Purifying selection can obscure the ancient age of viral lineages
Open accessAbstract
Statistical methods for molecular dating of viral origins have been used extensively to infer the time of most common recent ancestor for many rapidly evolving pathogens. However, there are a number of cases, in which epidemiological, historical, or genomic evidence suggests much older viral origins than those obtained via molecular dating. We demonstrate how pervasive purifying selection can mask the ancient origins of recently sampled pathogens, in part due to the inability of nucleotide-based substitution models to properly account for complex patterns of spatial and temporal variability in selective pressures. We use codon-based substitution models to infer the length of branches in viral phylogenies; these models produce estimates that are often considerably longer than those obtained with traditional nucleotide-based substitution models. Correcting the apparent underestimation of branch lengths suggests substantially older origins for measles, Ebola, and avian influenza viruses. This work helps to reconcile some of the inconsistencies between molecular dating and other types of evidence concerning the age of viral lineages.
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Exogenous free-living RNA viruses are subject to remarkably strong purifying selection.
“Despite a reputation for rapid adaptive evolution, exogenous free-living RNA viruses are subject to remarkably strong purifying selection (Holmes 2003;Pybus et al. 2007;Wertheim and Kosakovsky Pond 2011).”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Wertheim and Kosakovsky Pond 2011
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Cites
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- Authors
- Wertheim, J. O., & Kosakovsky Pond, S. L.
- Affiliations
- University of California San Diego (US)
- Corresponding author
- Wertheim, Joel O.
- ORCID
- Wertheim, Joel O.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-06-24
- Volume
- 28
- Issue
- 12
- Pages
- 3355-3365
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3247791
- OpenAlex
- W2099464974
- Cited by
- 200
- References
- 4
- Citations by year
- 2026: 10 · 2025: 11 · 2024: 13 · 2023: 7 · 2022: 12 · 2021: 9 · 2020: 12 · 2019: 7 · 2018: 19 · 2017: 16 · 2016: 15 · 2015: 19 · 2014: 27 · 2013: 10 · 2012: 9
- FWCI
- 9.31
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Molecular Biology and Evolution (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0714991)
- National Institutes of Health (AI47745, AI74621, AI-36214)
- Center for AIDS Research, University of Washington
- University of California, San Diego
- National Institute of General Medical Sciences (GM093939, R01GM093939)
- National Institute of Allergy and Infectious Diseases (R01AI057167, AI-74621, AI-47745, AI57167, R21AI047745, AI 43638, R24AI106039, R56AI047745, AI-36214, R01AI047745, U01AI043638, P01AI074621, P30AI036214, T32AI007384)
- Division of Mathematical Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
- Keywords
- purifying selection, viral origin, divergence time estimation, branch length estimation, viral phylogeny, measles virus, Ebola virus, avian influenza virus
- MeSH terms
- Codon, Measles virus, Mutation, Influenza A virus, Phylogeny, Rinderpest virus, RNA Viruses, RNA, Viral, Selection, Genetic, Sequence Alignment, Peste-des-petits-ruminants virus, Evolution, Molecular, Amino Acid Substitution, Ebolavirus
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