The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Comparisons of dN/dS are time dependent for closely related bacterial genomes
Open accessAbstract
The 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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Cites
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Self-citationThe hitch-hiking effect of a favourable gene
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Cited by
The Population Genetics of dN/dS
Kryazhimskiy, S., & Plotkin, J. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000304 · Cited by 962
Horizontal gene transfer and adaptive evolution in bacteria.
Arnold, B. J., Huang, I.-T., & Hanage, W. P. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00650-4 · Cited by 869
High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography
Hershberg, R., Lipatov, M., Small, P. M., Sheffer, H., Niemann, S., Homolka, S., Roach, J. C., Kremer, K., Petrov, D. A., Feldman, M. W., et al. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060311 · Cited by 593
Genome plasticity of BCG and impact on vaccine efficacy
Brosch, R., Gordon, S. V., Garnier, T., Eiglmeier, K., Frigui, W., Valenti, P., Dos Santos, S., Duthoy, S., Lacroix, C., Garcia-Pelayo, C., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700869104 · Cited by 574
Ford, C. B., Shah, R. R., Maeda, M. K., Gagneux, S., Murray, M. B., Cohen, T., Johnston, J. C., Gardy, J., Lipsitch, M., & Fortune, S. M. (2013) · Nature Genetics · doi:10.1038/ng.2656 · Cited by 457
Metadata
- Authors
- Rocha, E. P. C., Smith, J. M., Hurst, L. D., Holden, M. T. G., Cooper, J. E., Smith, N. H., & Feil, E. J.
- Venue
- Journal of Theoretical Biology
- Publisher
- Elsevier BV
- Published
- 2006-03
- Volume
- 239
- Issue
- 2
- Pages
- 226-235
- ISSN
- 0022-5193 (ISSN-L)
- OpenAlex
- W2072550492
- Cited by
- 428
- References
- 45
- FWCI
- 6.55
- Type
- journal article
- Language
- en
- Open access
- green
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- Rocha, E. P. C., Smith, J. M., Hurst, L. D., Holden, M. T. G., Cooper, J. E., Smith, N. H., & Feil, E. J. (2006). Comparisons of dN/dS are time dependent for closely related bacterial genomes. Journal of Theoretical Biology. https://doi.org/10.1016/j.jtbi.2005.08.037
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