Negative epistasis between beneficial mutations in an evolving bacterial population

scientific article published in June 2011

Negative epistasis between beneficial mutations in an evolving bacterial population is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1126/SCIENCE.1203801
P698PubMed publication ID21636772
P5875ResearchGate publication ID51187210

P50authorRichard LenskiQ713637
Timothy F. CooperQ123559146
P2093author name stringDominique Schneider
Duy M Dinh
Aisha I Khan
P2860cites workThe biochemical architecture of an ancient adaptive landscapeQ34461523
Tests of parallel molecular evolution in a long-term experiment with Escherichia coliQ34694847
Epistasis correlates to genomic complexityQ35080659
Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitatQ35760235
The dynamics of adaptation on correlated fitness landscapesQ37399576
Epistasis and the adaptability of an RNA virusQ41907301
Interactions between stressful environment and gene deletions alleviate the expected average loss of fitness in yeast.Q42065537
Epistatic buffering of fitness loss in yeast double deletion strainsQ42613014
Exploring the effect of sex on empirical fitness landscapesQ46501857
The fate of competing beneficial mutations in an asexual population.Q54262235
LONG-TERM EXPERIMENTAL EVOLUTION IN ESCHERICHIA COLI. III. VARIATION AMONG REPLICATE POPULATIONS IN CORRELATED RESPONSES TO NOVEL ENVIRONMENTS.Q54617461
THE EVOLUTION OF POSTZYGOTIC ISOLATION: ACCUMULATING DOBZHANSKY-MULLER INCOMPATIBILITIESQ56227508
Sex and deleterious mutationQ59036312
Evolution of mutational robustness in an RNA virusQ21563619
Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 GenerationsQ22066139
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coliQ22066316
Genome evolution and adaptation in a long-term experiment with Escherichia coliQ22122199
Sex increases the efficacy of natural selection in experimental yeast populationsQ22122472
Mutational robustness can facilitate adaptationQ24624037
Second-order selection for evolvability in a large Escherichia coli populationQ24635911
Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptationQ24794572
Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populationsQ28245607
Selection for robustness in mutagenized RNA virusesQ28469235
Darwinian evolution can follow only very few mutational paths to fitter proteinsQ29616042
The properties of adaptive walks in evolving populations of fungusQ30947119
Understanding the evolutionary fate of finite populations: the dynamics of mutational effectsQ33281050
Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein regionQ33853183
Evolvability of an RNA virus is determined by its mutational neighbourhoodQ33914492
The population genetics of ecological specialization in evolving Escherichia coli populationsQ33922714
Parallel changes in gene expression after 20,000 generations of evolution in EscherichiacoliQ34171913
Perspective: Sign epistasis and genetic constraint on evolutionary trajectoriesQ34437784
Test of synergistic interactions among deleterious mutations in bacteriaQ34448329
P433issue6034
P407language of work or nameEnglishQ1860
P921main subjectbeneficial mutationQ111187232
P1104number of pages4
P304page(s)1193-1196
P577publication date2011-06-01
P1433published inScienceQ192864
P1476titleNegative epistasis between beneficial mutations in an evolving bacterial population
P478volume332

Reverse relations

cites work (P2860)
Q41658937A Model for Designing Adaptive Laboratory Evolution Experiments
Q36182021A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut
Q42551296A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain
Q58827491A meta-analysis of the effects of plant traits and geographical scale on the magnitude of adaptive differentiation as measured by the difference between QST and FST
Q43110160A model of substitution trajectories in sequence space and long-term protein evolution.
Q51826213A shift from magnitude to sign epistasis during adaptive evolution of a bacterial social trait.
Q35764270A tortoise-hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria
Q37175865Adaptation in protein fitness landscapes is facilitated by indirect paths
Q37263496Adaptation of Enterococcus faecalis to daptomycin reveals an ordered progression to resistance
Q54253302Adaptation of Escherichia coli to glucose promotes evolvability in lactose.
Q35175854Adaptation of a cyanobacterium to a biochemically rich environment in experimental evolution as an initial step toward a chloroplast-like state
Q28647522Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli
Q34130237Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli.
Q34312048Adaptive evolution: evaluating empirical support for theoretical predictions
Q30419009Adaptive walks on the fitness landscape of music
Q59831979Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose
Q47587442Additive Phenotypes Underlie Epistasis of Fitness Effects
Q52758683Additive genetic architecture underlying a rapidly evolving sexual signaling phenotype in the Hawaiian cricket genus Laupala.
