Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.

@article{Clarke2015MethodsFT,
  title={Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.},
  author={Julia A. Clarke and Clint A. Boyd},
  journal={Systematic biology},
  year={2015},
  volume={64 1},
  pages={
          25-41
        }
}
Approaches quantifying the relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding… 

Figures and Tables from this paper

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins
TLDR
The FBD model and a model of morphological trait evolution are incorporated into a Bayesian total‐evidence approach to dating species phylogenies and it is shown that including stem‐fossil diversity can greatly improve the estimates of the divergence times of crown taxa.
Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time
TLDR
The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in this empirical study, and the modified GER was the index least susceptible to bias.
Sampled ancestors and dating in Bayesian phylogenetics
TLDR
A Bayesian Markov chain Monte Carlo framework for inferring sampled ancestor phylogenies is developed, properties of the sampled ancestor tree space are investigated, and Bayesian methods to date phylogenies are reviewed and a computational problem connected to calibration methods is addressed.
Environmentally driven extinction and opportunistic origination explain fern diversification patterns
TLDR
A novel Bayesian model is developed to simultaneously estimate correlations between diversification dynamics and multiple environmental trajectories and indicates that the prime driver of fern diversity dynamics is environmentally driven extinction, with origination being an opportunistic response to diminishing ecospace occupancy.
The Coral of Life
  • J. Podani
  • Environmental Science
    Evolutionary Biology
  • 2019
TLDR
This paper argues that corals, as suggested by Darwin in his early notebooks, are superior to trees as metaphors, and may also be used as mathematical models, and is supplemented with a figure, The Coral of Life, which is the first attempt to combine all of the above features in a single diagram for the entirety of life.
First discovery of Eocene coastal-estuarine ostracods from Japan, with the geological history of the migration of estuarine genera in the Far East
Abstract The genus Neomonoceratina, which dominated the ostracod assemblage in the uppermost part of the Akasaki Formation (Miroku Group) of the Kyushu Island, Japan, is associated with the benthic
A Comparative Study of Metadiscourse in English Research Article Abstracts in Hard Disciplines by L1 Chinese and L1 English Scholars
This study investigates how L1 Chinese scholars in hard science disciplines use metadiscourse in their English academic writing, by comparing the deployment of metadiscoursal resources written by L1

References

SHOWING 1-10 OF 54 REFERENCES
The impact of fossils and taxon sampling on ancient molecular dating analyses.
  • L. Hug, A. Roger
  • Environmental Science, Biology
    Molecular biology and evolution
  • 2007
TLDR
From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates.
A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points
TLDR
A central challenge facing the temporal calibration of molecular phylogenies is finding a quantitative method for estimating maximum age constraints on lineage divergence times and this method, exploiting the fact that the relative branch lengths on the ultrametric tree are proportional to time is provided.
Assessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points.
TLDR
A recently developed fossil cross-validation method is expanded on to evaluate whether alternative nodal assignments of multiple fossils produce calibration sets that differ in their internal consistency, finding that a correlation exists between s values, devised to measure the consistency among the calibration points of a calibration set, and nodal distances among calibration points.
Uncertainty in the age of fossils and the stratigraphic fit to phylogenies.
TLDR
The effect of age uncertainty on measures of stratigraphic fit to phylogenies is explored here for two indices based on the extension of ghost lineages (MSM* and GER), with a solution based on randomization of the ages of terminal taxa resulting in a range of possible values.
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
TLDR
The results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic.
Assessing Concordance of Fossil Calibration Points in Molecular Clock Studies: An Example Using Turtles
TLDR
A new cross‐validation method is presented that identifies inconsistent fossils when multiple fossil calibrations are available for a clade and it is found that despite their overall antiquity as a lineage, the most species‐rich clades of turtles diversified well within the Cenozoic.
Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches.
TLDR
Saturation significantly influenced the fossils that were selected as most reliable for all three methods evaluated and highlighted the need to critically evaluate the fossils selected by data with different rates of nucleotide substitution and how data withDifferent evolutionary rates affect the results of each method for evaluating fossils.
Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).
TLDR
The level of agreement reached between different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases, thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.
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.
Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea).
...
...