2015
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2015, 526: 569-573. PMID: 26444237, DOI: 10.1038/nature15697.Peer-Reviewed Original ResearchSolving 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 relationshipsSequenceSoil
2011
PhyDesign: an online application for profiling phylogenetic informativeness
López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.Peer-Reviewed Original ResearchConceptsPhylogenetic informativenessPhylogenetic studiesPhylogenetic informativeness analysesBroad taxonomic samplingMolecular phylogenetic studiesTree of lifeOrthologous genesPhylogenetic samplingTaxonomic samplingPhylogenetic questionsPhylogenetic purposesEfficiency of sequencingSequence alignmentMarker selectionUltrametric treeDiverse suiteUtility of locusLociTreesUser-friendly toolGenomeGenesSequencingSpeciesDiversity
2010
Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny
Ohenoja E, Wang Z, Townsend JP, Mitchel D, Voitk A. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia 2010, 102: 1089-1095. PMID: 20943508, DOI: 10.3852/09-317.Peer-Reviewed Original Research
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
2006
Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions Of The Royal Society B Biological Sciences 2006, 361: 1947-1963. PMID: 17062413, PMCID: PMC1764934, DOI: 10.1098/rstb.2006.1923.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGlobal geographic rangeGeographic rangeSpecies recognitionFungal speciesGenetic isolationEukaryotic microbesSmall organismsNon-exclusive reasonsPhylogenetic species recognitionEndemic speciesRecognizable morphological changesEukaryotic speciesMorphological changesPhylogenetic speciesGeographic limitsReproductive isolationMorphological speciesKingdom FungiMorphological charactersMicrobial organismsGenetic changesSpeciesMorphological differencesOrganismsFungi
2005
Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species
Townsend JP, Taylor JW. Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species. Methods In Enzymology 2005, 395: 597-617. PMID: 15865986, DOI: 10.1016/s0076-6879(05)95031-3.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsGene expressionGenome-wide gene expressionGene regulation differencesDifferential gene expressionMultiple developmental stagesMultiple environmental conditionsMultiple speciesDevelopmental stagesRegulation differencesSpeciesEnvironmental conditionsMultiple individualsMicroarrayExpressionSuch studiesStatistical powerExperimental protocol