Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni

Wilson, Daniel J.; Gabriel, Edith; Leatherbarrow, A. J. H.; Cheesbrough, J.; Gee, Steven; Bolton, Eric; Fox, Andrew S.; Hart, C. A.; Diggle, Peter J.; Fearnhead, Paul

doi:10.1093/molbev/msn264

Cited by 172 publications

(207 citation statements)

References 61 publications

(89 reference statements)

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“…The strategy for choosing summary statistics in the ABC study of Wilson et al (2009) was to use previously developed method-of-moments estimators (a similar approach is justified theoretically in Fearnhead and Prangle (2012)). Note that Wilson et al (2009) developed their ABC to analyze a single data set, and could afford for summary statistics that require a noticeable computation time. By contrast, we present a general method for choosing a subset of summary statistics based on the calculation of the Cp index.…”

Section: Discussionmentioning

confidence: 99%

“…Although this ratio is widely used as an indicator of molecular adaptation (for example, Nielsen and Yang, 1998;Wilson and McVean, 2006;Wilson et al, 2009), this methodology is not free from some controversy. One of the main criticisms is its use in single-population samples, where the close ancestry of the sequences may break the relation of this ratio to the adaptation coefficient (Kryazhimskiy and Plotkin, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…As far as we know, only Wilson and McVean (2006) and Wilson et al (2009) have proposed methods for the co-estimation of recombination and adaptation rates from coding sequences. The former used an approximation to the coalescent with recombination based on the product of approximating conditionals likelihood and the copying model of Li and Stephens (2003), which was implemented in the package OmegaMap using a Markov chain Monte Carlo framework.…”

Section: Introductionmentioning

confidence: 99%

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Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

et al. 2013

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The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

et al. 2013

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“…We quantified g by dividing the average Ks value (synonymous substitutions per synonymous site) of all core genes with no obvious signal of recent recombination by the mutation rate of bacterial genomes (5.4 Â 10 À10 substitution/site/generation; Drake et al, 1998), as suggested earlier (Wilson et al, 2009;Jarvik et al, 2010). (Synonymous substitutions are thought to be neutral and thus, reflect the intrinsic mutational rate).…”

Section: Clonal or Sexual Speciation?mentioning

confidence: 99%

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea

et al. 2010

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High-throughput sequencing studies during the last decade have uncovered that bacterial genomes are very diverse and dynamic, resulting primarily from the frequent and promiscuous horizontal gene exchange that characterizes the bacterial domain of life. However, a robust understanding of the rates of genetic exchange for most bacterial species under natural conditions and the influence of the ecological settings on the rates remain elusive, severely limiting our view of the microbial world. Here, we analyzed the complete genomic sequences and expressed transcriptomes of several Shewanella baltica isolates recovered from different depths in the Baltic Sea and found that isolates from more similar depths had exchanged a larger fraction of their core and auxiliary genome, up to 20% of the total, compared with isolates from more different depths. The exchanged genes seem to be ecologically important and contribute to the successful adaptation of the isolates to the unique physicochemical conditions of the depth. Importantly, the latter genes were exchanged in very recent past, presumably as an effect of isolate's seasonal migration across the water column, and reflected sexual speciation within the same depth. Therefore, our findings reveal that genetic exchange in response to environmental settings may be surprisingly rapid, which has important broader impacts for understanding bacterial speciation and evolution and for modeling bacterial responses to human-induced environmental impacts.

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“…To cope with this problem, the use of the coalescent theory (Schierup and Wiuf, 2010) and gene genealogies has been increasing in bacteria (Moodley et al, 2009;Wilson et al, 2009;Doroghazi and Buckley, 2010).…”

Section: Introductionmentioning

confidence: 99%

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

et al. 2011

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We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during R. solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral phylotype, phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination and evidences of long-distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether R. solanacearum lineages will eventually evolve in distinct species remains an open question. The intensification of cropping and increase of geographical dispersion may favour situations of phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool.

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Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni

Cited by 172 publications

References 61 publications

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

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