02147nas a2200205   4500000000100000008004100001653002300042653003300065653002500098100001400123700001600137700001500153700001400168700001400182245007500196856026000271300000700531520138900538022001401927       2018                            d10aBayesian inference10aBacterial phylogenetic trees10aBayesian methodology1 aDidelot X1 aCroucher NJ1 aBentley SD1 aHarris SR1 aWilson DJ00aBayesian inference of ancestral dates on bacterial phylogenetic trees.  uhttps://watermark.silverchair.com/gky783.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAiswggInBgkqhkiG9w0BBwagggIYMIICFAIBADCCAg0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMjP5Kc-6O9sSc_bedAgEQgIIB3u4wMjBVaruzrRbbPrZrwaDwpa6DyD3bzNjChYZY8GC_t2c0  a113 a<p>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.</p>
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