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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The rate of gene evolution is governed by the overall mutation rate and the proportion of sites at which changes are neutral.
“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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Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution
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Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo
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A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy
Kolaczkowski, B. D., & Thornton, J. W. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn042 · Cited by 94 · see citing works
Plastid endosymbiosis, genome evolution and the origin of green plants
Stiller, J. W. (2007) · Trends in Plant Science · doi:10.1016/j.tplants.2007.08.002 · Cited by 93 · see citing works
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The origin of mitochondria in light of a fluid prokaryotic chromosome model
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Phylogenetic Inference via Sequential Monte Carlo
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Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily
Lundin, D., Poole, A. M., Sjöberg, B., & Högbom, M. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.367458 · Cited by 90 · see citing works
The quest for natural selection in the age of comparative genomics
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Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires
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Self-citationDated phylogeny suggests early Neolithic origin of Sino-Tibetan languages
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The languages of Halmahera and West New Guinea
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The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models
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Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution
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The Problem of Rooting Rapid Radiations
Grievink, L. S., Penny, D., Hendy, M. D., & Holland, B. R. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm178 · Cited by 82 · see citing works
Self-citationTesting the Hypothesis of Common Ancestry
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A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
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Testing for Covarion-like Evolution in Protein Sequences
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Bayesian phylogenetic analysis of linguistic data using BEAST
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Covarion Structure in Plastid Genome Evolution: A New Statistical Test
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Deep Residual Neural Networks Resolve Quartet Molecular Phylogenies
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How Much Can Evolved Characters Tell us about the Tree that Generated Them?
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Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy
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Testing for Differences in Rates-Across-Sites Distributions in Phylogenetic Subtrees
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Bifunctional aldehyde/alcohol dehydrogenase (ADHE) in chlorophyte algal mitochondria
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Building trees of algae: some advances in phylogenetic and evolutionary analysis
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Epistasis and the Dynamics of Reversion in Molecular Evolution
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Early evolution comes full circle
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Phylogenetic Analyses of Parasites in the New Millennium
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Heterotachy and Functional Shift in Protein Evolution
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Self-citation
- 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
About these checks
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.
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