and speciose assemblage of North American rodents. The composition and phylogenetic relationships within this group have been addressed using multiple character systems but remain unresolved, particularly the branching pattern of deeply rooted lineages. The relationships and status of several taxa formerly included within Peromyscus also are controversial. We present a new phylogenetic hypothesis based on combined mitochondrial and nuclear sequences using cytochrome b, interphotoreceptor retinoid-binding protein, and growth hormone receptor gene sequences, and include all major peromyscine lineages. Bayesian and parsimony approaches recover a congruent, well-resolved phylogeny, wherein Peromyscus forms a monophyletic assemblage only if a number of putative genera are included within it. Onychomys rather than Reithrodontomys is the sister taxon to Peromyscus (within which are included Habromys, Osgoodomys, Megadontomys, Podomys, and Neotomodon). Reithrodontomys in turn is the sister taxon to Isthmomys, and these 2 genera are the nearest outlier to Onychomys plus an expanded concept of Peromyscus, consistent with the recent recognition of this entire group as the tribe Reithrodontomyini. The Baiomyini, Ochrotomyini, and Neotoma (Neotomini) appear as successive outgroups to this clade: Based on these results, we present a systematic review of higher-level relationships among peromyscine rodents.
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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 | 0.001 | 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 | 0.003 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.001 |
| 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".