The evolution of methods for establishing evolutionary timescales
- Environmental Science, GeographyPhilosophical Transactions of the Royal Society B: Biological Sciences
The utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record is discussed, including node-calibrations where lineage divergence times are constrained using probability densities and tip-cal calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata.
Tips and nodes are complementary not competing approaches to the calibration of molecular clocks
- GeographyBiology Letters
It is shown that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages.
Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference
- Environmental Science, GeographyFrontiers in Ecology and Evolution
Time calibrated trees are challenging to estimate for many extinct groups of species due to the incompleteness of the rock and fossil records. Additionally, the precise age of a sample is typically…
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales
- Biology, Environmental ScienceCurrent Biology
Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes
- Environmental SciencebioRxiv
A flexible new approach to Bayesian node dating that combines advantages of traditional node dating and the fossilized birth-death model is developed, and reliable age estimates that are robust to model violation are found.
The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates
- Environmental Science, GeographyPalaeontology
The molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied…
Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes.
- Environmental Science, BiologySystematic biology
This work develops a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model, and defines calibration densities on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades.
Dating placentalia: Morphological clocks fail to close the molecular fossil gap
- Environmental ScienceEvolution; international journal of organic evolution
The results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data, and that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution.
Bayesian Phylogenetic Estimation of Clade Ages Supports Trans‐Atlantic Dispersal of Cichlid Fishes
- Environmental ScienceSystematic biology
A flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model is developed, and calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades.
Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process
It is found that including all relevant fossils without pruning off those inappropriate for the FBD process can lead to underestimation of divergence times, and the interplay of taxon-sampling density and other factors is highlighted.
SHOWING 1-10 OF 259 REFERENCES
Molecular timescales and the fossil record: a paleontological perspective.
- Geography, Environmental ScienceTrends in genetics : TIG
The fossilized birth–death process for coherent calibration of divergence-time estimates
- Environmental ScienceProceedings of the National Academy of Sciences
The fossilized birth–death process is introduced—a fossil calibration method that unifies extinct and extant species with a single macroevolutionary model, eliminating the need for ad hoc calibration priors and yielding more accurate node age estimates while providing a coherent measure of statistical uncertainty.
Calibrating and constraining molecular clocks
In explaining the role of fossils in establishing timescales, the historical sequ ence in which key observations were made is reviewed, and a list of 63 key dates is presented, with thorough evidence and error expressions, for a wide range of organisms.
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
- Biology, GeographyProceedings of the Royal Society B: Biological Sciences
A powerful Bayesian method is used to analyse 36 nuclear genomes and 274 mitochondrial genomes to reject a pre K–Pg model of placental ordinal diversification, and it is suggested other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach.
Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.
- Environmental Science, GeographySystematic biology
This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.
Best Practices for Justifying Fossil Calibrations
- Environmental ScienceSystematic biology
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.
Exploring uncertainty in the calibration of the molecular clock
- BiologyBiology Letters
It is demonstrated that the parameters distinguishing calibration densities have a major impact upon the prior and posterior of the divergence times, and it is critically important that users evaluate the joint prior distribution of divergence times used by their dating programmes.
Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci
- BiologySystematic biology
The results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way for improving the precision of posterior time estimation, however, even if a huge amount of sequence data is analyzed, considerable uncertainty will persist in time estimates.
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times.
- BiologySystematic biology
The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies, and a variety of local- and relaxed-clock methods have been proposed and implemented.
Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals
- BiologyProceedings of the Royal Society B: Biological Sciences
The large discrepancies between clock- and fossil-based estimates for divergence dates might be attributable to relatively small changes in evolutionary rates through time, although other explanations need to be investigated.