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Cited by 86Genomics and Phylogenetic StudiesEvolution and Paleontology StudiesEvolution and Genetic Dynamics

Estimating Divergence Times in the Presence of an Overdispersed Molecular Clock

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Cutler, David J.·2000·Molecular Biology and Evolution
DOI 10.1093/oxfordjournals.molbev.a026264
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Abstract

Molecular loci that fail relative-rate tests are said to be "overdispersed." Traditional molecular-clock approaches to estimating divergence times do not take this into account. In this study, a method was developed to estimate divergence times using loci that may be overdispersed. The approach was to replace the traditional Poisson process assumption with a more general stationary process assumption. A probability model was developed, and an accompanying computer program was written to find maximum-likelihood estimates of divergence times under both the Poisson process and the stationary process assumptions. In simulation, it was shown that confidence intervals under the traditional Poisson assumptions often vastly underestimate the true confidence limits for overdispersed loci. Both models were applied to two data sets: one from land plants, the other from the higher metazoans. In both cases, the traditional Poisson process model could be rejected with high confidence. Maximum-likelihood analysis of the metazoan data set under the more general stationary process suggested that their radiation occurred well over a billion years ago, but confidence intervals were extremely wide. It was also shown that a model consistent with a Cambrian (or nearly Cambrian) origination of the animal phyla, although significantly less likely than a much older divergence, fitted the data well. It is argued that without an a priori understanding of the variance in the time between substitutions, molecular data sets may be incapable of ever establishing the age of the metazoan radiation.

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  • The molecular clock assumption can be relaxed in a variety of ways.

    “The molecular clock assumption can be relaxed in a variety of ways [ 13– 15, 17, 49– 52].”

    From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [51]

  • Observations indicate that the pattern of substitution intervals for many genes has a broader distribution, which might be described as an 'overdispersed' Poisson distribution.

    “In fact, the molecular clock is generally even sloppier: observations indicate that the pattern of substitution intervals for many genes has a broader distribution, which might be described as an 'overdispersed' Poisson distribution 11,13,14 .”

    From The modern molecular clock (2003) · cites this paper as [14]

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Research works printed but not linked: 2

  1. [19]19. LANGLEY, C. H., and W. M. FITCH. 1973. The constancy of evolution: a statistical analysis of the ␣ and ␤ haemoglo- bins, cytochrome c, and fibrinopeptide A. Pp. 246-262 in N. E. MORTON, ed. Genetic structure of populations. Uni- versity of Hawaii Press, Honolulu.
  2. [28]28. PRESS, W. H., S. A. TEUKOLSKY, W. T. VETTERLING, and B. P. FLANNERY. 1992. Numerical recipes in C: the art of scien- tific computing. 2nd edition. Cambridge University Press, Cambridge, England.

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Authors
Cutler, D. J.
Affiliations
University of California, Davis (US)
Corresponding author
Cutler, David J.
ORCID
Cutler, David J.
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2000-11-01
Volume
17
Issue
11
Pages
1647-1660
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/oxfordjournals.molbev.a026264
OpenAlex
W2110131668
Cited by
86
References
39
Citations by year
2025: 1 · 2024: 1 · 2022: 1 · 2018: 1 · 2016: 1 · 2015: 2 · 2014: 1 · 2012: 3
FWCI
3.14
Type
journal article
Language
en
Open access
Locations
  • Molecular Biology and Evolution (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
divergence time estimation, confidence intervals, land plants, relative rate tests
MeSH terms
Animals, Humans, Models, Genetic, Phylogeny, Plants, Time Factors, Genetic Variation, Evolution, Molecular

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