Q36306331An in vivo system for directed experimental evolution of rabbit haemorrhagic disease virus
Q48133871Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection
Q28534615Bacterial adaptation through loss of function
Q38103942Bacterial genome evolution within a clonal population: from in vitro investigations to in vivo observations
Q37173084Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness
Q38254752Beyond genome sequencing: lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer.
Q34443462Biased estimates of diminishing-returns epistasis? Empirical evidence revisited
Q35204371Biophysical fitness landscapes for transcription factor binding sites
Q90350496CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli
Q34594904Can you sequence ecology? Metagenomics of adaptive diversification
Q28727500Cancer in light of experimental evolution
Q36485051Chromosomal duplication is a transient evolutionary solution to stress.
Q30300777Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations.
Q34497324Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1.
Q42379133Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model
Q27938036Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.
Q42906922Conservative sex and the benefits of transformation in Streptococcus pneumoniae
Q28647800Contingency and entrenchment in protein evolution under purifying selection
Q42204146Contribution of silent mutations to thermal adaptation of RNA bacteriophage Qβ
Q33608467Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli
Q29011147Deleterious Passengers in Adapting Populations
Q29002206Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps
Q64929525Detecting adaptive convergent amino acid evolution.
Q42633184Detecting epistasis from an ensemble of adapting populations.
Q34992854Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq
Q34264500Differential epigenetic compatibility of qnr antibiotic resistance determinants with the chromosome of Escherichia coli.
Q36279809Differential paralog divergence modulates genome evolution across yeast species.
Q27683542Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme
Q53717083Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus.
Q54219938Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.
Q28584571Disentangling genetic and epigenetic determinants of ultrafast adaptation
Q51300318Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations.
Q90212325Diversification and Evolution of Vancomycin-Resistant Enterococcus faecium during Intestinal Domination
Q27693280Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution
Q38187602Dynamics and constraints of enzyme evolution
Q47877246Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria.
Q26783005Elucidating the molecular architecture of adaptation via evolve and resequence experiments
Q89723844Emerging Frontiers in the Study of Molecular Evolution
Q38218962Empirical fitness landscapes and the predictability of evolution
Q34313206Engineering ecosystems and synthetic ecologies
Q37412772Environment determines epistatic patterns for a ssDNA virus
Q55436455Environmental change exposes beneficial epistatic interactions in a catalytic RNA.
Q50716194Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila.
Q39162611Epistasis and the Evolution of Antimicrobial Resistance
Q40725548Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model?
Q28653314Epistasis can accelerate adaptive diversification in haploid asexual populations
Q51332673Epistasis from functional dependence of fitness on underlying traits.
Q53156835Epistatic interactions between ancestral genotype and beneficial mutations shape evolvability in Pseudomonas aeruginosa.
Q54304014Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations.
Q33583647Epistatically interacting substitutions are enriched during adaptive protein evolution
Q34332944Evolution in response to climate change: in pursuit of the missing evidence
Q90743445Evolution in the light of fitness landscape theory
Q34596522Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress
Q42369791Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome
Q43101601Evolution of clonal populations approaching a fitness peak.
Q41227508Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli
Q39675173Evolution of sex: Using experimental genomics to select among competing theories
Q92879130Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures
Q34005257Evolutionary accessibility of mutational pathways
Q36242283Evolutionary adaptation after crippling cell polarization follows reproducible trajectories
Q89545822Evolutionary constraints in fitness landscapes
Q51461404Evolutionary history and genetic parallelism affect correlated responses to evolution.
Q41132191Evolutionary implications of Liebig's law of the minimum: Selection under low concentrations of two nonsubstitutable nutrients
Q37983903Evolutionary insight from whole-genome sequencing of experimentally evolved microbes.
Q83227516Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle
Q35867457Evolvability of an Optimal Recombination Rate
Q57174769Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution
Q90345321Experimental Studies of Evolutionary Dynamics in Microbes
Q34289524Experimental evolution
Q38683209Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations
Q28661568Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii.
Q34362047Experiments on the role of deleterious mutations as stepping stones in adaptive evolution
Q42695844Exploiting ecology in drug pulse sequences in favour of population reduction
Q38414823Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health
Q36410897First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes
Q51313054Fisher's geometric model predicts the effects of random mutations when tested in the wild.
