ArticleProceedings of the National Academy of Sciences of the United States of America2018
Impact of the tree prior on estimating clock rates during epidemic outbreaks.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
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- Phylogeographic History of Tomato Chlorosis Virus.Viruses · 2025Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial.Scientific reports · 2024Article
- Comparing the transmission potential from sequence and surveillance data of 2009 North American influenza pandemic waves.Infectious Disease Modelling · 2023Article
- Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.Communications biology · 2023Article
- Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink.Virus evolution · 2023Article
- Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.Virus evolution · 2022Review
- Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating.Journal of fungi (Basel, Switzerland) · 2021Review
- Monitoring the Microevolution ofFrontiers in microbiology · 2021Article
- Genomic epidemiology of a densely sampled COVID-19 outbreak in China.Virus evolution · 2021Article
- Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data.Microbial genomics · 2020Article
- Evidence of increasing diversification of emerging Severe Acute Respiratory Syndrome Coronavirus 2 strains.Journal of medical virology · 2020Article
- A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex.Genome biology · 2020Article
- Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks.Interface focus · 2020Article
- Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics.PLoS neglected tropical diseases · 2020Article
- Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak.PLoS pathogens · 2020Article
- The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses.Viruses · 2019Article
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Abstract
Bayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary and population dynamic parameters based on genetic sequences. It has been noted that the clock rate, one of the evolutionary parameters, decreases with an increase in the sampling period of sequences. In particular, clock rates of epidemic outbreaks are often estimated to be higher compared with the long-term clock rate. Purifying selection has been suggested as a biological factor that contributes to this phenomenon, since it purges slightly deleterious mutations from a population over time. However, other factors such as methodological biases may also play a role and make a biological interpretation of results difficult. In this paper, we identify methodological biases originating from the choice of tree prior, that is, the model specifying epidemiological dynamics. With a simulation study we demonstrate that a misspecification of the tree prior can upwardly bias the inferred clock rate and that the interplay of the different models involved in the inference can be complex and nonintuitive. We also show that the choice of tree prior can influence the inference of clock rate on real-world Ebola virus (EBOV) datasets. While commonly used tree priors result in very high clock-rate estimates for sequences from the initial phase of the epidemic in Sierra Leone, tree priors allowing for population structure lead to estimates agreeing with the long-term rate for EBOV.
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