2025
Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes
Wang Y, Wang F, Meng G, Lopez-Giraldez F, Dong C, Wang Z, Townsend J. Rates of Evolution of Developmental Changes in Gene Expression in Sordariomycetes. Molecular Biology And Evolution 2025, 42: msaf131. PMID: 40452442, PMCID: PMC12203517, DOI: 10.1093/molbev/msaf131.Peer-Reviewed Original ResearchConceptsRate of gene expression evolutionGene expression evolutionExpression evolutionGene expressionPhenotypic evolutionHeterogeneous rates of evolutionNonsynonymous to synonymous substitution ratesRates of phenotypic evolutionDevelopmental stagesSingle-copy orthologsGene sequence evolutionSynonymous substitution ratesRate of evolutionExpression of genesFunctional pathway analysisCarbon metabolismEvolutionary forcesConsequent phenotypesSexual reproductionSequence evolutionConserved pathwaysMeiosis pathwaysSubstitution ratesCell cyclePathway analysis
2014
The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise
Su Z, Wang Z, López-Giráldez F, Townsend J. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers In Ecology And Evolution 2014, 2: 11. DOI: 10.3389/fevo.2014.00011.Peer-Reviewed Original ResearchPhylogenetic inferencePhylogenetic signalRate of evolutionMolecular evolutionary modelsAccurate phylogenetic inferenceFour-taxon treesYeast genus CandidaMolecular evolutionConsensus treeNucleotide substitutionsPrediction of signalsDistribution of signalsEvolutionary modelsModel choiceGenus CandidaUnrealistic modelsCorrect modelInferenceTreesRPB1PhylogenyCladePhylogeneticsRPB2Markov model
2012
Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny
Townsend JP, Su Z, Tekle YI. Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny. Systematic Biology 2012, 61: 835-849. PMID: 22389443, DOI: 10.1093/sysbio/sys036.Peer-Reviewed Original ResearchConceptsPhylogenetic signalPhylogenetic noisePhylogenetic treeAdditional sequence dataRate of evolutionPhylogenetic researchPhylogenetic experimental designSequence dataImpact of collectionInternodesPower of resolutionFundamental unitTreesPhylogeneticsPhylogenyPolytomyGenesLociPotential signalsSignalsExample data setsData sets
2010
Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships
Townsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Systematic Biology 2010, 59: 446-457. PMID: 20547780, DOI: 10.1093/sysbio/syq025.Peer-Reviewed Original ResearchConceptsPhylogenetic experimental designOptimal rateAsymptotic impactAnalytical predictionsAddition of charactersOptimal selectionObvious applicationApproximate ideaEstimation of ratesCurrent phylogenetic studiesOptimal efficiencyTheoryDeep internodesTaxon additionRate of evolutionExperimental designNew taxonPhylogenetic informativenessPhylogenetic relationships
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