Phylogeographic and Phylogenetic Exploration of <i>Plethodon</i> (Plethodontidae, Caudata) Salamanders in the Pacific Northwest
Bibliographic record
Abstract
Genetic studies of amphibians often reveal substantial population structure due to either historical demographics from changing climate and geographic features over varying timeframes. Eight species of terrestrial salamanders (Family: Plethodontidae, Genus: Plethodon) reside in forests of the Pacific Northwest (PNW). Plethodon vehiculum is the most widespread and abundant terrestrial salamander in the PNW yet evolutionary studies are lacking. Using mitochondrial DNA (mtDNA) sequence data (D-loop and cytb) questions regarding the phylogeography of P. vehiculum and phylogenetics of western Plethodons are explored. Two major clades were defined in P. vehiculum, a southern clade in the Klamath-Siskiyou region and a northern clade ranging from northern Oregon to British Columbia using parsimony and maximum likelihood trees and a haplotype network. High divergence levels between the north and south clades are observed warranting further investigation into the southern clade's unique evolutionary trajectory. The northern populations were not highly differentiated with high levels of haplotype sharing, not common in other terrestrial salamander species. A large recent range expansion or high habitat connectivity for these salamanders is suggested. The Columbia River did not act as barrier to dispersal in this species, however, Vancouver Island and the population of Washington's Olympic Peninsula revealed unique haplotypes only to those areas, due to the presence of geographic barriers to dispersal and/or multiple glacial refugia. The D-loop and cytb provided evidence for recent range expansion in the northern clade. This was the first study to incorporate all western Plethodon salamanders in a phylogenetic study. Parsimony and maximum likelihood methods offered strong support for recognized relationships among western Plethodons, however relationships between the major groups remain unhighly supported. Lack of genetic diversity in the mtDNA cytb gene in P. vehiculum is highly inconsistent with other Plethodon salamanders and highlights the importance of understanding mtDNA evolution in ectotherms. Divergence measures were used to estimate divergence times among species, dating all speciation before the Pleistocene glaciations. The southern OR clade of P. vehiculum was dated to have been separated from the northern clade at the start of the Pleistocene. The deep phylogeographic break here justifies the possibility of reclassification of the southern clade.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".