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
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
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 rateCoelacanthHox cluster genomics in the horn shark, Heterodontus francisci
Kim C, Amemiya C, Bailey W, Kawasaki K, Mezey J, Miller W, Minoshima S, Shimizu N, Wagner G, Ruddle F. Hox cluster genomics in the horn shark, Heterodontus francisci. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 1655-1660. PMID: 10677514, PMCID: PMC26491, DOI: 10.1073/pnas.030539697.Peer-Reviewed Original ResearchConceptsHox gene clustersHox clustersHOXA clusterGene clusterHeterodontus francisciVertebrate body planHorn sharkGene-coding sequencesDivergence timesEvolutionary historyBody planHoxD clusterEvolutionary significanceSequence motifsVertebrate phylogenyDevelopmental processesGenetic entitiesStructural similarityControl motifsSharksCluster organizationMotifPhylogenyGenomicsNoncoding
1999
Evolution of Chordate Hox Gene Clustersa
RUDDLE F, AMEMIYA C, CARR J, KIM C, LEDJE C, SHASHIKANT C, WAGNER G. Evolution of Chordate Hox Gene Clustersa. Annals Of The New York Academy Of Sciences 1999, 870: 238-248. PMID: 10415487, DOI: 10.1111/j.1749-6632.1999.tb08884.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceChickensDNA, ComplementaryEvolution, MolecularFishesHomeodomain ProteinsHumansMiceMolecular Sequence DataMultigene FamilyWhalesZebrafishConceptsHox cluster duplicationsCluster duplicationBody plan evolutionTerms of genomeGene duplicationHox genesDevelopmental evolutionGene enhancerDuplication modelDuplicationVertebratesNew functionsChordatesInvertebratesGenomeImportant roleEvolutionUrogenital systemGenesEnhancerRoleDaughter clustersNeuromuscular interactionNovel features
1996
Evidence 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