2025
Template switching during DNA replication is a prevalent source of adaptive gene amplification
Chuong J, Nun N, Suresh I, Matthews J, De T, Avecilla G, Abdul-Rahman F, Brandt N, Ram Y, Gresham D. Template switching during DNA replication is a prevalent source of adaptive gene amplification. ELife 2025, 13: rp98934. PMID: 39899365, PMCID: PMC11790251, DOI: 10.7554/elife.98934.Peer-Reviewed Original ResearchConceptsCopy number variantsLong terminal repeatTemplate switchingDNA replicationDynamics of copy number variantsCNV formationEffect of copy number variantsOrigin of DNA replicationSource of genetic variationFitness effectsLocal DNA featuresSaccharomyces cerevisiae</i>Gene amplificationGenome architectureGenome evolutionGenomic elementsGenomic locationsDNA elementsAdaptive evolutionLagging strandEngineered strainGenetic variationHomologous recombinationFrequent amplificationRate of adaptationTemplate switching during DNA replication is a prevalent source of adaptive gene amplification
Chuong J, Ben Nun N, Suresh I, Matthews J, De T, Avecilla G, Abdul-Rahman F, Brandt N, Ram Y, Gresham D. Template switching during DNA replication is a prevalent source of adaptive gene amplification. ELife 2025, 13 DOI: 10.7554/elife.98934.3.Peer-Reviewed Original ResearchCopy number variantsGAP1 CNVsLong terminal repeatTemplate switchingDNA replicationDynamics of copy number variantsCNV formationEffect of copy number variantsOrigin of DNA replicationSource of genetic variationFitness effectsLocal DNA featuresGene amplificationGAP1 geneGenome architectureGenome evolutionGenomic elementsGenomic locationsDNA elementsSaccharomyces cerevisiaeAdaptive evolutionLagging strandEngineered strainGenetic variationHomologous recombination
2024
Experimental Evolution Studies in Φ6 Cystovirus
Singhal S, Balitactac A, Nayagam A, Bahrami P, Nayeem S, Turner P. Experimental Evolution Studies in Φ6 Cystovirus. Viruses 2024, 16: 977. PMID: 38932268, PMCID: PMC11209170, DOI: 10.3390/v16060977.Peer-Reviewed Original ResearchConceptsExperimental evolution studiesFitness effects of spontaneous mutationsSpontaneous mutationsEffects of spontaneous mutationsEvolution of RNA virusesEvolution studiesEvolution of host rangeFast generation timesResponse to selectionMultiple phagesNon-pathogenic modelRNA genomeConsequence of evolutionOuter membraneHost rangeRNA virusesNovel traitsMutation rateHost cellsFitness effectsPopulation sizeMutationsCystovirusesBacteriophageGeneration time
2023
Environmental modulation of global epistasis in a drug resistance fitness landscape
Diaz-Colunga J, Sanchez A, Ogbunugafor C. Environmental modulation of global epistasis in a drug resistance fitness landscape. Nature Communications 2023, 14: 8055. PMID: 38052815, PMCID: PMC10698197, DOI: 10.1038/s41467-023-43806-x.Peer-Reviewed Original ResearchConceptsGlobal epistasisEnvironmental variationGene-by-gene interactionsFitness landscapeGenotype-phenotype mapAdaptive trajectoriesEvolution of drug resistanceEssential enzymeEpistasisFitness effectsGenetic backgroundMutationsAntimicrobial drugsDrug resistanceEnvironmental modulationDrug doseLandscapeGenesPathogensDrugFitnessEvolutionOncogenic context shapes the fitness landscape of tumor suppression
Blair L, Juan J, Sebastian L, Tran V, Nie W, Wall G, Gerceker M, Lai I, Apilado E, Grenot G, Amar D, Foggetti G, Do Carmo M, Ugur Z, Deng D, Chenchik A, Paz Zafra M, Dow L, Politi K, MacQuitty J, Petrov D, Winslow M, Rosen M, Winters I. Oncogenic context shapes the fitness landscape of tumor suppression. Nature Communications 2023, 14: 6422. PMID: 37828026, PMCID: PMC10570323, DOI: 10.1038/s41467-023-42156-y.Peer-Reviewed Original Research
2022
Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs
