The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
Open accessAbstract
Time-scales of viral evolution and emergence have been studied widely, but are often poorly understood. Molecular analyses of viral evolutionary time-scales generally rely on estimates of rates of nucleotide substitution, which vary by several orders of magnitude depending on the timeframe of measurement. We analysed data from all major groups of viruses and found a strong negative relationship between estimates of nucleotide substitution rate and evolutionary timescale. Strikingly, this relationship was upheld both within and among diverse groups of viruses. A detailed case study of primate lentiviruses revealed that the combined effects of sequence saturation and purifying selection can explain this time-dependent pattern of rate variation. Therefore, our analyses show that studies of evolutionary time-scales in viruses require a reconsideration of substitution rates as a dynamic, rather than as a static, feature of molecular evolution. Improved modelling of viral evolutionary rates has the potential to change our understanding of virus origins.
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Citations
Cites
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · cited 2×
“We also evaluated the posterior distributions of the coefficient of rate variation, which should deviate from zero in the presence of substantial rate variation among branches [31].”
MethodSelf-citationRNA VIRUS MUTATIONS AND FITNESS FOR SURVIVAL
Domingo, E., & Holland, J. J. (1997) · Annual Review of Microbiology · doi:10.1146/annurev.micro.51.1.151 · Cited by 1,514
Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models
Suchard, M. A., Weiss, R. E., & Sinsheimer, J. S. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003872 · Cited by 791
Bayesian Model Adequacy and Choice in Phylogenetics
Bollback, J. P. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004175 · Cited by 215
Purifying selection can obscure the ancient age of viral lineages
Wertheim, J. O., & Kosakovsky Pond, S. L. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr170 · Cited by 200
Cited by
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A., & Robertson, D. L. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0771-4 · Cited by 1,014
“These differences reflect the fact that rate estimates can vary considerably with the time scale of measurement, a frequently observed phenomenon in viruses known as time-dependent evolutionary rates (Aiewsakun and Katzourakis, 2016; Duchene et al., 2014; Membrebe et al., 2019).”
BackgroundInfluentialOff-season RSV epidemics in Australia after easing of COVID-19 restrictions
Eden, J.-S., Sikazwe, C., Xie, R., Deng, Y.-M., Sullivan, S. G., Michie, A., Levy, A., Cutmore, E., Blyth, C. C., Britton, P. N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30485-3 · Cited by 340
Self-citationThe evolution of Ebola virus: Insights from the 2013-2016 epidemic
Holmes, E. C., Dudas, G., Rambaut, A., & Andersen, K. G. (2016) · Nature · doi:10.1038/nature19790 · Cited by 314
Self-citationSabin, S., Herbig, A., Vågene, Å. J., Ahlström, T., Bozovic, G., Arcini, C., Kühnert, D., & Bos, K. I. (2020) · Genome Biology · doi:10.1186/s13059-020-02112-1 · Cited by 97
Metadata
- Authors
- Duchêne, S., Holmes, E. C., & Ho, S. Y. W.
- Venue
- Proceedings of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2014-07-07
- Volume
- 281
- Issue
- 1786
- Pages
- 20140732
- ISSN
- 0080-4649 (ISSN-L)
- 0962-8452
- 1471-2954
- OpenAlex
- W2110480399
- Cited by
- 197
- References
- 5
- FWCI
- 11.49
- Type
- journal article
- Language
- en
- Open access
- green
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- Duchêne, S., Holmes, E. C., & Ho, S. Y. W. (2014). Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proceedings of the Royal Society B: Biological Sciences. https://doi.org/10.1098/rspb.2014.0732
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