Inference of bacterial microevolution using multilocus sequence data
Inference of bacterial microevolution using multilocus sequence data
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DOI：
10.1534/genetics.106.063305
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发表时间：
2007-03-01
期刊：
影响因子：
3.3
通讯作者：
Falush, Daniel
中科院分区：
文献类型：
--
作者：
Didelot, Xavier;Falush, Daniel
我们描述了一种基于模型的方法，使用多位点序列数据来推断细菌的克隆关系和同源重组事件的染色体位置，这些事件破坏了克隆模式的遗传。我们的模型的关键假设是重组事件引入了一个恒定速率的替换到一个连续的序列区域。该方法既适用于少数基因座的多位点序列分型（MLST）数据，也适用于多个细菌基因组的比对。它可以用来确定一个分离的子集是否有共同的祖先，估计共同祖先的年龄，从而解决各种流行病学和生态学问题，这些问题取决于细菌传播的模式。在将特定的遗传事件与其引起的表型变化联系起来时，它也应该是有用的。我们证明该模型优于现有的利用MLST数据细分重组细菌的方法，并提供了沙门氏菌和芽孢杆菌的例子。本文中使用的软件ClonalFrame可从http://bacteria.stats.ox.ac.uk/获得。
We describe a model-based method for using multilocus sequence data to infer the clonal relationships of bacteria and the chromosomal position of homologous recombination events that disrupt a clonal pattern of inheritance. The key assumption of our model is that recombination events introduce a constant rate of substitutions to a contiguous region of sequence. The method is applicable both to multilocus sequence typing (MLST) data from a few loci and to alignments of multiple bacterial genomes. It can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor, and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. It Should also be useful in associating particular genetic events with the changes in phenotype that they cause. We show that the model Outperforms existing methods of subdividing recombinogenic bacteria using MLST data and provide examples from Salmonella and Bacillus. The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/.