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Comparisons of dN/dS are time dependent for closely related bacterial genomes
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posted on 2023-06-08, 00:44 authored by Eduardo P C Rocha, John Maynard Smith, Laurence D Hurst, Matthew T G Holden, Jessica E Cooper, Noel H Smith, Edward FeilThe ratio of non-synonymous (dN) to synonymous (dS) changes between taxa is frequently computed to assay the strength and direction of selection. Here we note that for comparisons between closely related strains and/or species a second parameter needs to be considered, namely the time since divergence of the two sequences under scrutiny. We demonstrate that a simple time lag model provides a general, parsimonious explanation of the extensive variation in the dN/dS ratio seen when comparing closely related bacterial genomes. We explore this model through simulation and comparative genomics, and suggest a role for hitch-hiking in the accumulation of non-synonymous mutations. We also note taxon-specific differences in the change of dN/dS over time, which may indicate variation in selection, or in population genetics parameters such as population size or the rate of recombination. The effect of comparing intra-species polymorphism and inter-species substitution, and the problems associated with these concepts for asexual prokaryotes, are also discussed. We conclude that, because of the critical effect of time since divergence, inter-taxa comparisons are only possible by comparing trajectories of dN/dS over time and it is not valid to compare taxa on the basis of single time points.
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Publication status
- Published
Journal
Journal of Theoretical BiologyISSN
0022-5193Publisher
ElsevierExternal DOI
Issue
2Volume
239Page range
226-235Department affiliated with
- Biology and Environmental Science Publications
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- No
Peer reviewed?
- Yes
Legacy Posted Date
2012-02-06Usage metrics
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