2018
Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers In Cellular And Infection Microbiology 2018, 8: 193. PMID: 29971217, PMCID: PMC6018220, DOI: 10.3389/fcimb.2018.00193.Peer-Reviewed Original ResearchConceptsSerovar CopenhageniPublic health relevanceSevere casesSerogroup IcterohaemorrhagiaeSerovar IcterohaemorrhagiaeWorldwide zoonosisHealth relevanceIcterohaemorrhagiaeCopenhageniVirulent strainHigh discriminatory powerSerovarsGlobal isolatesFrameshift mutationDiscriminatory powerFirst studyPathogenic speciesIsolates
2017
Detection 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
Early and multiple origins of metastatic lineages within primary tumors
Zhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP. Early and multiple origins of metastatic lineages within primary tumors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 2140-2145. PMID: 26858460, PMCID: PMC4776530, DOI: 10.1073/pnas.1525677113.Peer-Reviewed Original ResearchConceptsMetastatic lineagesGenetic changesEarly genetic divergenceMolecular evolutionary modelsSingle genetic changeDivergent lineagesTumor phylogeneticsDivergence timesAncestral stateGenetic divergenceCancer lineagesPhylogenetic analysisEvolutionary processesLineagesCancer evolutionMultiple originsDriver genesCancer biologyCancer progressionSomatic mutationsTumor developmentEvolutionary modelsDriver mutationsChronogramMutations
2014
The peopling of the African continent and the diaspora into the new world
Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA. The peopling of the African continent and the diaspora into the new world. Current Opinion In Genetics & Development 2014, 29: 120-132. PMID: 25461616, PMCID: PMC4308437, DOI: 10.1016/j.gde.2014.09.003.Peer-Reviewed Original ResearchConceptsAfrican diasporaModern humansHuman historyHuman migrationNew WorldDemographic historyAfrican descentAfrican continentDemographic eventsHistoryDiasporaEvolutionary questionsAfrican populationsPhenotypic variationContinentGenomic dataAfricaGeographic originDisease susceptibilityPeoplingBirthplaceRecent findingsCorresponding developmentWorldComputational methods
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
2008
The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
Townsend JP, López-Giráldez F, Friedman R. The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree. Journal Of Molecular Evolution 2008, 67: 437-447. PMID: 18696029, DOI: 10.1007/s00239-008-9142-0.Peer-Reviewed Original ResearchConceptsAmino acid sequencePhylogenetic informativenessAcid sequenceVertebrate treeDNA sequencesMolecular evolutionary patternsEarly placental mammalsGenes c-mycDivergence timesMolecular evolutionPhylogenetic conflictEarly vertebratesEvolutionary patternsPlacental mammalsNucleotide sequenceMuroid rodentsFunctional constraintsGenesC-MycSupport valuesSequenceNucleotidesNumber of charactersHigh informativenessTrees
2007
Quantifying variation in gene expression
CLARK TA, TOWNSEND JP. Quantifying variation in gene expression. Molecular Ecology 2007, 16: 2613-2616. PMID: 17594433, DOI: 10.1111/j.1365-294x.2007.03354.x.Commentaries, Editorials and Letters
2005
Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii
Johannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii. Genetics 2005, 171: 109-117. PMID: 15965255, PMCID: PMC1456504, DOI: 10.1534/genetics.105.040923.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, FungalCoccidioidesCoccidioidomycosisDNA, FungalEvolution, MolecularGene ConversionGenetic VariationHumansMembrane GlycoproteinsMutationPhylogenyPolymorphism, GeneticRecombination, GeneticRepetitive Sequences, Nucleic AcidSequence Analysis, DNASpecies SpecificityTandem Repeat SequencesConceptsPathogenic fungus Coccidioides immitisConcerted evolutionProtein-coding genesC. posadasiiGenetic distance analysisPoint mutation rateHost-pathogen interactionsCell surface proteinsGenome dynamicsPathogen's benefitMultigene familyUnequal crossingGeographic rangeFungus Coccidioides immitisRepetitive domainEntire geneMutation rateRepetitive arraysSurface proteinsDistance analysisGenesHost immune systemImmune systemImmunodominant proteinsParasitic phaseHorizontal gene transfer, genome innovation and evolution
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 2005, 3: 679-687. PMID: 16138096, DOI: 10.1038/nrmicro1204.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsEvolution, MolecularGene Transfer TechniquesGenetic VariationGenomeModels, GeneticPhylogenyConceptsHorizontal gene transferHGT eventsImportance of HGTLife historyConcatenation of genesGene transferTypes of genesGroups of organismsGene historiesReticulation eventsPhylogenetic signalTaxonomic samplingMicrobial evolutionSelective sweepsGenome innovationPhylogenetic reconstructionEvolutionary biologyProkaryotic genomesSuch genesMicrobial communitiesPhylogenetic analysisGene swappingHorizontal transferTaxonomic classificationGenes
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 ResearchMeSH KeywordsAnimalsDNA, MitochondrialDrosophila melanogasterFemaleGenetic VariationGenetics, PopulationGenomeMutationRegression AnalysisConceptsMtDNA 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 relationships
2003
Horizontal Acquisition of Divergent Chromosomal DNA in Bacteria: Effects of Mutator Phenotypes
Townsend JP, Nielsen KM, Fisher DS, Hartl DL. Horizontal Acquisition of Divergent Chromosomal DNA in Bacteria: Effects of Mutator Phenotypes. Genetics 2003, 164: 13-21. PMID: 12750317, PMCID: PMC1462543, DOI: 10.1093/genetics/164.1.13.Peer-Reviewed Original ResearchMeSH KeywordsData Interpretation, StatisticalEscherichia coliEvolution, MolecularGene Transfer, HorizontalGenetic VariationModels, GeneticConceptsGenetic variabilityDNA fragmentsBacterial populationsMore amino acid changesSpecific amino acid substitutionsAmino acid changesAmino acid substitutionsStudy of recombinationPresence of mutatorsRate of adaptationEnvironmental DNALong DNA fragmentsBacterial adaptationAdaptive potentialMutator phenotypeHorizontal acquisitionChromosomal DNAPopulation adaptationAcid substitutionsAcid changesMutatorDonor bacteriaE. coliPhenotypeDivergence