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Nucleic Acids Res. 2018 Dec 14;46(22):e134. doi: 10.1093/nar/gky783.

Bayesian inference of ancestral dates on bacterial phylogenetic trees.

Author information

1
Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK.
2
The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
3
Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.

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.

PMID:
30184106
PMCID:
PMC6294524
DOI:
10.1093/nar/gky783
[Indexed for MEDLINE]
Free PMC Article

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