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Inference of the properties of the recombination process from whole bacterial genomes
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Ansari, M. Azim and Didelot, Xavier (2014) Inference of the properties of the recombination process from whole bacterial genomes. Genetics, 196 (1). pp. 253-265. doi:10.1534/genetics.113.157172 ISSN 0016-6731.
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Official URL: http://dx.doi.org/10.1534/genetics.113.157172
Abstract
Patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require us to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a data set of Bacillus cereus genomes and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this article are implemented in a software package that is freely available for download at http://code.google.com/p/clonalorigin/.
Item Type: | Journal Article | ||||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
Journal or Publication Title: | Genetics | ||||||||
Publisher: | Genetics Society of America | ||||||||
ISSN: | 0016-6731 | ||||||||
Official Date: | 2014 | ||||||||
Dates: |
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Volume: | 196 | ||||||||
Number: | 1 | ||||||||
Page Range: | pp. 253-265 | ||||||||
DOI: | 10.1534/genetics.113.157172 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) |
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