2018
Neutral Theory and the Somatic Evolution of Cancer
Cannataro VL, Townsend JP. Neutral Theory and the Somatic Evolution of Cancer. Molecular Biology And Evolution 2018, 35: 1308-1315. PMID: 29684198, PMCID: PMC5967571, DOI: 10.1093/molbev/msy079.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, BiologicalAnimalsEvolution, MolecularGenetic DriftHumansNeoplasmsSelection, Genetic
2017
Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana
Park B, Rutter MT, Fenster CB, Symonds VV, Ungerer MC, Townsend JP. Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics 2017, 206: 2105-2117. PMID: 28550014, PMCID: PMC5560809, DOI: 10.1534/genetics.116.199190.Peer-Reviewed Original ResearchMeSH KeywordsArabidopsisEvolution, MolecularModels, GeneticMutation AccumulationQuantitative Trait LociSelection, GeneticConceptsMutation accumulation dataDirectional selectionNatural selectionMutational effectsPhenotypic traitsDirectional natural selectionQuantitative trait lociDivergent lineagesRosette diameterTrait lociHistorical selectionQuantitative traitsLineagesArabidopsisTraitsDensity traitsAccumulation dataDivergenceKey roleUltimate sourceLociSelectionOrganismsKey componentMutationsDetection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence
Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Molecular Biology And Evolution 2017, 34: 3006-3022. PMID: 28962009, PMCID: PMC5850860, DOI: 10.1093/molbev/msx213.Peer-Reviewed Original ResearchConceptsPoisson random fieldRandom fieldsEnsemble of modelsRandom field frameworkField frameworkClustering modelHistorical demographic trendsAmino acid-altering substitutionsSelection intensityEnsembleHigh powerUniform selectionProtein-coding genesProtein coding genesHeterogeneity of selectionDNA sequence polymorphismsComparison of polymorphisms
2016
Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India
Lewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14601-14608. PMID: 27791071, PMCID: PMC5187705, DOI: 10.1073/pnas.1604985113.Peer-Reviewed Original ResearchConceptsPlague resistanceEnvironmental driversIntense natural selectionWild host populationsIntense selective pressureEvolutionary driversPossible evolutionary basisHost evolutionNatural selectionDisease resistanceEvolutionary selectionFlea population dynamicsEvolutionary basisSelective pressureEvolutionary processesPopulation dynamicsHost populationsWildlife hostsLocal persistencePlague dynamicsCommensal ratsDisease agentsPowerful insightsDisease transmissionEcology
2012
Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size
Rice DP, Townsend JP. Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size. G3: Genes, Genomes, Genetics 2012, 2: 905-911. PMID: 22908039, PMCID: PMC3411246, DOI: 10.1534/g3.112.003228.Peer-Reviewed Original ResearchMeSH KeywordsAllelesModels, GeneticPhenotypeQuantitative Trait LociQuantitative Trait, HeritableSelection, GeneticA Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data
Rice DP, Townsend JP. A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data. Genetics 2012, 190: 1533-1545. PMID: 22298701, PMCID: PMC3316662, DOI: 10.1534/genetics.111.137075.Peer-Reviewed Original ResearchConceptsMutation accumulation dataPhenotypic traitsMutational effectsMutation accumulation experimentsPopulation genetics theoryQuantitative trait lociQuantitative phenotypic traitsAccumulation dataHistory of selectionLocus effect sizesEvolutionary biologistsNeutral evolutionGenetic architectureQTL dataStrong selectionTrait lociSelection strengthDistribution of mutationsNatural selectionPhenotypic diversityHistorical selectionMolecular dataQuantitative traitsGenetic theoryQTLCodon 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
Factors affecting the reversal of antimicrobial-drug resistance
Johnsen PJ, Townsend JP, Bøhn T, Simonsen GS, Sundsfjord A, Nielsen KM. Factors affecting the reversal of antimicrobial-drug resistance. The Lancet Infectious Diseases 2009, 9: 357-364. PMID: 19467475, DOI: 10.1016/s1473-3099(09)70105-7.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2006
Population structure and gene evolution in Saccharomyces cerevisiae
Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 2006, 6: 702-715. PMID: 16879422, DOI: 10.1111/j.1567-1364.2006.00059.x.Peer-Reviewed Original ResearchMeSH KeywordsCloning, MolecularEvolution, MolecularPhylogenyRecombination, GeneticSaccharomyces cerevisiaeSelection, GeneticConceptsPopulation genetic variationPopulation structureS. cerevisiaeDistinct population structureSaccharomyces sensu strictoSulfur-based fungicidesSulfite exporterGene evolutionGene treesGene SSU1Historical selectionTranscription factorsHigh polymorphismNatural isolatesProtein productsCerevisiaeSequence analysisSSU1Oak forestsGreater polymorphismSensu strictoWine yeastSequence studiesFZF1Expression levels