2025
Viral genomic features predict Orthopoxvirus reservoir hosts
Tseng K, Koehler H, Becker D, Gibb R, Carlson C, Pilar Fernandez M, Seifert S. Viral genomic features predict Orthopoxvirus reservoir hosts. Communications Biology 2025, 8: 309. PMID: 40000824, PMCID: PMC11862092, DOI: 10.1038/s42003-025-07746-0.Peer-Reviewed Original ResearchConceptsHost speciesViral genomic featuresHost ecological traitsPotential host speciesGenomic featuresHistorical rangeEcological traitsParts of Southeast AsiaWildlife surveillanceHuman populationCausative agent of smallpoxHost predictionAgent of smallpoxSpeciesSoutheast AsiaCausative agentGeographic regionsOrthopoxviruses
2022
Virus isolation data improve host predictions for New World rodent orthohantaviruses
Mull N, Carlson C, Forbes K, Becker D. Virus isolation data improve host predictions for New World rodent orthohantaviruses. Journal Of Animal Ecology 2022, 91: 1290-1302. PMID: 35362148, DOI: 10.1111/1365-2656.13694.Peer-Reviewed Original ResearchConceptsRisk of pathogen spilloverHost associationsMulti-host pathogensRT-PCR dataVirus isolation dataBRT modelsTrait profilesEcological traitsReservoir host speciesPathogen spilloverRT-PCRHost speciesPathogen maintenancePathogen hostsRegression treesBRTHost predictionHost competenceHantavirus cardiopulmonary syndromeZoonotic reservoirsPrioritizing surveillanceRodent phylogenyMultiple data typesIsolation dataMuroid rodents
2018
An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila
Shapiro L, Paulson J, Arnold B, Scully E, Zhaxybayeva O, Pierce N, Rocha J, Klepac-Ceraj V, Holton K, Kolter R. An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila. MBio 2018, 9: 10.1128/mbio.01307-18. PMID: 30279283, PMCID: PMC6168856, DOI: 10.1128/mbio.01307-18.Peer-Reviewed Original ResearchConceptsTemperate eastern North AmericaEastern North AmericaErwinia tracheiphila</i>,Host plant speciesPlant speciesCrop plantsCausal agent of bacterial wiltAgent of bacterial wiltVirulence gene repertoireLow genetic heterogeneityLarge-scale sequencingSusceptible to isolatesNorth AmericaDriving diversificationPhylogenomic analysisPopulation bottlenecksGenetic clustersEcological traitsIsolate collectionGene repertoirePopulation expansionGeographic rangeEvolutionary trajectoriesGenetic heterogeneityCausal agent
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
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