2023
Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts
Dighe A, Maziarz J, Ibrahim-Hashim A, Gatenby R, Kshitiz, Levchenko A, Wagner G. Experimental and phylogenetic evidence for correlated gene expression evolution in endometrial and skin fibroblasts. IScience 2023, 27: 108593. PMID: 38174318, PMCID: PMC10762354, DOI: 10.1016/j.isci.2023.108593.Peer-Reviewed Original ResearchGene expression changesGene expression evolutionEndometrial stromal fibroblastsExpression evolutionExpression changesCell typesGene expressionSimilar gene expression changesSubstantial gene expression changesGene expression profilesSkin fibroblastsMultiple cell typesEvolutionary correlationPhylogenetic evidenceEvolutionary changeDermal skin fibroblastsMammalian speciesExpression profilesPlacental invasivenessComparative datasetCancer growthCultured skin fibroblastsStromal fibroblastsFibroblastsMouse strains
2022
Body Plan Identity: A Mechanistic Model
DiFrisco J, Wagner G. Body Plan Identity: A Mechanistic Model. Evolutionary Biology 2022, 49: 123-141. DOI: 10.1007/s11692-022-09567-z.Peer-Reviewed Original ResearchBody planBody plan evolutionMajor taxonomic groupsSegment polarity networkTransient embryonic structureAbstract Mechanistic modelsAnimal cladesPhylotypic stageMajor cladesPolarity networkTaxonomic groupsEvolutionary changeEvolutionary phenomenaDevelopmental complexityEmbryonic structuresDevelopmental mechanismsEnvironmental perturbationsMechanistic modelMechanistic architectureCladeArthropodsBiological causesGround planChordatesVertebrates
2015
Evolutionary innovations and novelties: Let us get down to business!
Wagner G. Evolutionary innovations and novelties: Let us get down to business! Zoologischer Anzeiger 2015, 256: 75-81. DOI: 10.1016/j.jcz.2015.04.006.Peer-Reviewed Original ResearchCore gene regulatory networkGene regulatory networksRegulatory networksNovel body partsEvolutionary innovationEvolutionary developmental biologyCore regulatory networkBody part identityEvolutionary noveltyEvolutionary biologistsEvolutionary biologyDevelopmental biologyEvolutionary changeBiological processesCell typesImportant unanswered questionsBiologyCritical insightsGenomicsRecent advancesMechanistic aspectsGenesBiologistsUnanswered questionsBody parts
2008
Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals
Lynch VJ, Tanzer A, Wang Y, Leung FC, Gellersen B, Emera D, Wagner GP. Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 14928-14933. PMID: 18809929, PMCID: PMC2567470, DOI: 10.1073/pnas.0802355105.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsHoxa-11Evolutionary changePlacental mammalsEutherian mammalsTranscription factorsCis-regulatory evolutionDirect regulatory targetsGene expression domainsStrong positive selectionNovel developmental pathwayPRL expressionTherian ancestorGene regulationExpression domainsPositive selectionRegulatory targetsNovel functionDevelopmental pathwaysMammalsSpatial expressionProlactin expressionGenesExpressionAdaptive changes
2006
EVIDENCE FOR THE REVERSIBILITY OF DIGIT LOSS: A PHYLOGENETIC STUDY OF LIMB EVOLUTION IN BACHIA (GYMNOPHTHALMIDAE: SQUAMATA)
Kohlsdorf T, Wagner GP. EVIDENCE FOR THE REVERSIBILITY OF DIGIT LOSS: A PHYLOGENETIC STUDY OF LIMB EVOLUTION IN BACHIA (GYMNOPHTHALMIDAE: SQUAMATA). Evolution 2006, 60: 1896-1912. PMID: 17089974, DOI: 10.1111/j.0014-3820.2006.tb00533.x.Peer-Reviewed Original ResearchConceptsDigit lossSouth American genusMolecular phylogenyLimb evolutionComplex traitsPhylogenetic studiesEvolutionary changeBachiaAmerican generaGenetic informationDigit numberReevolutionMost membersSpecific phenotypesTraitsStrong evidencePhylogenyVisible effectTaxaGenusGenesMorphological structurePhenotypeEvolutionLimited numberEVIDENCE FOR THE REVERSIBILITY OF DIGIT LOSS: A PHYLOGENETIC STUDY OF LIMB EVOLUTION IN BACHIA (GYMNOPHTHALMIDAE: SQUAMATA)
