2008
The gene regulatory logic of transcription factor evolution
Wagner GP, Lynch VJ. The gene regulatory logic of transcription factor evolution. Trends In Ecology & Evolution 2008, 23: 377-385. PMID: 18501470, DOI: 10.1016/j.tree.2008.03.006.Peer-Reviewed Original ResearchConceptsTranscription factor proteinsDevelopmental evolutionGene regulatory logicMinimal pleiotropic effectsTranscription factor evolutionFactor proteinTranscription factor functionEvolution of developmentTranscription factor genesCis-regulatory elementsFunction of proteinsAdaptive evolutionDevelopmental biologyRegulatory logicNovel functionFactor genesFactor functionProtein changesPleiotropic effectsProteinRecent studiesEvolutionGenesRelative contributionBiologyPleiotropic scaling of gene effects and the ‘cost of complexity’
Wagner GP, Kenney-Hunt JP, Pavlicev M, Peck JR, Waxman D, Cheverud JM. Pleiotropic scaling of gene effects and the ‘cost of complexity’. Nature 2008, 452: 470-472. PMID: 18368117, DOI: 10.1038/nature06756.Peer-Reviewed Original ResearchConceptsQuantitative trait lociEffects of pleiotropyOrganismal complexityGenetic sequence dataHigher organismsEvolutionary biologyTrait lociMouse genomeSequence dataBiology questionsSkeletal traitsGene effectsMost mutationsCost of complexityGenetic mutationsTraitsMutationsMultiple effectsGenomeSkeletal characteristicsPleiotropyLociPleiotropicOrganismsBiology
2007
The developmental genetics of homology
Wagner GP. The developmental genetics of homology. Nature Reviews Genetics 2007, 8: 473-479. PMID: 17486120, DOI: 10.1038/nrg2099.Peer-Reviewed Original ResearchA stochastic model for the evolution of transcription factor binding site abundance
Wagner GP, Otto W, Lynch V, Stadler PF. A stochastic model for the evolution of transcription factor binding site abundance. Journal Of Theoretical Biology 2007, 247: 544-553. PMID: 17475285, DOI: 10.1016/j.jtbi.2007.03.001.Peer-Reviewed Original Research
2005
The “Fish-Specific” Hox Cluster Duplication Is Coincident with the Origin of Teleosts
Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. The “Fish-Specific” Hox Cluster Duplication Is Coincident with the Origin of Teleosts. Molecular Biology And Evolution 2005, 23: 121-136. PMID: 16162861, DOI: 10.1093/molbev/msj020.Peer-Reviewed Original ResearchConceptsHox cluster duplicationsCluster duplicationHox genesHox clustersTeleost lineageDifferent teleost lineagesHox gene complementOrigin of teleostsRecent common ancestorDuplication eventsGene complementTeleost radiationGene genealogiesStem lineageCommon ancestorGnathostome vertebratesBasal actinopterygiansLineagesZebrafishTeleostsGenesDuplicationFuguSharksFish
2004
Adaptive evolution of HoxA11 and HoxA13 at the origin of the uterus in mammals
Lynch V, Roth J, Takahashi K, Dunn C, Nonaka D, Stopper G, Wagner G. Adaptive evolution of HoxA11 and HoxA13 at the origin of the uterus in mammals. Proceedings Of The Royal Society B 2004, 271: 2201-2207. PMID: 15539344, PMCID: PMC1691855, DOI: 10.1098/rspb.2004.2848.Peer-Reviewed Original ResearchConceptsAdaptive evolutionTranscription factorsMolecular evolutionHoxa-11Hoxa-13Cis-regulatory evolutionAdaptive molecular evolutionEvolution of developmentMammalian female reproductive systemStrong positive selectionCis-regulatory elementsAmniote taxaDevelopmental genesStem lineageDevelopmental evolutionEvolutionary changeEutherian mammalsSpatial regulationPositive selectionMorphological charactersFemale reproductive organsGenesFemale reproductive systemReproductive organsMammals
2002
Evolution of functionally conserved enhancers can be accelerated in large populations: a populationgenetic model
Carter A, Wagner G. Evolution of functionally conserved enhancers can be accelerated in large populations: a populationgenetic model. Proceedings Of The Royal Society B 2002, 269: 953-960. PMID: 12028779, PMCID: PMC1690979, DOI: 10.1098/rspb.2002.1968.Peer-Reviewed Original ResearchConceptsPopulation sizeRelated Drosophila speciesCis-regulatory elementsPopulation genetic modelsRate of evolutionModerate population sizesDrosophila speciesDrosophila EnhancerVertebrate enhancersDynamics of fixationDifferent taxaCompensatory mutationsNeutral rateGeneration timeSmall populationEnhancerTaxaSpatial organizationLarge populationSpeciesMutationsSequenceVertebratesEvolutionPopulation
2001
The Test Distribution of Modularity Statistics: A Correction and a Clarification
Housworth E, Mezey J, Cheverud J, Wagner G. The Test Distribution of Modularity Statistics: A Correction and a Clarification. Genetics 2001, 158: 1381-1381. PMID: 11478289, PMCID: PMC1461726, DOI: 10.1093/genetics/158.3.1381.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsEpistasis and the Mutation Load: A Measurement-Theoretical Approach