Q33575800Fisher's geometrical model emerges as a property of complex integrated phenotypic networks
Q41849560Fitness conferred by replaced amino acids declines with time
Q64101025Fluctuating environments select for short-term phenotypic variation leading to long-term exploration
Q58703918From Local Adaptation to Speciation: Specialization and Reinforcement
Q36586464Functional evolution of an anthocyanin pathway enzyme during a flower color transition
Q35004076Generation and study of the strains of streptomycetes - heterologous hosts for production of moenomycin
Q43184230Genetic background affects epistatic interactions between two beneficial mutations
Q38639465Genetic variation in adaptability and pleiotropy in budding yeast
Q28651650Genome dynamics during experimental evolution
Q21560957Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment
Q22122302Genome-scale engineering for systems and synthetic biology
Q28082330Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments
Q34708295Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter
Q34489656Hidden epistastic interactions can favour the evolution of sex and recombination
Q55285004High mutation rates limit evolutionary adaptation in Escherichia coli.
Q36372082High-order epistasis shapes evolutionary trajectories
Q41292956Hitchhiking and epistasis give rise to cohort dynamics in adapting populations
Q35943086Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.
Q37184676How Good Are Statistical Models at Approximating Complex Fitness Landscapes?
Q48142732How Many Biochemistries Are Available To Build a Cell?
Q92283288IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations
Q36368892Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation
Q99207734Idiosyncratic epistasis creates universals in mutational effects and evolutionary trajectories
Q30380900In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization.
Q92471939Increasing growth rate slows adaptation when genotypes compete for diffusing resources
Q33730568Inferring fitness landscapes by regression produces biased estimates of epistasis.
Q47102776Inferring genetic interactions from comparative fitness data.
Q52591835Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides.
Q30560970Interaction-based feature selection and classification for high-dimensional biological data
Q35616623Investigating the Role of Gene-Gene Interactions in TB Susceptibility
Q45345601Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.
Q51438302Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria.
Q43231261Long-term diversity and genome adaptation of Acinetobacter baylyi in a minimal-medium chemostat
Q45261637Long-term dynamics of adaptation in asexual populations
Q40567914Love the one you're with: replicate viral adaptations converge on the same phenotypic change
Q37311367Low selection pressure aids the evolution of cooperative ribozyme mutations in cells
Q34241242Many pathways in laboratory evolution can lead to improved enzymes: how to escape from local minima.
Q35105723Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations.
Q35764471Measuring ruggedness in fitness landscapes.
Q38053191Mechanisms and selection of evolvability: experimental evidence.
Q34405876Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli
Q36330218Metabolic specialization and the assembly of microbial communities
Q39169158Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity
Q42771933Microbiology. Antibiotic resistance, not shaken or stirred
Q59789922Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Q64232908Modular epistasis and the compensatory evolution of gene deletion mutants
Q58709856Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene
Q28647014Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process
Q40134218Multi-hierarchical profiling: an emerging and quantitative approach to characterizing diverse biological networks
Q43245159Multiple Resistance at No Cost: Rifampicin and Streptomycin a Dangerous Liaison in the Spread of Antibiotic Resistance.
Q57118367Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis
Q35583838Multiplexed tracking of combinatorial genomic mutations in engineered cell populations
Q34679960Mutations in global regulators lead to metabolic selection during adaptation to complex environments
Q31039375Network-Based Analysis of eQTL Data to Prioritize Driver Mutations
Q37997288New insights into bacterial adaptation through in vivo and in silico experimental evolution
Q92216184Noise-precision tradeoff in predicting combinations of mutations and drugs
Q37493368On the (un)predictability of a large intragenic fitness landscape
Q46337805On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations
Q41987306Optimizing complex phenotypes through model-guided multiplex genome engineering
Q28595783Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1
Q45994253Parallel emergence of negative epistasis across experimental lineages.
Q92568694Patterns and Mechanisms of Diminishing Returns from Beneficial Mutations
Q41864870Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene
Q50914574Phase transition in random adaptive walks on correlated fitness landscapes.
Q51367880Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes.
Q38966881Potential for adaptation overrides cost of resistance.
Q58760610Power law fitness landscapes and their ability to predict fitness
Q35079781Properties of selected mutations and genotypic landscapes under Fisher's geometric model.
Q92601578Pseudomonas aeruginosa Interstrain Dynamics and Selection of Hyperbiofilm Mutants during a Chronic Infection
Q55208702Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines.
Q41911214Rates of fitness decline and rebound suggest pervasive epistasis
Q38254854Recent advances in the evolutionary engineering of industrial biocatalysts
Q90244482Recent insights into the genotype-phenotype relationship from massively parallel genetic assays
Q28540044Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1
Q41592999Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering
Q46298833Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria.
