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

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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

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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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Authors: Penny, D., McComish, B. J., Charleston, M. A., & Hendy, M. D.
Affiliations: Massey University (NZ)
ORCID: McComish, Bennet J.
Charleston, Michael A.
Hendy, Michael D.
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: green
figshare.com
Licence: cc-by
www.springer.com/tdm (tdm)
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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Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution

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