Trade-off shapes diversity in eco-evolutionary dynamics

Farahpour, Farnoush; Saeedghalati, Mohammadkarim; Brauer, Verena S.; Hoffmann, Daniel

doi:10.1101/184432

Cited by 9 publications

(10 citation statements)

References 95 publications

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“…Due to very high frequencies of mutator clones within populations 2 and 4, we do not present Muller plots for these populations. Muller plots were produced using the R package MullerPlot ( Farahpour et al. 2016 ).…”

Section: Resultsmentioning

confidence: 99%

Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase

Katz

Avrani

Yavneh

et al. 2021

Molecular Biology and Evolution

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Many bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years, following exhaustion of external resources, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time E. coli continuously adapts genetically, through the accumulation of mutations. For non-mutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accumulation. Despite the rapid and convergent manner in which populations adapt under LTSP, they continue to harbor extensive genetic variation. The dynamics of evolution of mutation rates under LTSP are particularly interesting. The emergence of mutators affects overall mutation accumulation rates as well as the mutational spectra and the ultimate spectrum of adaptive alleles acquired under LTSP. With time, mutators can evolve even higher mutation rates, through the acquisition of additional mutation-rate enhancing mutations. Different mutator and non-mutator clones within a single population and time point can display extreme variation in their mutation rates, resulting in differences in both the dynamics of adaptation and their associated deleterious burdens. Despite these differences, clones that vary greatly in their mutation rates tend to co-exist within their populations for many years, under LTSP.

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Section: Resultsmentioning

confidence: 99%

Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase

Katz

Avrani

Yavneh

et al. 2021

Molecular Biology and Evolution

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“…Frequencies are recorded every

generations over

generations. The plot was produced with R-package MullerPlot ( Farahpour et al, 2016 ). ( b ) Distribution over trait space: Snapshot of distribution of strains and species in trait space after

generations.…”

Section: Resultsmentioning

confidence: 99%

Trade-off shapes diversity in eco-evolutionary dynamics

Farahpour

Saeedghalati

Brauer

et al. 2018

eLife

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We introduce an Interaction- and Trade-off-based Eco-Evolutionary Model (ITEEM), in which species are competing in a well-mixed system, and their evolution in interaction trait space is subject to a life-history trade-off between replication rate and competitive ability. We demonstrate that the shape of the trade-off has a fundamental impact on eco-evolutionary dynamics, as it imposes four phases of diversity, including a sharp phase transition. Despite its minimalism, ITEEM produces a remarkable range of patterns of eco-evolutionary dynamics that are observed in experimental and natural systems. Most notably we find self-organization towards structured communities with high and sustained diversity, in which competing species form interaction cycles similar to rock-paper-scissors games.

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“…Despite adaptive evolution in steady environments, deficient genomes evolved in a jack-of-all-trades-and-master-of-all manner, which was theoretically proposed as one of three mechanisms for specialism that is widespread in nature 50 , in comparison to the wild-type genome, which adopted a tradeoff mechanism, which was generally explained by constraints in phenotypic space 51,52 . In nature, the trade-off strategy might be more frequent and reasonable for costless adaptation and niche expansion during eco-evolution 2,53,54 . As both the genome and the environment participate in ecological evolution, the coordination among genetic richness, adaptiveness and niche broadness revealed a quantitative linkage of adaptive evolution to ecology.…”

Section: Discussionmentioning

confidence: 99%

Local adaptation mediated niche expansion in correlation with genetic richness

Kurokawa

Nishimura

Ying

2021

Preprint

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As a central issue in evolution and ecology, the quantitative relationship among the genome, adaptation and the niche was investigated. Local adaptation of five Escherichia coli strains carrying either the wild-type genome or reduced genomes was achieved by experimental evolution. A high-throughput fitness assay of the ancestor and evolved populations across an environmental gradient of eight niches resulted in a total of 80 fitness curves generated from 2,220 growth curves. Further analyses showed that the increases in both local adaptiveness and niche broadness were negatively correlated with genetic richness. Local adaptation caused common niche expansion, whereas niche expansion for generality or speciality was decided by genetic richness. The order of the mutations accumulated stepwise was correlated with the magnitude of the fitness increase attributed to mutation accumulation. Pre-adaptation probably participated in coordination among genetic richness, local adaptation and niche expansion.

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Trade-off shapes diversity in eco-evolutionary dynamics

Cited by 9 publications

References 95 publications

Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase

Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase

Trade-off shapes diversity in eco-evolutionary dynamics

Local adaptation mediated niche expansion in correlation with genetic richness

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