The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates

@article{Marjanovi2019TheMO,
  title={The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates},
  author={D. Marjanovi{\'c}},
  journal={bioRxiv},
  year={2019}
}
Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by… Expand
Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods
  • S. Guindon
  • Computer Science, Medicine
  • Frontiers in Genetics
  • 2020
TLDR
It is argued that the fossilized birth-death process relies on assumptions about the mechanisms underlying fossilization and the data collection process that may negatively impact the date estimates, and node-dating approaches make better use of the data available, even though they rest on paleontologists' intervention to prepare raw fossil data. Expand
The First Age of Reptiles? Comparing Reptile and Synapsid Diversity, and the Influence of Lagerstätten, During the Carboniferous and Early Permian
Terrestrial ecosystems during the Pennsylvanian (late Carboniferous) and Cisuralian (early Permian) are usually described in the literature as being dominated by synapsids, the mammal-line amniotes.Expand
Iguanian lizards from the Split Rock Formation, Wyoming: exploring the modernization of the North American lizard fauna
Terrestrial ecosystems in North America changed substantially during the Neogene. Previous authors have documented changes in plants and mammals but squamates have received comparatively littleExpand
Giant lungfish genome elucidates the conquest of land by vertebrates
TLDR
The chromosome-quality genome of the Australian lungfish is determined, known to have the largest genome of any animal, and phylogenomic analyses confirm that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods. Expand
The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates
TLDR
This work reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results. Expand

References

SHOWING 1-10 OF 777 REFERENCES
Fossils, molecules, divergence times, and the origin of lissamphibians.
A review of the paleontological literature shows that the early dates of appearance of Lissamphibia recently inferred from molecular data do not favor an origin of extant amphibians fromExpand
An updated paleontological timetree of lissamphibians, with comments on the anatomy of Jurassic crown-group salamanders (Urodela)
TLDR
The conclusion that the fossil record of Lissamphibia is dense enough to provide reliable calibration constraints for molecular divergence dating is upheld and some of the divergence dates the authors infer from the tree are up to 15 Ma younger than previously published. Expand
Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses.
TLDR
Predictive models are developed that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa can be predicted to some extent before any phylogenetic analysis. Expand
Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction
TLDR
The completeness of the eutherian fossil record through geological time is evaluated and supports the “explosivemodel” of early placental evolution, whereby placentalmammals originated around the time of the K/Pg boundary and diversified soon after. Expand
Best Practices for Justifying Fossil Calibrations
TLDR
A specimen-based protocol for selecting and documenting relevant fossils is presented and future directions for evaluating and utilizing phylogenetic and temporal data from the fossil record are discussed, to establish the best practices for justifying fossils used for the temporal calibration of molecular phylogenies. Expand
Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses
TLDR
Predictive models are developed that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any analysis. Expand
Phylogenetic relationships of the Cretaceous frog Beelzebufo from Madagascar and the placement of fossil constraints based on temporal and phylogenetic evidence
TLDR
A metric is derived, Δt, to quantify temporal divergence among chronograms and finds that errors resulting from mis‐specified calibrations are localized when additional nodes throughout the tree are properly calibrated. Expand
Phylogeny and systematic history of early salamanders
TLDR
While this study has not resolved the relationships between salamander families it has allowed a deeper understanding of the data, and assesses the confidence with which the placement of key fossils can be made in a new way. Expand
Effects of phylogenetic uncertainty on fossil identification illustrated by a new and enigmatic Eocene iguanian
TLDR
A skull fossil of a new pleurodontan lizard taxon is described from the Eocene deposits of the Willwood Formation, Wyoming, and used as a case-study to explore the effects of phylogenetic uncertainty on fossil identification. Expand
Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography
  • D. Cannatella
  • Medicine, Biology
  • Cytogenetic and Genome Research
  • 2015
TLDR
The estimates of divergence times indicate that overwater dispersal, rather than vicariance due to the splitting of Africa and South America, may explain the presence of Xenopus in Africa and its closest fossil relatives in South America. Expand
...
1
2
3
4
5
...