Pennings P, Ogbunugafor C, Hershberg R. Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs. G3: Genes, Genomes, Genetics 2022, 12: jkac190. PMID: 35920784, PMCID: PMC9434179, DOI: 10.1093/g3journal/jkac190.Peer-Reviewed Original ResearchConceptsCompensatory mutationsPopulation geneticsExperimental evolutionDynamics of adaptationMutation rateWild typeEvolution of antibiotic resistanceQuality of mutationsTheoretical population geneticsDynamics of compensationEvolution of mutationsMutation supplyMicrobial evolutionNonmutant strainsProbability of reversalMutated strainsEvolutionary dynamicsFitness costsAntibiotic resistanceFitness effectsMutationsAdaptive dynamicsGeneticsStrainPotential roleThe mutation effect reaction norm (mu‐rn) highlights environmentally dependent mutation effects and epistatic interactions
Ogbunugafor C. The mutation effect reaction norm (mu‐rn) highlights environmentally dependent mutation effects and epistatic interactions. Evolution 2022, 76: 37-48. PMID: 34989399, DOI: 10.1111/evo.14428.Peer-Reviewed Original ResearchConceptsReaction normsFitness effects of mutationsPhenotypic consequences of mutationsEvolution of antimicrobial resistanceEffects of mutationsConsequences of mutationsGenetic interactionsPopulation geneticsEpistatic interactionsPhenotypic consequencesGenetic informationMutational effectsFunction of environmental contextUnpredictability of evolutionFitness effectsMutationsAntimicrobial resistanceLayer of complexityEnvironmental contextModern SynthesisPerformance of genotypesReverse evolutionEpistasisGeneticsPublic health
2021
Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection
Abdul-Rahman F, Tranchina D, Gresham D. Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection. Molecular Biology And Evolution 2021, 38: 4362-4375. PMID: 34132791, PMCID: PMC8476146, DOI: 10.1093/molbev/msab173.Peer-Reviewed Original ResearchConceptsDistribution of fitness effectsNeutral fitness effectsGenetic diversityFitness effectsFluctuating environmentsMaintenance of genetic diversityGene deletion collectionHigh-fitness genotypesTemporally fluctuating environmentsShort-term fitnessVariable selection effectDynamics of selectionDeletion collectionBarcode sequencesFit genotypesNutrient limitationUnique genotypesGenetic variationContinuous cultureEvolutionary biologyEnvironmental fluctuationsDiversityEnvironmental conditionsGenotypesPopulation diversity
2006
Adaptive Mutations In RNA-Based Regulatory Mechanisms: Computational and Experimental Investigations
Barash D, Sikorski J, Perry E, Nevo E, Nudler E. Adaptive Mutations In RNA-Based Regulatory Mechanisms: Computational and Experimental Investigations. Israel Journal Of Ecology And Evolution 2006, 52: 263-279. DOI: 10.1560/ijee_52_3-4_263.Peer-Reviewed Original ResearchTPP riboswitchRegulatory mechanismsEvolution CanyonTermination efficiencyTranscription terminationNorth-facing slopesAdaptive mutationsEvolutionary time scalesGenetic control elementsRNA genetic control elementsBeneficial fitness effectsClass of RNAsMesic north-facing slopeParticipation of proteinsLevel of RNAModel systemOrganism's fitnessFitness effectsBeneficial mutationsTranslation initiationAncient originGC contentNonrandom mutationsPromoter regionMutational differences
2003
Role of duplicate genes in genetic robustness against null mutations
Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH. Role of duplicate genes in genetic robustness against null mutations. Nature 2003, 421: 63-66. PMID: 12511954, DOI: 10.1038/nature01198.Peer-Reviewed Original ResearchConceptsDuplicate genesGenetic robustnessNull mutationSevere fitness effectsGenome-wide evaluationAlternative metabolic pathwaysFitness effectsLoss of functionSequence similarityRegulatory networksDeletion mutantsS. cerevisiaeGenesMetabolic pathwaysDuplicate copiesGene deletionFunctional compensationFitness dataCopiesMutationsMutantsCerevisiaeRelative importanceOrganismsSecond mechanism
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