Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

@article{Sanderson2002EstimatingAR,
  title={Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.},
  author={Michael J. Sanderson},
  journal={Molecular biology and evolution},
  year={2002},
  volume={19 1},
  pages={
          101-9
        }
}
  • M. Sanderson
  • Published 2002
  • Biology, Medicine
  • Molecular biology and evolution
Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny… Expand
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References

SHOWING 1-10 OF 54 REFERENCES
Performance of a divergence time estimation method under a probabilistic model of rate evolution.
TLDR
Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included and new parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Expand
A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization ofExpand
Estimating divergence dates from molecular sequences.
TLDR
This work presents a maximum-likelihood approach to estimating divergence times that deals explicitly with the problem of rate variation, and presents tests of the accuracy of the method, which show it to be robust to the effects of some modes of rate variations. Expand
Reconstructing shifts in diversification rates on phylogenetic trees.
TLDR
Tests of hypotheses about key innovations do require Information about phylogenetic relationships, and some of these tests can be implemented without any information about time, but every effort should be made to obtain information aboutTime, which greatly increases the power of such tests. Expand
Estimating divergence times in the presence of an overdispersed molecular clock.
  • D. Cutler
  • Biology, Medicine
  • Molecular biology and evolution
  • 2000
TLDR
A method was developed to estimate divergence times using loci that may be overdispersed, and a model consistent with a Cambrian origination of the animal phyla, although significantly less likely than a much older divergence, fitted the data well. Expand
A molecular timescale for vertebrate evolution
TLDR
The clock-like accumulation of sequence differences in some genes provides an alternative method by which the mean divergence time can be estimated, and the molecular times agree with most early and late fossil-based times, but indicate major gaps in the Mesozoic fossil record. Expand
Estimating Rate and Time in Molecular Phylogenies: Beyond the Molecular Clock?
TLDR
The study of rates of character evolution has been a cornerstone of evolutionary biology since the pioneering work of Simpson (1944) and molecular rate constancy continues to be viewed as a reasonable model even across vast reaches of the tree of life (Wray et al., 1996). Expand
Among-site rate variation and its impact on phylogenetic analyses.
  • Z. Yang
  • Biology, Medicine
  • Trends in ecology & evolution
  • 1996
TLDR
Analysis of reliable methods for studying rate variation shows that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies. Expand
Can fast early rates reconcile molecular dates with the Cambrian explosion?
  • L. Bromham, M. Hendy
  • Biology, Medicine
  • Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 2000
TLDR
A new method which uses multiple calibration dates and an empirically determined range of possible substitution rates to place bounds on the basal date of divergence of lineages is used to ask whether faster rates of molecular evolution early in the metazoan radiation could possibly account for the discrepancy between molecular and palaeontological date estimates. Expand
A compound poisson process for relaxing the molecular clock.
TLDR
This work introduces a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process and uses Markov chain Monte Carlo integration to evaluate the posterior probability distribution. Expand
...
1
2
3
4
5
...