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MBE Advance Access published online on November 4, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn252
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp.

Kevin J. Balbi1, Eduardo P.C. Rocha2,3 and Edward J. Feil1,*

1 Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
2 Institut Pasteur, Microbial Evolutionary Genomics; CNRS, URA2171, F-75015 Paris, France
3 UPMC Univ Paris 06, Atelier de BioInformatique, F-75005, Paris, France

* Corresponding author: Edward J. Feil, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK. email: e.feil{at}bath.ac.uk, Tel : +44 (0)1225 383021, Fax +44 (0)1225 386779.

Received for publication August 20, 2008. Revision received October 29, 2008. Accepted for publication October 29, 2008.

The Shigella are recently emerged clones of E. coli which have independently adopted an intracellular pathogenic lifestyle. We examined the molecular evolutionary consequences of this niche specialisation by comparing the normalised, directional frequency profiles of unique polymorphisms within 2098 orthologues representing the intersection of five E. coli and four Shigella genomes. We note a surfeit of AT enriching changes (GC->AT), transversions and non-synonymous changes in the Shigella genomes. By examining these diffferences within a temporal framework, we conclude that our results are consistent with relaxed or inefficient selection in Shigella owing to a reduced effective population size. Alternative interpretations, and the interesting exception of S. sonnei, are discussed. Finally, this analysis lends support to the view that nucleotide composition typically does not lie at mutational equilibrium, but that selection plays a role in maintaining a higher GC content than would result solely from mutation bias. This argument sheds light on the enrichment of adenine and thymine in the genomes of bacterial endosymbionts where purifying selection is very weak.

Key Words: Genetic drift • Purifying selection • Base composition • Escherichia coli • Shigella


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