Molecular clocks keep dispersal hypotheses afloat: evidence for trans‐Atlantic rafting by rodents
Bibliographic record
Abstract
Abstract Aim In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time‐frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the African and South American continents has been an irreconcilable controversy for evolutionary biologists, presenting enigmas for both Gondwanan vicariance and Late Eocene dispersal hypotheses. In an attempt to resolve this discordance, we aim to provide a more robust phylogenetic hypothesis and improve divergence‐date estimates, which are essential to assessing the null hypothesis of vicariance biogeography. Location The primary centres of distribution are in Africa and South America. Methods We implemented parsimony, maximum‐likelihood and Bayesian methods to generate a phylogeny of 37 hystricognath taxa, the most comprehensive taxonomic sampling of this group to date, on the basis of two nuclear gene regions. To increase phylogenetic resolution at the basal nodes, these data were combined with previously published data for six additional nuclear gene regions. Divergence dates were estimated using two relaxed‐molecular‐clock methods, Bayesian multidivtime and nonparametric rate smoothing. Results Our data do not support reciprocal monophyly of African and South American lineages. Indeed, Old World porcupines (i.e. Hystricomorpha) appear to be more closely related to New World lineages (i.e. Caviomorpha) than to other Old World families (i.e. Bathyergidae, Petromuridae and Thryonomyidae). The divergence between the monophyletic assemblage of South American lineages and its Old World ancestor was estimated to have occurred c . 50 Ma. Main conclusions Our phylogenetic hypothesis and divergence‐date estimates are strongly at odds with Gondwanan‐vicariance isolating mechanisms. In contrast, our data suggest that transoceanic dispersal has played a significant role in governing the contemporary distribution of hystricognath rodents. Molecular‐clock analyses imply a trans‐Tethys dispersal event, broadly confined to the Late Cretaceous, and trans‐Atlantic dispersal within the Early Eocene. Our analyses also imply that the use of the oldest known South American rodent fossil as a calibration point has biased molecular‐clock inferences.
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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 | 0.004 |
| 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 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".