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Cited by 298Genomics and Phylogenetic StudiesEvolution and Paleontology StudiesEvolution and Genetic Dynamics

Estimating divergence dates from molecular sequences.

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Rambaut, A., Bromham, L.·1998·Molecular Biology and Evolution
DOI 10.1093/oxfordjournals.molbev.a025940
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Abstract

The ability to date the time of divergence between lineages using molecular data provides the opportunity to answer many important questions in evolutionary biology. However, molecular dating techniques have previously been criticized for failing to adequately account for variation in the rate of molecular evolution. We present a maximum-likelihood approach to estimating divergence times that deals explicitly with the problem of rate variation. This method has many advantages over previous approaches including the following: (1) a rate constancy test excludes data for which rate heterogeneity is detected; (2) date estimates are generated with confidence intervals that allow the explicit testing of hypotheses regarding divergence times; and (3) a range of sequences and fossil dates are used, removing the reliance on a single calculated calibration rate. We present tests of the accuracy of our method, which show it to be robust to the effects of some modes of rate variation. In addition, we test the effect of substitution model and length of sequence on the accuracy of the dating technique. We believe that the method presented here offers solutions to many of the problems facing molecular dating and provides a platform for future improvements to such analyses.

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  • Local molecular clock models estimate a separate molecular rate for each user-circumscribed group of branches in the tree.

    “For example, local molecular clock models estimate a separate molecular rate for each user-circumscribed group of branches in the tree [ 6, 13, 16].”

    From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [13]

    In “Estimating the Divergence Date” (page unavailable), the paper assigns and estimates separate rates for two specified groups of branches in a quartet. This supports the branch-group rate mechanism, but the paper describes a two-rate quartet model, not the broader claim that local clock models estimate a rate for each user-circumscribed group in a tree. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Intermediate models employing relaxed molecular clocks have been described.

    “Recently, it has been realized that less drastic alternatives to the unrooted model of phylogeny may exist. Instead of dispensing with the molecular clock entirely, attempts have been made to relax the molecular clock assumption by allowing the rate to vary across the tree [ 13– 15].”

    From Relaxed Phylogenetics and Dating with Confidence (2006) · cites this paper as [13]

  • 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 [13]

  • Confidence intervals allow molecular dates to be used to test evolutionary hypotheses within the bounds of the accuracy and precision of molecular clocks, by asking whether the range of possible date estimates is consistent with a specific evolutionary hypothesis.

    “Such confidence intervals allow molecular dates to be used to test evolutionary hypotheses within the bounds of the accuracy and precision of molecular clocks, by asking whether the range of possible date estimates is consistent with a specific evolutionary hypotheses 26 (for example, that the animal phyla arose in the early Cambrian 27 ) (BOX 2).”

    From The modern molecular clock (2003) · cites this paper as [26]

  • The method presented here is more reliable than previous molecular dating techniques.

    “The combination of a rate constancy test with high resolution of long DNA sequences (two data sets totaling over 7,000 bp), use of a wide range of taxa and fossil dates (rather than reliance on a single calibration rate), and a maximum likelihood analysis makes this method more reliable than previous molecular dating techniques (11).”

    From Testing the Cambrian explosion hypothesis by using a molecular dating technique (1998) · cites this paper as [11]

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Research works printed but not linked: 2

  1. HILLIS, D. M., B. K. MABLE, and C. MORITZ. 1996. Applica- tions of molecular systematics: the state of the field and a look to the future. Pp. 515-543 in D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Molecular systematics. Sinauer, Sun- derland, Mass.
  2. HUELSENBECK, J. P., D. M. HILLIS, and R. JONES. 1996. Para- metric bootstrapping in molecular phylogenetics: applica- tions and performance. Pp. 19-45 in J. FERRARIS and S. PALUMBI, eds. Molecular zoology: strategies and protocols. Wiley, New York.

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Authors
Rambaut, A., & Bromham, L.
Affiliations
University of Oxford (GB)
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
1998-04-01
Volume
15
Issue
4
Pages
442-448
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/oxfordjournals.molbev.a025940
OpenAlex
W1966957912
Cited by
298
References
22
Citations by year
2026: 2 · 2025: 3 · 2024: 3 · 2023: 3 · 2022: 1 · 2021: 2 · 2020: 5 · 2019: 8 · 2018: 9 · 2017: 3 · 2016: 2 · 2015: 8 · 2014: 24 · 2013: 3 · 2012: 5
FWCI
4.54
Type
journal article
Language
en
Open access
Locations
  • Molecular Biology and Evolution (publishedVersion)
  • PubMed (publishedVersion)
Funders
Wellcome Trust
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, rate heterogeneity, fossil calibration, substitution models, sequence length, confidence intervals, phylogenetics
MeSH terms
Animals, Birds, Models, Genetic, Phylogeny, Confidence Intervals, Likelihood Functions, Sequence Alignment, Evolution, Molecular

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