Q41987123Regulatory revolution: evolving the "anti-LacI" repressor
Q41905788Repeatability of evolution on epistatic landscapes
Q28607370Reverse evolution leads to genotypic incompatibility despite functional and active site convergence
Q41758914Rewiring of genetic networks in response to modification of genetic background
Q45071448Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift.
Q36269559Seeking Goldilocks During Evolution of Drug Resistance
Q47378055Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking
Q42324334Selection Limits to Adaptive Walks on Correlated Landscapes
Q44581995Selection biases the prevalence and type of epistasis along adaptive trajectories
Q34325560Selection-driven gene loss in bacteria
Q35761876Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung
Q60960612Sex-specific dominance reversal of genetic variation for fitness
Q35035921Should evolutionary geneticists worry about higher-order epistasis?
Q28597478Should tissue structure suppress or amplify selection to minimize cancer risk?
Q93013409Simulations reveal challenges to artificial community selection and possible strategies for success
Q36504175Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance
Q28547894Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
Q35748281Stickbreaking: a novel fitness landscape model that harbors epistasis and is consistent with commonly observed patterns of adaptive evolution
Q92488321Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory
Q28551065Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein
Q37346935Substrate ambiguous enzymes within the Escherichia coli proteome offer different evolutionary solutions to the same problem
Q53247059Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli.
Q38017457Synthetic approaches to understanding biological constraints
Q28391909Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and "swarm intelligence"
Q37909892Systems-biology approaches for predicting genomic evolution
Q34535938Tempo and mode of genome evolution in a 50,000-generation experiment
Q41846993Testing the role of genetic background in parallel evolution using the comparative experimental evolution of antibiotic resistance.
Q55002438The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography.
Q47136281The Nonstationary Dynamics of Fitness Distributions: Asexual Model with Epistasis and Standing Variation
Q38689208The Utility of Fisher's Geometric Model in Evolutionary Genetics
Q28646039The Valley-of-Death: reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment
Q36490860The basis of antagonistic pleiotropy in hfq mutations that have opposite effects on fitness at slow and fast growth rates
Q54347187The battle of the SNPs.
Q26860873The causes of epistasis
Q58570246The causes of evolvability and their evolution
Q35172659The changing geometry of a fitness landscape along an adaptive walk
Q34917226The conditional nature of genetic interactions: the consequences of wild-type backgrounds on mutational interactions in a genome-wide modifier screen
Q34399491The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds
Q34893085The cost of antibiotic resistance depends on evolutionary history in Escherichia coli.
Q42145476The dynamics of adapting, unregulated populations and a modified fundamental theorem
Q34468851The effect of bacterial recombination on adaptation on fitness landscapes with limited peak accessibility
Q51137906The effect of epistasis on sexually antagonistic genetic variation.
Q45120597The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes
Q34671988The environment affects epistatic interactions to alter the topology of an empirical fitness landscape
Q40519553The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is shaped by strong epistatic interactions
Q35579831The evolutionarily stable distribution of fitness effects
Q45344370The evolutionary epidemiology of multilocus drug resistance
Q28706318The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments
Q28649903The functional basis of adaptive evolution in chemostats
Q55510467The genomics of adaptation.
Q41012991The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus
Q34864177The impact of macroscopic epistasis on long-term evolutionary dynamics
Q46185374The molecular diversity of adaptive convergence.
Q28732355The mystery of missing heritability: Genetic interactions create phantom heritability
Q35099403The origins of specialization: insights from bacteria held 25 years in captivity.
Q39024576The rule of declining adaptability in microbial evolution experiments.
Q26864257The spectrum of adaptive mutations in experimental evolution
Q40587253The strength of genetic interactions scales weakly with mutational effects
Q59353073The utility of fitness landscapes and big data for predicting evolution
Q41463308There and back again: consequences of biofilm specialization under selection for dispersal.
Q38690951Thoughts Toward a Theory of Natural Selection: The Importance of Microbial Experimental Evolution
Q27003480Towards the identification of the loci of adaptive evolution
Q51544809Understanding specialism when the Jack of all trades can be the master of all.
Q42389367Variance in epistasis links gene regulation and evolutionary rate in the yeast genetic interaction network
Q37651181Variant profiling of evolving prokaryotic populations
Q35224374Variation in the fitness effects of mutations with population density and size in Escherichia coli
Q26830367What can we learn from fitness landscapes?
Q36351996What is adaptation by natural selection? Perspectives of an experimental microbiologist
Q28818537Widespread Genetic Incompatibilities between First-Step Mutations during Parallel Adaptation of Saccharomyces cerevisiae to a Common Environment
Q54332246[Genetic adaptation of bacteria].

Search more.