2015
Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection
Hodgins-Davis A, Rice DP, Townsend JP. Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection. Molecular Biology And Evolution 2015, 32: 2130-2140. PMID: 25901014, PMCID: PMC4592357, DOI: 10.1093/molbev/msv094.Peer-Reviewed Original ResearchConceptsGene expression evolvesGene expressionPhenotypic evolutionGenetic architectureExpression evolvesEvolutionary quantitative genetic modelsMutation accumulation linesNatural genetic variationStrength of selectionGenomic mutation rateQuantitative genetic modelGenomic data setsGene expression levelsEffects of selectionEvolutionary timeRegulatory evolutionStabilizing selectionAccumulation linesGene regulationMost genesNatural selectionGenetic variationMutational effectsFruit flyPhenotype space
2014
Detecting rare gene transfer events in bacterial populations
Nielsen KM, Bøhn T, Townsend JP. Detecting rare gene transfer events in bacterial populations. Frontiers In Microbiology 2014, 4: 415. PMID: 24432015, PMCID: PMC3882822, DOI: 10.3389/fmicb.2013.00415.Peer-Reviewed Original ResearchHorizontal gene transferHGT eventsHost fitnessBacterial populationsDetection of HGTNew hostPopulation sizeGene transfer eventsKey population genetics parametersStrong positive selectionPopulation genetic parametersGene transfer mechanismsPopulation genetic modelingLarge population sizesGenetic diversityRelative population sizeGenetic compatibilityHGT ratesPositive selectionGenetic variationMutational processesNovel functionDonor organismHighlight knowledge gapsStructured populations
2012
Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae
Hodgins-Davis A, Adomas AB, Warringer J, Townsend JP. Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae. Genome Biology And Evolution 2012, 4: 1061-1079. PMID: 23019066, PMCID: PMC3514956, DOI: 10.1093/gbe/evs084.Peer-Reviewed Original ResearchMeSH KeywordsCluster AnalysisCopperDNA-Binding ProteinsDose-Response Relationship, DrugGene Expression ProfilingGene Expression Regulation, FungalGene-Environment InteractionGenes, FungalGenetic VariationMetabolic Networks and PathwaysMicroarray AnalysisNuclear ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsTranscriptomeConceptsPopulation variationReaction normsGene expression reaction normsGene expressionNovel ecological contextsGenome-wide mRNA levelsGenetic backgroundRelevant copper concentrationsAbundance of variationMitotic fitnessSulfur homeostasisPlastic phenotypesDownstream metabolic consequencesPlastic variationMost genesCopper stressPhenotypic variationGene networksAbundant genesGenetic variationCopper gradientExpression variationEcological contextDifferential expressionGenes
2009
Evolving gene expression: from G to E to G×E
Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to G×E. Trends In Ecology & Evolution 2009, 24: 649-658. PMID: 19699549, PMCID: PMC2805859, DOI: 10.1016/j.tree.2009.06.011.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene expressionMode of evolutionGene expression data setsTerms of geneticsExpression data setsGenetic variationBreadth of conclusionsEnvironmental responsesGxE interactionsMultiple individualsGeneticsExpressionSingle strainEnvironmental controlEvolutionEnvironmental effectsKey componentSpeciesG×EInteractionStrains
2008
Sleuthing the difference a nucleotide can make
Townsend JP. Sleuthing the difference a nucleotide can make. Molecular Ecology 2008, 17: 2793-2795. PMID: 18565029, DOI: 10.1111/j.1365-294x.2008.03824.x.Peer-Reviewed Original ResearchConceptsGene expression polymorphismsExpression polymorphismsGenetic variationGene expressionGenome-wide gene expressionPotential evolutionary impactCis-regulatory regionsAmino acid sensorsDifferential gene expressionSingle nucleotide insertionEcological genomicsEvolutionary impactNatural populationsDifferential fitnessYeast SaccharomycesTranscription factorsGenetic basisNatural isolatesHomonucleotide repeatsNatural variationNucleotide insertionEnvironment interactionPolymorphismAcid sensorsSSY1
2006
Ecological and evolutionary genomics of Saccharomyces cerevisiae
LANDRY CR, TOWNSEND JP, HARTL DL, CAVALIERI D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 2006, 15: 575-591. PMID: 16499686, DOI: 10.1111/j.1365-294x.2006.02778.x.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEvolutionary genomic studiesPrime model systemImportant genetic variationPowerful model speciesEvolutionary genomicsEvolutionary geneticsEvolutionary forcesFunctional genomicsYeast genomeNumerous habitatsModel speciesGenomic studiesUnicellular fungiGenetic variationBiology questionsS. cerevisiaeNatural isolatesGenetic levelGenomicsSaccharomycesModel systemYeastEukaryotesGenomeHabitats
2004
Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster
Townsend JP, Rand DM. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 2004, 93: 98-103. PMID: 15138453, DOI: 10.1038/sj.hdy.6800484.Peer-Reviewed Original ResearchConceptsMtDNA length variationNew World samplesDrosophila melanogasterFounder eventsMitochondrial genome size variationLength variationMtDNA length variantsGenome size variationDifferent mutational pressureOld World populationsD-loop regionNew World populationsMutation-selection dynamicsPatterns of variationLevel of heteroplasmyMitochondrial genomeRelaxed selectionMutational pressureControl regionGenetic variationRange expansionLength variantsMutational dynamicsNew WorldLinkage relationshipsGene expression profiling in evolutionary genetics
Hartl D, Meiklejohn C, Castillo-Davis C, Cavalieri D, Ranz J, Townsend J. Gene expression profiling in evolutionary genetics. 2004, 74-93. DOI: 10.1017/cbo9780511542619.007.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsNatural populationsPopulation geneticsKey model organismGenotypes of organismsGene expression profilingDNA sequencing strategyEvolutionary geneticsComparative genomicsEvolutionary timeModel organismsChain termination methodHuman genomePopulation geneticistsGenomic sequencesGenetic variationSingle speciesComplete sequenceExpression profilingMolecular geneticsGenetic differencesGenomeMolecular biologySequencing strategyMolecular levelDNA sequencing
2003
Population Genetic Variation in Genome-Wide Gene Expression
Townsend JP, Cavalieri D, Hartl DL. Population Genetic Variation in Genome-Wide Gene Expression. Molecular Biology And Evolution 2003, 20: 955-963. PMID: 12716989, DOI: 10.1093/molbev/msg106.Peer-Reviewed Original ResearchConceptsGene expression levelsGene expressionNatural populationsGenetic variationNatural isolatesExpression levelsGenome-wide gene expressionPopulation genetic variationGenome-wide scaleComparative gene expressionDifferential gene expressionDNA microarray technologyAmino acid metabolismWine yeast SaccharomycesSulfur assimilationEvolutionary biologistsGenomic scaleYeast SaccharomycesNatural selectionS. cerevisiaeProtein degradationSuch traitsDifferential reproductionMicroarray technologyOrganic evolution