Hansen T, Wagner G. Epistasis and the Mutation Load: A Measurement-Theoretical Approach. Genetics 2001, 158: 477-485. PMID: 11333254, PMCID: PMC1461645, DOI: 10.1093/genetics/158.1.477.Peer-Reviewed Original ResearchConceptsMutation-selection equilibriumGene interactionsEpistatic interactionsMutation loadStrength of epistasisMutation-selection balanceGenomic mutation rateHigher-order gene interactionsSynergistic epistasisMean fitnessOptimal genotypeEpistatic effectsTwofold disadvantageEpistasisMutation rateGenetic backgroundSynergistic interactionSystematic relationshipGenesLociInteraction intensityInteractionFitnessInteraction densityGenotypesModeling Genetic Architecture: A Multilinear Theory of Gene Interaction
Hansen T, Wagner G. Modeling Genetic Architecture: A Multilinear Theory of Gene Interaction. Theoretical Population Biology 2001, 59: 61-86. PMID: 11243929, DOI: 10.1006/tpbi.2000.1508.Peer-Reviewed Original ResearchConceptsGenotype-phenotype mapGene interactionsQuantitative genetic variationEffects of epistasisGenetic canalizationGenetic experimentsGenetic variationGene substitutionGenetic backgroundEpistasisTractable modelComplex functionsCentral importanceLociBiologyCanalizationPhenotypeGenotypesInteractionSum of linear
2000
Is the Genotype-Phenotype Map Modular?: A Statistical Approach Using Mouse Quantitative Trait Loci Data
Mezey J, Cheverud J, Wagner G. Is the Genotype-Phenotype Map Modular?: A Statistical Approach Using Mouse Quantitative Trait Loci Data. Genetics 2000, 156: 305-311. PMID: 10978294, PMCID: PMC1461239, DOI: 10.1093/genetics/156.1.305.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAnimalsBiological EvolutionGenotypeMandibleMiceModels, GeneticPhenotypeQuantitative Trait, HeritableModeling the Evolution of Genetic Architecture: A Continuum of Alleles Model with Pairwise A×A Epistasis
WAGNER G, MEZEY J. Modeling the Evolution of Genetic Architecture: A Continuum of Alleles Model with Pairwise A×A Epistasis. Journal Of Theoretical Biology 2000, 203: 163-175. PMID: 10704300, DOI: 10.1006/jtbi.2000.1074.Peer-Reviewed Original Research
1999
Is Hsp90 a regulator of evolvability?
Wagner G, Chiu C, Hansen T. Is Hsp90 a regulator of evolvability? Journal Of Experimental Zoology 1999, 285: 116-118. PMID: 10440722, DOI: 10.1002/(sici)1097-010x(19990815)285:2<116::aid-jez3>3.0.co;2-p.Commentaries, Editorials and LettersMeSH KeywordsAnimalsBiological EvolutionGene Expression RegulationGenetic VariationHSP90 Heat-Shock ProteinsModels, GeneticMutationPhenotype
1998
Genetic measurement theory of epistatic effects
Wagner G, Laubichler M, Bagheri-Chaichian H. Genetic measurement theory of epistatic effects. Genetica 1998, 102-103: 569-580. PMID: 9766965, DOI: 10.1023/a:1017088321094.Peer-Reviewed Original ResearchConceptsEpistatic effectsGenotype-phenotype mapMendelian genetic systemMathematical population geneticsAverage additive effectPairs of lociGenetic architecturePopulation geneticsEvolutionary changeEvolutionary phenomenaGenetic systemGenotypic varianceMetabolic fluxSecond locusEpistasisGene substitutionMutation effectsAdditive effectAdult body weightGene effectsSecond mutationLocus BLociMutationsNegative interactions
1996
Apparent Stabilizing Selection and the Maintenance of Neutral Genetic Variation
Wagner G. Apparent Stabilizing Selection and the Maintenance of Neutral Genetic Variation. Genetics 1996, 143: 617-619. PMID: 8722811, PMCID: PMC1207295, DOI: 10.1093/genetics/143.1.617.Peer-Reviewed Original ResearchEvidence for Four Hox Clusters in the KillifishFundulus heteroclitus(Teleostei)
Misof B, Wagner G. Evidence for Four Hox Clusters in the KillifishFundulus heteroclitus(Teleostei). Molecular Phylogenetics And Evolution 1996, 5: 309-322. PMID: 8728389, DOI: 10.1006/mpev.1996.0026.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBiological EvolutionDNA PrimersFishesGenes, HomeoboxHomeodomain ProteinsHumansKillifishesKineticsMiceModels, GeneticMolecular Sequence DataMultigene FamilyPhylogenyPolymerase Chain ReactionProbabilitySequence Homology, Amino AcidSequence Homology, Nucleic AcidConceptsHox clustersMammalian Hox genesTeleost Fundulus heteroclitusDiploid teleostsHox genesHomeobox sequencesPCR surveySequence comparisonLower vertebratesFundulus heteroclitusCognate groupsFirst evidenceSequenceOrthologsCluster AVertebratesTeleostsGenesNumber of representativesHeteroclitusClustersHumansMiceFragmentsRepresentatives
1985
On the evolution of dominance modifiers II: a non-equilibrium approach to the evolution of genetic systems
Wagner G, Bürger R. On the evolution of dominance modifiers II: a non-equilibrium approach to the evolution of genetic systems. Journal Of Theoretical Biology 1985, 113: 475-500. PMID: 3999784, DOI: 10.1016/s0022-5193(85)80034-5.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionDrosophilaGenes, DominantMathematicsModels, GeneticMothsSelection, Genetic