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Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution
Open accessAbstract
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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“According to this model, the rate of gene evolution is governed by the overall mutation rate and the proportion of sites at which changes are neutral 6 (FIG. 1b).”
From The modern molecular clock (2003) · cites this paper as [6]
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Self-citation
Metadata
- Authors
- Penny, D., McComish, B. J., Charleston, M. A., & Hendy, M. D.
- Affiliations
- Massey University (NZ)
- Venue
- Journal of Molecular Evolution
- Published
- 2001-12
- Volume
- 53
- Issue
- 6
- Pages
- 711-723
- ISSN
- 0022-2844 (ISSN-L)
- 1432-1432
- 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
- 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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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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