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 assessmentGenesMeasuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.Peer-Reviewed Original ResearchTranscription factor-binding sitesCis-regulatory elementsHOXA clusterSelective pressureGene expression evolutionMethionine biosynthesis pathwayLow sequence similarityFactor-binding sitesClade-specific differencesTurnover rateExpression evolutionSpecies treeBiosynthesis pathwayRelated speciesSequence similaritySite turnoverDifferent organismsSequence evolutionTranscription factorsDifferent cladesFungal dataProgesterone response elementMaximum likelihood modelVertebratesTurnover