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Bayesian inference of clonal expansions in a dated phylogeny

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Helekal, David, Ledda, Alice, Volz, Erik, Wyllie, David and Didelot, Xavier (2021) Bayesian inference of clonal expansions in a dated phylogeny. Systematic Biology . syab095. doi:10.1093/sysbio/syab095

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Official URL: https://doi.org/10.1093/sysbio/syab095

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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 analyse 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 datasets. Inference under our clonal expansion model can reveal important features in the evolution and epidemiology of infectious disease pathogens.

Item Type: Journal Article
Subjects: Q Science > QH Natural history
R Medicine > RB Pathology
Divisions: Faculty of Science > Life Sciences (2010- )
Faculty of Science > Statistics
SWORD Depositor: Library Publications Router
Library of Congress Subject Headings (LCSH): Genetic epidemiology , Genetic epidemiology -- Statistical methods, Microbial genomics, Phylogeny
Journal or Publication Title: Systematic Biology
Publisher: Oxford University Press (OUP)
ISSN: 1076-836X
Official Date: 6 December 2021
Dates:
DateEvent
6 December 2021Published
29 November 2021Accepted
Article Number: syab095
DOI: 10.1093/sysbio/syab095
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
EP/S022244/1 [EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
UNSPECIFIEDNational Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272
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