2020
Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification
Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2020, 13: evaa228. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.Peer-Reviewed Original ResearchConceptsLeukocyte tyrosine kinaseEvolutionary historyPhylogenetic analysisProtein-coding genesComparative genomic analysisEarly embryonic expressionMetazoan genomesComparative genomicsPhylogenetic contextModel organismsEmbryonic expressionModel speciesHuman genesKey genesGenomic analysisImportant genesMammal systemsFunctional convergenceTyrosine kinaseMolecular homologyGenesFunctional roleVertebratesMammal modelsHomologyUnmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi
Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi. Molecular Biology And Evolution 2020, 37: 2228-2240. PMID: 32191325, PMCID: PMC7403615, DOI: 10.1093/molbev/msaa077.Peer-Reviewed Original ResearchMeSH KeywordsAscomycotaBasidiomycotaBiological EvolutionFruiting Bodies, FungalGene Expression Regulation, DevelopmentalMultigene FamilyConceptsComplex multicellularityGene familyMulticellular fruiting bodiesGene family levelLarge phylogenetic distancesSimilar selection pressuresRecent common ancestorFungal ancestorsFungal genomesGenomic repertoireMolecular convergenceMulticellular fungiPhylogenetic distanceConvergent evolutionEvolutionary convergenceLarge cladeEvolutionary trajectoriesCommon ancestorIndependent evolutionNatural selectionSelection pressureEvolutionary predispositionMulticellularityCladeFruiting bodies
2017
The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics 2017, 13: e1006867. PMID: 28704372, PMCID: PMC5509106, DOI: 10.1371/journal.pgen.1006867.Peer-Reviewed Original ResearchConceptsGene expressionFilamentous fungiCommon garden environmentBody developmentWide gene expressionGene expression phenotypesGene deletion studiesGene expression measurementsMulticellular developmentDivergent speciesSexual phenotypeGene familyEvolved increasesDivergent morphologyKnockout phenotypesAncestral levelsWhole genomeGarden environmentExpression phenotypesDeletion studiesRelevant genesPhenotypic analysisDevelopmental stagesExpression measurementsBody morphology
2015
Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples – an example of saddle fungi
Hwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP. Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples – an example of saddle fungi. Environmental Microbiology Reports 2015, 7: 658-667. PMID: 26033481, DOI: 10.1111/1758-2229.12303.Peer-Reviewed Original ResearchConceptsPotential plant hostsEnvironmental sequencesDiversity of ecologyEctomycorrhizal fungiEcological roleGenetic divergenceGeographic distributionUnculturable fungiPhylogenetic informativenessPlant hostsEcologyITS phylogenyITS sequencesRoot tipsEnvironmental samplesSpeciesMetagenomic investigationSequence alignmentHost typeHelvellaDiversityFungiDiversity of relationshipsSequenceSoilUtility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects
Su Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. BMC Ecology And Evolution 2015, 15: 86. PMID: 25968460, PMCID: PMC4429678, DOI: 10.1186/s12862-015-0364-7.Peer-Reviewed Original ResearchMeSH KeywordsBayes TheoremBiological EvolutionComputer SimulationLikelihood FunctionsModels, GeneticPhylogenyConceptsGeneralized signalCorrect treeAnalytical predictionsNoise analysisDifferent inference methodsBayesian approachLength spaceInference methodsQuartet treesMaximum likelihoodSimulation studyBranch lengthsInferenceModel treePhylogenetic inferenceUtility of charactersAsymmetrical topologyLong-branch effectsConvergenceTopologyPredictionSpaceSignalsEvolution
2013
Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma
Samils N, Gioti A, Karlsson M, Sun Y, Kasuga T, Bastiaans E, Wang Z, Li N, Townsend JP, Johannesson H. Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings Of The Royal Society B 2013, 280: 20130862. PMID: 23782882, PMCID: PMC3712418, DOI: 10.1098/rspb.2013.0862.Peer-Reviewed Original ResearchConceptsMating typesFilamentous ascomycete Neurospora tetraspermaNeurospora tetraspermaMating-type locusGene expression levelsExpression divergenceTranscriptional divergencePhenotypic divergenceFungal AnaloguesRecombinational suppressionMat ASequence divergenceN. tetraspermaMale developmentDivergent regionsFemale developmentMolecular phenotypesGenesSexual dimorphismMale tissuesExpression levelsDivergencePhenotypeAgar mediumGenome
2012
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13: 43. PMID: 22435713, PMCID: PMC3368730, DOI: 10.1186/1471-2105-13-43.Peer-Reviewed Original ResearchConceptsCodon usage biasNucleotide compositionUsage biasGenome evolutionGene functionProtein functionCodon usageNatural selectionCodon positionsTranslational efficiencySelective pressureSequence compositionGene expressionSequence analysisSimulated sequencesSequenceGenomeGenesFundamental importanceMutationsInformative estimationExpression
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