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Bayesian inference of ancestral dates on bacterial phylogenetic trees

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Didelot, Xavier, Croucher, Nicholas J., Bentley, Stephen D., Harris, Simon R. and Wilson, Daniel J. (2018) Bayesian inference of ancestral dates on bacterial phylogenetic trees. Nucleic Acids Research, 46 (22). e134. doi:10.1093/nar/gky783

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Official URL: http://dx.doi.org/10.1093/nar/gky783

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Abstract

The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated phylogeny, in which the dates of all common ancestors are estimated. Here, we propose a new Bayesian methodology to construct dated phylogenies which is specifically designed for bacterial genomics. Unlike previous Bayesian methods aimed at building dated phylogenies, we consider that the phylogenetic relationships between the genomes have been previously evaluated using a standard phylogenetic method, which makes our methodology much faster and scalable. This two-step approach also allows us to directly exploit existing phylogenetic methods that detect bacterial recombination, and therefore to account for the effect of recombination in the construction of a dated phylogeny. We analysed many simulated datasets in order to benchmark the performance of our approach in a wide range of situations. Furthermore, we present applications to three different real datasets from recent bacterial genomic studies. Our methodology is implemented in a R package called BactDating which is freely available for download at https://github.com/xavierdidelot/BactDating.

Item Type: Journal Article
Subjects: Q Science > QA Mathematics
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Phylogeny, Bacterial genomes, Bayesian statistical decision theory
Journal or Publication Title: Nucleic Acids Research
Publisher: Oxford University Press
ISSN: 0305-1048
Official Date: 14 December 2018
Dates:
DateEvent
14 December 2018Published
3 September 2018Available
21 August 2018Accepted
Volume: 46
Number: 22
Article Number: e134
DOI: 10.1093/nar/gky783
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
MR/N010760/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
UNSPECIFIED[NIHR] National Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272
HPRU-2012-10080Public Health Englandhttp://dx.doi.org/10.13039/501100002141
101237/Z/13/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
101237/Z/13/Z[RS] Royal Societyhttp://dx.doi.org/10.13039/501100000288

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