ArticleBioinformatics (Oxford, England)2012
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62 citing papers in PubMed.
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- Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.Journal of molecular evolution · 2025Article
- Association of poultry vaccination with interspecies transmission and molecular evolution of H5 subtype avian influenza virus.Science advances · 2025Article
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- Higher HIV-1 evolutionary rate is associated with cytotoxic T lymphocyte escape mutations in infants.Journal of virology · 2024Article
- The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus.Nature communications · 2024Article
- Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species.mBio · 2024Article
- Genome-informed investigation of the molecular evolution and genetic reassortment of severe fever with thrombocytopenia syndrome virus.PLoS neglected tropical diseases · 2023Article
- Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.Nature communications · 2023Article
- Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.Research square · 2023Article
- Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages.PLoS neglected tropical diseases · 2023Article
- Article
- Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History.Molecular biology and evolution · 2022Article
- Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent.Virus genes · 2022Article
- Evolution of the North American Lineage H7 Avian Influenza Viruses in Association with H7 Virus's Introduction to Poultry.Journal of virology · 2022Article
2 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
motivationStatistical methods for comparing relative rates of synonymous and non-synonymous substitutions maintain a central role in detecting positive selection. To identify selection, researchers often estimate the ratio of these relative rates (dN/dS) at individual alignment sites. Fitting a codon substitution model that captures heterogeneity in dN/dS across sites provides a reliable way to perform such estimation, but it remains computationally prohibitive for massive datasets. By using crude estimates of the numbers of synonymous and non-synonymous substitutions at each site, counting approaches scale well to large datasets, but they fail to account for ancestral state reconstruction uncertainty and to provide site-specific dN/dS estimates.
resultsWe propose a hybrid solution that borrows the computational strength of counting methods, but augments these methods with empirical Bayes modeling to produce a relatively fast and reliable method capable of estimating site-specific dN/dS values in large datasets. Importantly, our hybrid approach, set in a Bayesian framework, integrates over the posterior distribution of phylogenies and ancestral reconstructions to quantify uncertainty about site-specific dN/dS estimates. Simulations demonstrate that this method competes well with more-principled statistical procedures and, in some cases, even outperforms them. We illustrate the utility of our method using human immunodeficiency virus, feline panleukopenia and canine parvovirus evolution examples.
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