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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, 71 (5). pp. 1073-1087. syab095. doi:10.1093/sysbio/syab095 ISSN 1076-836X.
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WRAP-Bayesian-inference-of-clonal-expansions-in-a-dated-phylogeny-Didelot-2021.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (1265Kb) | Preview |
Official URL: https://doi.org/10.1093/sysbio/syab095
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 | |||||||||
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| Subjects: | Q Science > QH Natural history R Medicine > RB Pathology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Science > Statistics |
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| 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: |
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| Volume: | 71 | |||||||||
| Number: | 5 | |||||||||
| Page Range: | pp. 1073-1087 | |||||||||
| Article Number: | syab095 | |||||||||
| DOI: | 10.1093/sysbio/syab095 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 20 December 2021 | |||||||||
| Date of first compliant Open Access: | 21 December 2021 | |||||||||
| RIOXX Funder/Project Grant: |
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