ArticleSystematic biology2022
Bayesian Inference of Clonal Expansions in a Dated Phylogeny.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 18 citations in OpenAlex.
- Quantifying the predictability of evolution by analysis of coalescent rate variation.Molecular biology and evolution · 2026Article
- Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent pneumococcal conjugate vaccine introduction, South Africa.Microbial genomics · 2026Article
- treestructure: an R package to detect population structure in phylogenetic trees.Bioinformatics (Oxford, England) · 2026Article
- DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.Molecular biology and evolution · 2026Article
- Genomic and statistical models to characterizeMicrobial genomics · 2026Article
- Inference of Multiple Mergers while Dating a Pathogen Phylogeny.Systematic biology · 2025Article
- Plasmid-driven strategies for clone success in Escherichia coli.Nature communications · 2025Article
- Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children.Nature communications · 2024Article
- Five centuries of genome evolution and multi-host adaptation ofMicrobial genomics · 2024Article
- Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi.Microbial genomics · 2024Article
- Article
- Fitness, growth and transmissibility of SARS-CoV-2 genetic variants.Nature reviews. Genetics · 2023Review
- Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data.Journal of the Royal Society, Interface · 2023Article
- Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease.Bioinformatics (Oxford, England) · 2023Article
- A scalable analytical approach from bacterial genomes to epidemiology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Microbial population genetics models often assume that all lineages are constrained by the same population size dynamics over time. However, many neutral and selective events can invalidate this assumption and can contribute to the clonal expansion of a specific lineage relative to the rest of the population. Such differential phylodynamic properties between lineages result in asymmetries and imbalances in phylogenetic trees that are sometimes described informally but which are difficult to analyze formally. To this end, we developed a model of how clonal expansions occur and affect the branching patterns of a phylogeny. We show how the parameters of this model can be inferred from a given dated phylogeny using Bayesian statistics, which allows us to assess the probability that one or more clonal expansion events occurred. For each putative clonal expansion event, we estimate its date of emergence and subsequent phylodynamic trajectory, including its long-term evolutionary potential which is important to determine how much effort should be placed on specific control measures. We demonstrate the applicability of our methodology on simulated and real data sets. Inference under our clonal expansion model can reveal important features in the evolution and epidemiology of infectious disease pathogens. [Clonal expansion; genomic epidemiology; microbial population genomics; phylodynamics.].
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