Clonal interference in large populations

Park, Su‐Chan; Krug, Joachim

doi:10.1073/pnas.0705778104

Cited by 173 publications

(214 citation statements)

References 34 publications

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“…Although the average rate of fixations declines only modestly during the experiment, there is noticeable temporal variability as mutations often fix in “cohorts” of multiple linked mutations. These cohorts have been observed previously 1,29 and are expected in models of clonal interference 31,32 . However, they could also reflect transiently stable frequency-dependent interactions, as previously observed in Ara–1 29 .…”

Section: Dynamics and Fates Of New Mutationssupporting

confidence: 77%

The dynamics of molecular evolution over 60,000 generations

Good

McDonald

Barrick

et al. 2017

Nature

653

839

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The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. Here, we analyze the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at 500-generation intervals through 60,000 generations. Despite a declining rate of fitness gain, molecular evolution continues to be characterized by signatures of rapid adaptation, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present new evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.

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Section: Dynamics and Fates Of New Mutationssupporting

confidence: 77%

The dynamics of molecular evolution over 60,000 generations

Good

McDonald

Barrick

et al. 2017

Nature

653

839

View full text Add to dashboard Cite

show abstract

“…1B). Although theory (e.g., Rozen et al 2002;Park and Krug 2007) and data (e.g., Miralles et al 1999;De Visser and Rozen 2006) have previously demonstrated that competition between mutations in clonal lineages can lead to accelerated adaptation, ours is the first evidence that competition from mutations in competitors that are initially lower in fitness also influences the fitness effect of mutations that fix. The results imply that the evolutionary history of populations is written not only by the winners but by the losers as well.…”

Section: Discussionmentioning

confidence: 84%

Here’s to the Losers: Evolvable Residents Accelerate the Evolution of High-Fitness Invaders

Gifford¹,

Toll-Riera²,

Kojadinovic³

et al. 2015

The American Naturalist

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Recent work has shown that evolvability plays a key role in determining the long-term population dynamics of asexual clones. However, simple considerations suggest that the evolvability of a focal lineage of bacteria should also be influenced by the evolvability of its competitors. First, evolvable competitors should accelerate evolution by impeding the fixation of the focal lineage through a clonal interference-like mechanism. Second, evolvable competitors should increase the strength of selection by rapidly degrading the environment, increasing selection for adaptive mutations. Here we tested these ideas by allowing a high-fitness clone of the bacterium Pseudomonas aeruginosa to invade populations of two low-fitness resident clones that differ in their evolvability. Both competition from mutations in the resident lineage and environmental degradation lead to faster adaptation in the invader through fixing single mutations with a greater fitness advantage. The results suggest that competition from mutations in both the successful invader and the unsuccessful resident shapes the adaptive trajectory of the invader through both direct competition and indirect environmental effects. Therefore, to predict evolutionary outcomes, it will be necessary to consider the evolvability of all members of the community and the effects of adaptation on the quality of the environment. This is particularly relevant to mixed microbial communities where lineages differ in their adaptive potential, a common feature of chronic infections. abstract: Recent work has shown that evolvability plays a key role in determining the long-term population dynamics of asexual clones. However, simple considerations suggest that the evolvability of a focal lineage of bacteria should also be influenced by the evolvability of its competitors. First, evolvable competitors should accelerate evolution by impeding the fixation of the focal lineage through a clonal interference-like mechanism. Second, evolvable competitors should increase the strength of selection by rapidly degrading the environment, increasing selection for adaptive mutations. Here we tested these ideas by allowing a high-fitness clone of the bacterium Pseudomonas aeruginosa to invade populations of two low-fitness resident clones that differ in their evolvability. Both competition from mutations in the resident lineage and environmental degradation lead to faster adaptation in the invader through fixing single mutations with a greater fitness advantage. The results suggest that competition from mutations in both the successful invader and the unsuccessful resident shapes the adaptive trajectory of the invader through both direct competition and indirect environmental effects. Therefore, to predict evolutionary outcomes, it will be necessary to consider the evolvability of all members of the community and the effects of adaptation on the quality of the environment. This is particularly relevant to mixed microbial communities where lineages differ in their adaptive potential, a...

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“…The value ν c = 1/[N ln(N )] is thus the scale for clonal interference [23,30] and for the small island effect [24]. In fact, one can solve the difference equation (2) exactly by writing it as a first order difference equation for…”

Section: Neutral Dynamics With Pure Demographic Stochasticity (Dmentioning

confidence: 99%

Stability of two-species communities: Drift, environmental stochasticity, storage effect and selection

Danino

Kessler

Shnerb

2018

Theoretical Population Biology

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The dynamics of two competing species in a finite size community is one of the most studied problems in population genetics and community ecology. Stochastic fluctuations lead, inevitably, to the extinction of one of the species, but the relevant timescale depends on the underlying dynamics. The persistence time of the community has been calculated for neutral models, where the only drive of the system is drift (demographic stochasticity) and for models with strong selection. Following recent analyses that stress the importance of environmental stochasticity in empirical systems, we present here a general theory of persistence time of two-species community where drift, environmental variations and time independent selective advantage are all taken into account.

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Clonal interference in large populations

Cited by 173 publications

References 34 publications

The dynamics of molecular evolution over 60,000 generations

The dynamics of molecular evolution over 60,000 generations

Here’s to the Losers: Evolvable Residents Accelerate the Evolution of High-Fitness Invaders

Stability of two-species communities: Drift, environmental stochasticity, storage effect and selection

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