The rise and fall of deleterious mutation

Balbi, Kevin; Feil, Edward J.

doi:10.1016/j.resmic.2007.09.005

Cited by 23 publications

(20 citation statements)

References 61 publications

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“…Additionally, some other critical clues found in our study may, to some extent, explain the observation of high community rERs in extreme environments. As it was previously suggested that natural selection is less efficient in small populations30, our results supposed that relaxed purifying selection might occur more frequently in extreme environments because of the relatively smaller population sizes. Similarly, a more relaxed selective constraint was found in microbial communities in the deep sea rather than the surface water19.…”

Section: Discussionsupporting

confidence: 64%

Microbial communities evolve faster in extreme environments

Hua

Huang

et al. 2014

Sci Rep

121

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Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments.

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Section: Discussionsupporting

confidence: 64%

Microbial communities evolve faster in extreme environments

Hua

Huang

et al. 2014

Sci Rep

121

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“…It has been found that among closely related strains or species dN/dS ratios can be elevated in a time-dependent fashion [31],[32], and thus not reflect longer term selection pressures. This is because such comparisons are akin to the study of de novo mutations that have not yet been eliminated at the population level.…”

Section: Resultsmentioning

confidence: 99%

Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen

Larsson

Elfsmark²,

Svensson³

et al. 2009

PLoS Pathog

127

149

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Francisella tularensis is a potent mammalian pathogen well adapted to intracellular habitats, whereas F. novicida and F. philomiragia are less virulent in mammals and appear to have less specialized lifecycles. We explored adaptations within the genus that may be linked to increased host association, as follows. First, we determined the genome sequence of F. tularensis subsp. mediasiatica, the only subspecies that had not been previously sequenced. This genome, and those of 12 other F. tularensis isolates, were then compared to the genomes of F. novicida (three isolates) and F. philomiragia (one isolate). Signs of homologous recombination were found in ∼19.2% of F. novicida and F. philomiragia genes, but none among F. tularensis genomes. In addition, random insertions of insertion sequence elements appear to have provided raw materials for secondary adaptive mutations in F. tularensis, e.g. for duplication of the Francisella Pathogenicity Island and multiplication of a putative glycosyl transferase gene. Further, the five major genetic branches of F. tularensis seem to have converged along independent routes towards a common gene set via independent losses of gene functions. Our observations suggest that despite an average nucleotide identity of >97%, F. tularensis and F. novicida have evolved as two distinct population lineages, the former characterized by clonal structure with weak purifying selection, the latter by more frequent recombination and strong purifying selection. F. tularensis and F. novicida could be considered the same bacterial species, given their high similarity, but based on the evolutionary analyses described in this work we propose retaining separate species names.

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“…They include the effects of recent fixations and shared ancestral polymorphisms, but neglect the effect of lineage-specific polymorphisms. Their study was motivated by earlier studies on the effect of ancestral polymorphisms on estimates of mutation rate for closely related lineages, related to the apparent mutation rate acceleration (Ho and Larson 2006; Balbi and Feil 2007). A third study closely related to ours is the study by Kryazhimskiy and Plotkin (2008).…”

Section: Discussionmentioning

confidence: 99%

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

Mugal¹,

Wolf²,

Kaj³

2013

Molecular Biology and Evolution

125

138

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The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald–Kreitman test and other related statistics, in particular for closely related lineages.

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The rise and fall of deleterious mutation

Cited by 23 publications

References 61 publications

Microbial communities evolve faster in extreme environments

Microbial communities evolve faster in extreme environments

Molecular Evolutionary Consequences of Niche Restriction in Francisella tularensis, a Facultative Intracellular Pathogen

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

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