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Cited by 287Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.

Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution

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Penny, David, McComish, Bennet J., Charleston, Michael A., Hendy, Michael D.·2001·Journal of Molecular Evolution
DOI 10.1007/s002390010258
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Abstract

There is an apparent paradox in our understanding of molecular evolution. Current biochemically based models predict that evolutionary trees should not be recoverable for divergences beyond a few hundred million years. In practice, however, trees often appear to be recovered from much older times. Mathematical models, such as those assuming that sites evolve at different rates [including a Gamma distribution of rates across sites (RAS)] may in theory allow the recovery of some ancient divergences. However, such models require that each site maintain its characteristic rate over the whole evolutionary period. This assumption, however, contradicts the knowledge that tertiary structures diverge with time, invalidating the rate-constancy assumption of purely mathematical models. We report here that a hidden Markov version of the covarion model can meet both biochemical and statistical requirements for the analysis of sequence data. The model was proposed on biochemical grounds and can be implemented with only two additional parameters. The two hidden parts of this model are the proportion of sites free to vary (covarions) and the rate of interchange between fixed sites and these variable sites. Simulation results are consistent with this approach, providing a better framework for understanding anciently diverged sequences than the standard RAS models. However, a Gamma distribution of rates may approximate a covarion model and may possibly be justified on these grounds. The accurate reconstruction of older divergences from sequence data is still a major problem, and molecular evolution still requires mathematical models that also have a sound biochemical basis.

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Metadata

Authors
Penny, D., McComish, B. J., Charleston, M. A., & Hendy, M. D.
Affiliations
Massey University (NZ)
ORCID
Venue
Journal of Molecular Evolution
Publisher
Springer Science and Business Media LLC
Published
2001-12
Volume
53
Issue
6
Pages
711-723
ISSN
  • 0022-2844 (ISSN-L)
  • 1432-1432
DOI
10.1007/s002390010258
OpenAlex
W2139677507
Cited by
287
References
61
Citations by year
2026: 7 · 2025: 44 · 2024: 63 · 2023: 5 · 2022: 4 · 2021: 5 · 2020: 6 · 2019: 6 · 2018: 6 · 2017: 4 · 2016: 4 · 2015: 4 · 2014: 11 · 2013: 5 · 2012: 11
FWCI
3.70
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Molecular Evolution (publishedVersion)
  • PubMed (publishedVersion)
  • eCite Digital Repository (University of Tasmania) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
hidden Markov models, molecular evolution, phylogenetic inference
MeSH terms
Models, Biological, Models, Chemical, Evolution, Molecular

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