2024
A common allele increases endometrial Wnt4 expression, with antagonistic implications for pregnancy, reproductive cancers, and endometriosis
Pavličev M, McDonough-Goldstein C, Zupan A, Muglia L, Hu Y, Kong F, Monangi N, Dagdas G, Zupančič N, Maziarz J, Sinner D, Zhang G, Wagner G, Muglia L. A common allele increases endometrial Wnt4 expression, with antagonistic implications for pregnancy, reproductive cancers, and endometriosis. Nature Communications 2024, 15: 1152. PMID: 38346980, PMCID: PMC10861470, DOI: 10.1038/s41467-024-45338-4.Peer-Reviewed Original ResearchConceptsFrequency of deleterious allelesAssociated with multiple phenotypesResistance to invasionWnt4 locusAlpha binding sitesPleiotropic mutationsDeleterious allelesPleiotropic SNPsMouse genomeMultiple phenotypesWnt4 transcriptionPopulation frequencyMolecular mechanismsPreovulatory estrogen peakRs3820282Estrogen-responsive tissuesWnt4 expressionCRISPR/Cas 9AllelesTranscriptionEndometriotic fociEndometrial stromaMutationsEpithelial proliferationEstrogen peak
2022
The hierarchical basis of serial homology and evolutionary novelty
DiFrisco J, Love A, Wagner G. The hierarchical basis of serial homology and evolutionary novelty. Journal Of Morphology 2022, 284: e21531. PMID: 36317664, DOI: 10.1002/jmor.21531.Peer-Reviewed Original ResearchConceptsSerial homologyWing serial homologsTree of lifeExtent of homologyParalogous genesEvolutionary noveltyPhylogenetic historyPhylogenetic conceptsGene sequencesSerial homologsEvolutionary precursorPhylogenetic interpretationMost biologistsHomologyCell typesBiological phenomenaGenetic contributionEpidermal appendagesWidespread overlapGenesNew charactersHomologLineagesAppendagesFecundity
2009
Frame‐shifts of digit identity in bird evolution and Cyclopamine‐treated wings
Vargas AO, Wagner GP. Frame‐shifts of digit identity in bird evolution and Cyclopamine‐treated wings. Evolution & Development 2009, 11: 163-169. PMID: 19245548, DOI: 10.1111/j.1525-142x.2009.00317.x.Peer-Reviewed Original Research
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 changesThe 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 road to modularity
Wagner GP, Pavlicev M, Cheverud JM. The road to modularity. Nature Reviews Genetics 2007, 8: 921-931. PMID: 18007649, DOI: 10.1038/nrg2267.Peer-Reviewed Original ResearchConceptsProtein-protein interaction networkMolecular systems biologyPatterns of evolutionGene duplicationGene regulationEvolutionary biologyNeutral mutationsBiological organizationQuantitative traitsInteraction networksSystems biologyStructure of macromoleculesEnvironmental conditionsBiologyDuplicationTraitsMutationsRegulationSelectionModularityMacromoleculesThe 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
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 number
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
What is the promise of developmental evolution? Part II: A causal explanation of evolutionary innovations may be impossible
Wagner G. What is the promise of developmental evolution? Part II: A causal explanation of evolutionary innovations may be impossible. Journal Of Experimental Zoology 2001, 291: 305-309. PMID: 11754010, DOI: 10.1002/jez.1130.Commentaries, Editorials and LettersThe 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 workFoldingEvolutionRegionSequenceThe tetrapod limb: A hypothesis on its origin
Wagner G, Chiu C. The tetrapod limb: A hypothesis on its origin. Journal Of Experimental Zoology 2001, 291: 226-240. PMID: 11598912, DOI: 10.1002/jez.1100.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsTetrapod limbsExpression domainsHoxa-13Hoxa-11Fin-limb transitionExclusive expression domainsMajor morphological adaptationsProximal-distal axisVertebrate evolutionFin developmentHoxa-11 expressionTerrestrial lifestyleFin skeletonMorphological adaptationsDevelopmental mechanismsExpression patternsLimb budPaleontological evidenceGenetic hypothesisExpressionZebrafishEvolutionHomologyAquaticGenes
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 rateCoelacanthIs 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 ResearchWhat is the promise of developmental evolution? part I: Why is developmental biology necessary to explain evolutionary innovations?
Wagner G. What is the promise of developmental evolution? part I: Why is developmental biology necessary to explain evolutionary innovations? Journal Of Experimental Zoology 2000, 288: 95-98. PMID: 10931493, DOI: 10.1002/1097-010x(20000815)288:2<95::aid-jez1>3.0.co;2-5.Commentaries, Editorials and LettersCanalization in evolutionary genetics: a stabilizing theory?
Gibson G, Wagner G. Canalization in evolutionary genetics: a stabilizing theory? BioEssays 2000, 22: 372-380. PMID: 10723034, DOI: 10.1002/(sici)1521-1878(200004)22:4<372::aid-bies7>3.0.co;2-j.Commentaries, Editorials and Letters