The Experts below are selected from a list of 30357 Experts worldwide ranked by ideXlab platform
Alvaro Sanchez - One of the best experts on this subject based on the ideXlab platform.
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on the deformability of an empirical fitness landscape by Microbial Evolution
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Djordje Bajic, Jean C C Vila, Zachary D Blount, Alvaro SanchezAbstract:A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining Evolutionary trajectories and the predictability of Evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli Deformability is quantified by the noncommutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an Evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects Evolutionary trajectories in the short range. However, mutations with large environmental effects produce long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our results therefore suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast Evolution over small mutational distances despite the potential attenuation of that power over longer Evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-Evolutionary dynamics with complex genetics and genomics.
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on the deformability of an empirical fitness landscape by Microbial Evolution
bioRxiv, 2018Co-Authors: Djordje Bajic, Jean C C Vila, Zachary D Blount, Alvaro SanchezAbstract:A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining Evolutionary trajectories and the predictability of Evolution. Theory suggests that this topography can be "deformed" by mutations that produce substantial changes to the environment. In spite of its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium E. coli. Deformability is quantified by the non-commutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an Evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects Evolutionary trajectories in the short-range. However, mutations with large environmental effects leave these as a "legacy", producing long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our methods and results provide the basis for an integration between adaptive and eco-Evolutionary dynamics with complex genetics and genomics.
Richard E. Lenski - One of the best experts on this subject based on the ideXlab platform.
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Experimental Evolution and the dynamics of adaptation and genome Evolution in Microbial populations
The ISME Journal, 2017Co-Authors: Richard E. LenskiAbstract:Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria’s mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome Evolution and used parallel Evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other Microbial Evolution experiments and suggest how the fields of experimental Evolution and Microbial ecology might intersect going forward.
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what is adaptation by natural selection perspectives of an experimental microbiologist
PLOS Genetics, 2017Co-Authors: Richard E. LenskiAbstract:Ever since Darwin, the role of natural selection in shaping the morphological, physiological, and behavioral adaptations of animals and plants across generations has been central to understanding life and its diversity. New discoveries have shown with increasing precision how genetic, molecular, and biochemical processes produce and express those organismal features during an individual's lifetime. When it comes to microorganisms, however, understanding the role of natural selection in producing adaptive solutions has historically been, and sometimes continues to be, contentious. This tension is curious because microbes enable one to observe the power of adaptation by natural selection with exceptional rigor and clarity, as exemplified by the burgeoning field of experimental Microbial Evolution. I trace the development of this field, describe an experiment with Escherichia coli that has been running for almost 30 years, and highlight other experiments in which natural selection has led to interesting dynamics and adaptive changes in Microbial populations.
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dynamics of insertion sequence elements during experimental Evolution of bacteria
Research in Microbiology, 2004Co-Authors: Dominique Schneider, Richard E. LenskiAbstract:We review the intersection between two areas of Microbial Evolution that were research foci of Michel Blot. One focus is the behavior of insertion sequence (IS) elements, including their role in promoting the Evolutionary adaptation of their hosts. The other focus is experimental Evolution, an approach that allows the dynamics of genomic and phenotypic change to be observed in the laboratory. This review shows that IS elements are useful as markers for detecting genomic change over experimental time scales and, moreover, that IS elements generate some of the beneficial mutations that increase organismal fitness.
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diminishing returns from mutation supply rate in asexual populations
Science, 1999Co-Authors: J A G M De Visser, Clifford Zeyl, Philip J Gerrish, Jeffrey L Blanchard, Richard E. LenskiAbstract:Mutator genotypes with increased mutation rates may be especially important in Microbial Evolution if genetic adaptation is generally limited by the supply of mutations. In experimental populations of the bacterium Escherichia coli , the rate of Evolutionary adaptation was proportional to the mutation supply rate only in particular circumstances of small or initially well-adapted populations. These experiments also demonstrate a “speed limit” on adaptive Evolution in asexual populations, one that is independent of the mutation supply rate.
Djordje Bajic - One of the best experts on this subject based on the ideXlab platform.
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on the deformability of an empirical fitness landscape by Microbial Evolution
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Djordje Bajic, Jean C C Vila, Zachary D Blount, Alvaro SanchezAbstract:A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining Evolutionary trajectories and the predictability of Evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli Deformability is quantified by the noncommutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an Evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects Evolutionary trajectories in the short range. However, mutations with large environmental effects produce long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our results therefore suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast Evolution over small mutational distances despite the potential attenuation of that power over longer Evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-Evolutionary dynamics with complex genetics and genomics.
