2022
A phylogenetic approach to study the evolution of somatic mutational processes in cancer
Miura S, Vu T, Choi J, Townsend JP, Karim S, Kumar S. A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications Biology 2022, 5: 617. PMID: 35732905, PMCID: PMC9217972, DOI: 10.1038/s42003-022-03560-0.Peer-Reviewed Original ResearchConceptsMutational processesPattern of conservationFalse-positive discovery rateCollection of mutationsSomatic mutational processesPhylogenetic approachGenomic variationSomatic variationCell lineagesMutational signaturesTumor evolutionMutation signaturesPhylogenyCancer cellsDiscovery rateMutationsComputer-simulated datasetsRelative activityLineagesComputational methodsSignaturesConservationDivergenceEvolutionJoint analysis
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 ResearchConceptsMutation accumulation dataDirectional selectionNatural selectionMutational effectsPhenotypic traitsDirectional natural selectionQuantitative trait lociDivergent lineagesRosette diameterTrait lociHistorical selectionQuantitative traitsLineagesArabidopsisTraitsDensity traitsAccumulation dataDivergenceKey roleUltimate sourceLociSelectionOrganismsKey componentMutations
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
Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design
Moeller AH, Townsend JP. Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design. Molecular Phylogenetics And Evolution 2012, 66: 436. PMID: 23063589, DOI: 10.1016/j.ympev.2012.09.035.Commentaries, Editorials and Letters
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 ResearchConceptsGenetic 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