ArticleeLife2019
Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.Molecular biology and evolution · 2026Article
- Exploring cooperation among social pathogens: a computational perspective.FEMS microbiology reviews · 2026Review
- Segregating DNA lesions point to high selective advantage of tumor initiating cells.bioRxiv : the preprint server for biology · 2025Article
- Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data.Molecular biology and evolution · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- "A mathematical theory of evolution": phylogenetic models dating back 100 years.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Reading Yule in light of the history and present of macroevolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.bioRxiv : the preprint server for biology · 2025Article
- Early detection of highly transmissible viral variants using phylogenomics.Science advances · 2024Article
- Phylogenies increase power to detect highly transmissible viral genome variants.medRxiv : the preprint server for health sciences · 2023Article
- Epidemiological inference for emerging viruses using segregating sites.Nature communications · 2023Article
- The potential of genomics for infectious disease forecasting.Nature microbiology · 2022Review
- Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.Virus evolution · 2022Review
- Unifying Phylogenetic Birth-Death Models in Epidemiology and Macroevolution.Systematic biology · 2021Article
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- Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus.Frontiers in veterinary science · 2021Article
- Decomposing the sources of SARS-CoV-2 fitness variation in the United States.Virus evolution · 2021Article
- No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2.Nature communications · 2020Article
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Authors and funding
2 authors.
Funding
Abstract
Beneficial and deleterious mutations cause the fitness of lineages to vary across a phylogeny and thereby shape its branching structure. While standard phylogenetic models do not allow mutations to feedback and shape trees, birth-death models can account for this feedback by letting the fitness of lineages depend on their type. To date, these multi-type birth-death models have only been applied to cases where a lineage's fitness is determined by a single character state. We extend these models to track sequence evolution at multiple sites. This approach remains computationally tractable by tracking the genotype and fitness of lineages probabilistically in an approximate manner. Although approximate, we show that we can accurately estimate the fitness of lineages and site-specific mutational fitness effects from phylogenies. We apply this approach to estimate the population-level fitness effects of mutations in Ebola and influenza virus, and compare our estimates with in vitro fitness measurements for these mutations.
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