2023
Normalizing need not be the norm: count-based math for analyzing single-cell data
Church S, Mah J, Wagner G, Dunn C. Normalizing need not be the norm: count-based math for analyzing single-cell data. Theory In Biosciences 2023, 143: 45-62. PMID: 37947999, DOI: 10.1007/s12064-023-00408-x.Peer-Reviewed Original Research
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
2021
Devo-Evo of Cell Types
Wagner G. Devo-Evo of Cell Types. 2021, 511-528. DOI: 10.1007/978-3-319-32979-6_153.Peer-Reviewed Original ResearchEvolutionary developmental biologyCell typesDevelopmental biologyCore gene regulatory networkAncestral cell typeCell type identityTranscription factor proteinsGene regulatory networksGene treesGene duplicationEvolutionary descentRegulatory complexRegulatory networksPopulation of cellsMolecular mechanismsFactor proteinOrganisms increasesEvolutionary perspectiveLineagesBiologyType identityMajor current challengeSpecific setTreesGenes
2019
Devo-Evo of Cell Types
Wagner G. Devo-Evo of Cell Types. 2019, 1-18. DOI: 10.1007/978-3-319-33038-9_153-1.Peer-Reviewed Original ResearchEvolutionary developmental biologyCell typesDevelopmental biologyCore gene regulatory networkAncestral cell typeCell type identityTranscription factor proteinsGene regulatory networksGene treesGene duplicationEvolutionary descentRegulatory complexRegulatory networksPopulation of cellsMolecular mechanismsFactor proteinOrganisms increasesEvolutionary perspectiveLineagesBiologyType identityMajor current challengeSpecific setTreesGenes
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 partsHomology in the Age of Developmental Genomics
Wagner G. Homology in the Age of Developmental Genomics. 2015, 25-43. DOI: 10.1007/978-3-7091-1862-7_2.Peer-Reviewed Original ResearchModel organismsEvolutionary biologyHomology conceptRecent common ancestorDevelopmental genomicsPhylogenetic relationshipsCommon ancestorDarwinian traditionHomologySame organOrganismsSpeciesComparative anatomyDifferent animalsBiologistsBiologyFundamental roleRichard OwenImportant roleGenomicsAncestorGenesOrgansHumansRole
2012
Origin of the Endometrial Gene Regulatory Network of Placental Mammals.
Wagner G, Lynch V, Nnamani M. Origin of the Endometrial Gene Regulatory Network of Placental Mammals. Biology Of Reproduction 2012, 87: 33-33. DOI: 10.1093/biolreprod/87.s1.33.Peer-Reviewed Original ResearchGene regulatory networksTransposable elementsPlacental mammalsRegulatory networksComparative transcriptome sequencingSpecific transposable elementsRegulatory network changesCis-regulatory elementsGene expression patternsDecidual cell typesChromatin marksGene regulationStem lineageTranscriptome sequencingChromatin immunoprecipitationRegulatory elementsInvasive placentationExpression patternsDerived characterAryl hydrocarbon receptorGenesCell typesMammalsRegulatory activityStromal cellsComing to Grips with Evolvability
Pavlicev M, Wagner G. Coming to Grips with Evolvability. Evolution: Education And Outreach 2012, 5: 231-244. DOI: 10.1007/s12052-012-0430-1.Peer-Reviewed Original ResearchGenotype-phenotype mapOrganismal developmentMost genesCryptic mutationsPhenotypic traitsComplex organismsPhenotypic charactersMost traitsRandom mutationsReal organismsGenetic effectsEvolvabilityGenetic backgroundOrganismsGenesMutationsTraitsNew environmentRandom changesPhenotypeFitnessEvolutionSelectionConventional computer languages
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 contributionBiology
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 ResearchEvolutionary Genomics of Hox Gene Clusters
Prohaska S, Stadler P, Wagner G. Evolutionary Genomics of Hox Gene Clusters. 2007, 68-90. DOI: 10.1007/978-0-387-68990-6_5.Peer-Reviewed Original ResearchHox clustersHox gene clustersVertebrate clustersGenome duplicationEvolutionary genomicsHox genesGene clusterStringent structural constraintsVertebratesFunctional differentiationCluster organizationDuplicationRepetitive materialGenomicsAdaptive opportunitiesGenesDifferentiationClustersStructural constraintsDifferent patterns
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
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
2001
The 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 hypothesisExpressionZebrafishEvolutionHomologyAquaticGenesEpistasis 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 densityGenotypes
2000
Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1
Wagner G, Chiu C, Laubichler M. Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1. Integrative And Comparative Biology 2000, 40: 819-831. DOI: 10.1668/0003-1569(2000)040[0819:deaams]2.0.co;2.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsDevelopmental evolutionEvolutionary innovationDevelopmental mechanismsFunction of genesEvolutionary geneticsGenetic architectureEvolutionary originEvolutionary biologyAssessment of homologyDevelopmental dynamicsSpecies differencesBiologyGenetic factorsHomologyGenesMechanismGeneticsSpeciesEvolutionRoleElucidationOriginMechanistic scienceCharacterDevelopmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1
Wagner G, Chiu C, Laubichler M. Developmental Evolution as a Mechanistic Science: The Inference from Developmental Mechanisms to Evolutionary Processes1. Integrative And Comparative Biology 2000, 40: 819-831. DOI: 10.1093/icb/40.5.819.Peer-Reviewed Original ResearchDevelopmental evolutionEvolutionary innovationDevelopmental mechanismsFunction of genesEvolutionary geneticsGenetic architectureEvolutionary originEvolutionary biologyAssessment of homologyDevelopmental dynamicsSpecies differencesBiologyGenetic factorsHomologyGenesMechanismGeneticsSpeciesEvolutionRoleElucidationOriginMechanistic scienceCharacter