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on the deformability of an empirical fitness landscape by Microbial Evolution
bioRxiv, 2018Co-Authors: Djordje Bajic, Jean C C Vila, Zachary D Blount, Alvaro SanchezAbstract:A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining Evolutionary trajectories and the predictability of Evolution. Theory suggests that this topography can be "deformed" by mutations that produce substantial changes to the environment. In spite of its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium E. coli. Deformability is quantified by the non-commutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an Evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects Evolutionary trajectories in the short-range. However, mutations with large environmental effects leave these as a "legacy", producing long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our methods and results provide the basis for an integration between adaptive and eco-Evolutionary dynamics with complex genetics and genomics.
Michael M. Desai - One of the best experts on this subject based on the ideXlab platform.
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global epistasis emerges from a generic model of a complex trait
eLife, 2021Co-Authors: Gautam Reddy, Michael M. DesaiAbstract:Epistasis between mutations can make adaptation contingent on Evolutionary history. Yet despite widespread 'microscopic' epistasis between the mutations involved, Microbial Evolution experiments show consistent patterns of fitness increase between replicate lines. Recent work shows that this consistency is driven in part by global patterns of diminishing-returns and increasing-costs epistasis, which make mutations systematically less beneficial (or more deleterious) on fitter genetic backgrounds. However, the origin of this 'global' epistasis remains unknown. Here, we show that diminishing-returns and increasing-costs epistasis emerge generically as a consequence of pervasive microscopic epistasis. Our model predicts a specific quantitative relationship between the magnitude of global epistasis and the stochastic effects of microscopic epistasis, which we confirm by reanalyzing existing data. We further show that the distribution of fitness effects takes on a universal form when epistasis is widespread and introduce a novel fitness landscape model to show how phenotypic Evolution can be repeatable despite sequence-level stochasticity.
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global epistasis emerges from a generic model of a complex trait
bioRxiv, 2020Co-Authors: Gautam Reddy, Michael M. DesaiAbstract:Epistasis between mutations can make adaptation contingent on Evolutionary history. Yet despite widespread "microscopic" epistasis between the mutations involved, Microbial Evolution experiments show consistent patterns of fitness increases during laboratory adaptation. Recent work has found that this consistency is driven in part by global patterns of diminishing-returns and increasing-costs epistasis, which make mutations systematically less beneficial (or more deleterious) on more-fit genetic backgrounds. This global "macroscopic" epistasis is thought to make phenotypic Evolution repeatable, even while the genetic basis of this Evolution is highly stochastic. However, the mechanistic basis of consistent macroscopic epistasis remains unknown. Here we show, using a generic model of a complex trait, that global diminishing-returns and increasing-costs epistasis arise naturally as a consequence of pervasive microscopic epistasis, emerging simply as a statistical trend due to an imbalance between positive and negative contributions to the fitness. Our model predicts a specific quantitative relationship between the magnitude of global epistasis and the stochastic effects of microscopic epistasis, which we confirm by re-analyzing existing data. We also describe the predictions of this model for the patterns of fitness Evolution and for how the distribution of fitness effects shifts as a population adapts, and propose additional experimental tests of these results.
Zachary D Blount - One of the best experts on this subject based on the ideXlab platform.
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on the deformability of an empirical fitness landscape by Microbial Evolution
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Djordje Bajic, Jean C C Vila, Zachary D Blount, Alvaro SanchezAbstract:A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining Evolutionary trajectories and the predictability of Evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium Escherichia coli Deformability is quantified by the noncommutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an Evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects Evolutionary trajectories in the short range. However, mutations with large environmental effects produce long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our results therefore suggest that, even in situations in which mutations have strong environmental effects, fitness landscapes may retain their power to forecast Evolution over small mutational distances despite the potential attenuation of that power over longer Evolutionary trajectories. Our methods and results provide an avenue for integrating adaptive and eco-Evolutionary dynamics with complex genetics and genomics.
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on the deformability of an empirical fitness landscape by Microbial Evolution
bioRxiv, 2018Co-Authors: Djordje Bajic, Jean C C Vila, Zachary D Blount, Alvaro SanchezAbstract:A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining Evolutionary trajectories and the predictability of Evolution. Theory suggests that this topography can be "deformed" by mutations that produce substantial changes to the environment. In spite of its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically characterized the deformability of the genome-wide metabolic fitness landscape of the bacterium E. coli. Deformability is quantified by the non-commutativity of epistatic interactions, which we experimentally demonstrate in mutant strains on the path to an Evolutionary innovation. Our analysis shows that the deformation of fitness landscapes by metabolic mutations rarely affects Evolutionary trajectories in the short-range. However, mutations with large environmental effects leave these as a "legacy", producing long-range landscape deformations in distant regions of the genotype space that affect the fitness of later descendants. Our methods and results provide the basis for an integration between adaptive and eco-Evolutionary dynamics with complex genetics and genomics.