期刊
GENETICS
卷 205, 期 2, 页码 857-870出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.116.193425
关键词
bacterial evolution; recombination; phylogenetic inference
资金
- Marsden grant from the Royal Society of New Zealand [UOA1324]
- New Zealand Food Safety Science and Research Centre
- Allan Wilson Centre for Molecular Ecology and Evolution
Homologous recombination is a central feature of bacterial evolution, yet it confounds traditional phylogenetic methods. While a number of methods specific to bacterial evolution have been developed, none of these permit joint inference of a bacterial recombination graph and associated parameters. In this article, we present a new method which addresses this shortcoming. Our method uses a novel Markov chain Monte Carlo algorithm to perform phylogenetic inference under the ClonalOrigin model. We demonstrate the utility of our method by applying it to ribosomal multilocus sequence typing data sequenced from pathogenic and nonpathogenic Escherichia coli serotype O157 and O26 isolates collected in rural New Zealand. The method is implemented as an open source BEAST 2 package, Bacter, which is available via the project web page at http://tgvaughan.github.io/bacter.
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