Bayesian inference of ancestral dates on bacterial phylogenetic trees
Bayesian inference of ancestral dates on bacterial phylogenetic trees
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DOI：
10.1101/347385
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发表时间：
2018-06
影响因子：
14.9
通讯作者：
X. Didelot;N. Croucher;S. Bentley;S. Harris;Daniel J. Wilson
中科院分区：
文献类型：
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作者：
X. Didelot;N. Croucher;S. Bentley;S. Harris;Daniel J. Wilson
对来自单一物种或感兴趣的谱系的细菌基因组集合进行测序和比较分析可以导致对其进化，生态学或流行病学的关键见解。这种研究的工具通常是建立一个系统发育树，更具体地说，如果可能的话，一个日期的系统发育，其中所有共同祖先的日期估计。在这里，我们提出了一种新的贝叶斯方法来构建过时的细菌基因组学是专门设计的。与以前的贝叶斯方法，旨在建立过时的系统发育，我们认为，基因组之间的系统发育关系已经使用标准的系统发育方法进行了评估，这使得我们的方法更快，可扩展。这两步的方法也使我们能够直接利用现有的系统发育方法，检测细菌重组，并因此占重组的影响，在建设一个过时的系统发育。我们分析了许多模拟数据集，以基准测试我们的方法在各种情况下的性能。此外，我们目前的应用程序，以三个不同的真实的数据集，从最近的细菌基因组研究。我们的方法是在一个名为BactDating的R包中实现的，该包可在https://github.com/xavierdidelot/BactDating免费下载。
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-steps 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.