Bayesian inference of ancestral dates on bacterial phylogenetic trees.

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TitleBayesian inference of ancestral dates on bacterial phylogenetic trees.
Publication TypeJournal Article
AuthorsDidelot X, Croucher NJ, Bentley SD, Harris SR, Wilson DJ
Abbrev. JournalNucleic Acids Res.
JournalNucleic acids research
Year of Publication2018
Pagination11
Publication Languageeng
KeywordsBacterial phylogenetic trees, Bayesian inference, Bayesian methodology
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.

PubMed URL

http://www.ncbi.nlm.nih.gov/pubmed/30184106?dopt=Abstract

DOI10.1093/nar/gky783
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