Kohlsdorf T, Wagner G. EVIDENCE FOR THE REVERSIBILITY OF DIGIT LOSS: A PHYLOGENETIC STUDY OF LIMB EVOLUTION IN BACHIA (GYMNOPHTHALMIDAE: SQUAMATA). Evolution 2006, 60: 1896-1912. DOI: 10.1554/06-056.1.Peer-Reviewed Original ResearchDigit lossSouth American genusMolecular phylogenyLimb evolutionComplex traitsPhylogenetic studiesEvolutionary changeBachiaAmerican generaGenetic informationDigit numberReevolutionMost membersSpecific phenotypesTraitsStrong evidencePhylogenyVisible effectTaxaGenusGenesMorphological structurePhenotypeEvolutionLimited number
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
2001
The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change
STADLER B, STADLER P, WAGNER G, FONTANA W. The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change. Journal Of Theoretical Biology 2001, 213: 241-274. PMID: 11894994, DOI: 10.1006/jtbi.2001.2423.Peer-Reviewed Original ResearchConceptsGenotype-phenotype mapNeo-Darwinian modelGenotype-phenotype modelsPhenotypic innovationPhenotypic evolutionGenetic accessibilityEvolutionary trajectoriesEvolutionary changeNatural selectionPhenotypic charactersPhenotype spaceGenotype spaceRNA sequencesSecondary structureFitness landscapePossible phenotypesFitness considerationsRNA modelCharacter autonomyPhenotypeRecent computational workFoldingEvolutionRegionSequence
2000
Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin–Limb Transition
Chiu C, Nonaka D, Xue L, Amemiya C, Wagner G. Evolution of Hoxa-11 in Lineages Phylogenetically Positioned along the Fin–Limb Transition. Molecular Phylogenetics And Evolution 2000, 17: 305-316. PMID: 11083943, DOI: 10.1006/mpev.2000.0837.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SequenceAnimalsBinding SitesCell LineConserved SequenceDNAEvolution, MolecularExtremitiesFishesHeLa CellsHomeodomain ProteinsHumansIntronsMolecular Sequence DataPhylogenyProtein IsoformsSequence AlignmentSequence Analysis, DNASequence Homology, Amino AcidXenopusXenopus ProteinsZebrafishZebrafish ProteinsConceptsFin-limb transitionSequence evolutionAmino acid sequence comparisonsHoxa-11Domain IElectrophoretic mobility shift assaysMobility shift assaysAmino acid sequencePatterns of evolutionConsecutive alanine residuesWhole cell extractsEvolutionary timeAppendage developmentCharacter reconstructionEvolutionary changeTranscription factorsSequence comparisonIntron sequencesNucleotide conservationShift assaysAcid sequenceAlanine residuesLineagesAccelerated rateCoelacanthEvolutionarily Stable Configurations: Functional Integration and the Evolution of Phenotypic Stability
Wagner G, Schwenk K. Evolutionarily Stable Configurations: Functional Integration and the Evolution of Phenotypic Stability. Evolutionary Biology 2000, 155-217. DOI: 10.1007/978-1-4615-4185-1_4.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
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 interactionsGenetic measurement theory of epistatic effects
Wagner G, Laubichler M, Bagheri-Chaichian H. Genetic measurement theory of epistatic effects. Contemporary Issues In Genetics And Evolution 1998, 7: 569-580. DOI: 10.1007/978-94-011-5210-5_43.Peer-Reviewed Original ResearchEpistatic 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