2017
New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset
Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Molecular Phylogenetics And Evolution 2017, 110: 27-38. PMID: 28254474, DOI: 10.1016/j.ympev.2017.02.017.Peer-Reviewed Original Research
2016
Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data
Wang Z, Nilsson R, James T, Dai Y, Townsend J. Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data. Fungal Biology 2016, 25-46. DOI: 10.1007/978-3-319-29137-6_3.ChaptersFungal systematicsMolecular phylogenyEnvironmental DNA surveysHigh-throughput sequencingSequence-based classificationFungal treeFungal evolutionPhylogenetic informativenessFungal genomesIntegrative taxonomyDNA surveysFungal researchEvolutionary biologyPhylogenetic inferenceComparative biologyTaxonomic ranksEcological charactersFungal classificationInformative experimental designGenetic markersMycological researchPhylogenySanger sequencingSystematicsBiology
2015
Solving 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
2014
Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
Dornburg A, Townsend JP, Friedman M, Near TJ. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Ecology And Evolution 2014, 14: 169. PMID: 25103329, PMCID: PMC4236503, DOI: 10.1186/s12862-014-0169-0.Peer-Reviewed Original ResearchConceptsMolecular age estimatesMolecular divergence timesDivergence timesSequence dataMolecular divergence time estimationMitochondrial sequence dataPhylogenetic informativeness profilesDivergence time estimationRay-finned fishesTree of lifeMolecular clock methodsSubstitution rate heterogeneityMolecular clock modelBranch length estimatesPhylogenetic informativenessNuclear sequencesRecent divergenceMolecular clockIndividual genesPhylogenetic inferenceDNA sequence alignmentRate heterogeneityFossil recordSequence alignmentClock method
2013
Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets
López-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.Peer-Reviewed Original ResearchConceptsPhylogenomic data setsPhylogenetic informativenessPhylogenetic signalEffects of homoplasyPoor phylogenetic resolutionPhylogenetic resolutionSister cladeOutgroup taxaPhylogenetic researchTaxonomic groupsPhylogenetic inferenceAdvantageous genesGenesMetazoansCladeTaxaDiverse groupDiverse time scalesHomoplasyHaphazard samplingMammalsFungiOrganismsFungalMarkers
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
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
2009
The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits
Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology 2009, 58: 224-239. PMID: 20525580, DOI: 10.1093/sysbio/syp020.Peer-Reviewed Original ResearchConceptsCharacter state reconstructionCommon ancestorAncestral character state reconstructionPhylogenetic informativeness analysesSexual reproductive structuresAscus dehiscenceMaximum likelihood phylogenyPhylogenetic informativenessEcological traitsFungal systematicsAncestral reconstructionNutritional modesRibosomal genesLargest phylumMorphological traitsRelated speciesReproductive structuresProtein geneAscomycota TreePezizomycotinaMultiple originsState reconstructionSporocarpsGene assessmentGenes
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
Profiling Phylogenetic Informativeness
Townsend JP. Profiling Phylogenetic Informativeness. Systematic Biology 2007, 56: 222-231. PMID: 17464879, DOI: 10.1080/10635150701311362.Peer-Reviewed Original ResearchConceptsPhylogenetic informativenessRapid radiationPhylogenetic studiesCharacter samplingBroad phylogenetic studyRapid adaptive radiationGenome-scale dataAddition of charactersAdaptive radiationPhylogenetic signalSoft polytomiesPhylogenetic profilesPhylogenetic hypothesisAncestral lineagePhylogenetic experimentsEarly metazoansPhylogenetic charactersSequence dataMuroid rodentsHistorical radiationPolytomyBase pairsGenesC-MycGenes BRCA1