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 cells
2009
Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.Peer-Reviewed Original ResearchTranscription factor-binding sitesCis-regulatory elementsHOXA clusterSelective pressureGene expression evolutionMethionine biosynthesis pathwayLow sequence similarityFactor-binding sitesClade-specific differencesTurnover rateExpression evolutionSpecies treeBiosynthesis pathwayRelated speciesSequence similaritySite turnoverDifferent organismsSequence evolutionTranscription factorsDifferent cladesFungal dataProgesterone response elementMaximum likelihood modelVertebratesTurnover
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
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