Taxonomy And Phylogenetics Of The Peromyscus Maniculatus Species Group
Bibliographic record
Abstract
This dataset contains the digitized treatments in Plazi based on the original journal article Greenbaum, Ira F., Honeycutt, Rodney L., Chirhart, Scott E. (2019): Taxonomy And Phylogenetics Of The Peromyscus Maniculatus Species Group. Special Publications of the Museum of Texas Tech University 71: 559-575, DOI: 10.5281/zenodo.7221125ABSTRACTAn overview is provided herein of advancements in the species composition and phylogenetics of the Peromyscus maniculatus species group since Carleton’s 1989 review of the genus. These advancements primarily are the result of studies of chromosomal and nucleotide-sequence variation, with most sequence data derived from the mitochondrial genome. Evidence is summarized supporting the conclusion that variation in mitochondrial genes provides consistent and informative details relative to species-level identification and the phylogenetic relationships among major clades of deer mice. Based on studies of the mitochondrial cytochrome- b gene as well as previously published and new sequences of the mitochondrial ND3/ND4/ND4L genes, the number of species in the P. maniculatus group is increased to nine (P. melanotis, P. polionotus, P. keeni, P. arcticus, P. gambelii, P. sejugis, P. sonoriensis, P. labecula, and P. maniculatus). The newly identified species render P. maniculatus as being restricted to the northeastern United States and south-central Canada. The phylogenetic studies provide evidence of a sister-group relationship between the P. leucopus and P. maniculatus species groups and the placement of P. melanotis as basal to other members of the P. maniculatus group. The well-supported clade containing P. keeni and P. gambelii / P. sejugis appears to be best explained as having resulted from independent peripheral isolation. However, the available data fail to resolve the phylogenetic relationship of the clades corresponding to P. maniculatus sensu stricto, P. sonoriensis, P. polionotus, and P. keeni / P. gambelii / P. sejugis, and too little data exist to address the phylogenetic relationships of P. arcticus and P. labecula relative to the other species in the P. maniculatus species group. A more thorough resolution of the systematics of the species in the P. maniculatus group awaits broader and targeted geographic sampling and the inclusion of data from more rapidly evolving nucleotide sequences.
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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 | 0.006 | 0.005 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.012 | 0.004 |
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".