Peer Review #2 of "Tip dating with fossil sites and stratigraphic sequences (v0.1)"
Bibliographic record
Abstract
Tip dating, a method of phylogenetic analysis in which fossils are included as terminals and assigned an age, is becoming increasingly widely used in evolutionary studies.Current implementations of tip dating allow fossil ages to be assigned as a point estimate, or incorporate uncertainty through the use of uniform tip age priors.However, the use of tip age priors has the unwanted effect of decoupling the ages of fossils from the same fossil site.Here we introduce a new Markov Chain Monte Carlo (MCMC) proposal, which allows fossils from the same site to have linked ages, while still incorporating uncertainty in the age of the fossil site itself.We also include an extension, allowing fossil sites to be ordered in a stratigraphic column with age bounds applied only to the top and bottom of the sequence.These MCMC proposals are implemented in a new open-source BEAST2 package, palaeo.We test these new proposals on a dataset of early vertebrate fossils, concentrating on the effects on two sites with multiple acanthodian fossil taxa but wide age uncertainty, the Man On The Hill (MOTH) site from northern Canada, and the Turin Hill site from Scotland, both of Lochkovian (Early Devonian) age.The results show an increased precision of age estimates when fossils have linked tip ages compared to when ages are unlinked, and in this example leads to support for a younger age for the MOTH site compared with the Turin Hill site.There is also a minor effect on the tree topology of acanthodians.These new MCMC proposals should be widely applicable to studies that employ tip dating, particularly when the terminals are coded as individual specimens.
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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 | 0.011 | 0.093 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.006 | 0.004 |
| Science and technology studies | 0.005 | 0.001 |
| Scholarly communication | 0.010 | 0.006 |
| Open science | 0.004 | 0.007 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.570 | 0.425 |
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".