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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 ISSN 0305-1048.
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WRAP-Bayesian-inference-ancestral-dates-bacterial-phylogenetic-trees-Didelot-2018.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (1341Kb) | Preview |
Official URL: http://dx.doi.org/10.1093/nar/gky783
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 | ||||||||||||||||||
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| Subjects: | Q Science > QA Mathematics Q Science > QH Natural history > QH426 Genetics |
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| Divisions: | Faculty of Science, Engineering and Medicine > 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: |
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| 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 (Creative Commons) | ||||||||||||||||||
| Date of first compliant deposit: | 3 October 2018 | ||||||||||||||||||
| Date of first compliant Open Access: | 4 October 2018 | ||||||||||||||||||
| RIOXX Funder/Project Grant: |
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