Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits

François Lutzoni, Frank Kauff, Cymon J. Cox, David McLaughlin, Gail Celio, Celiobryn Dentinger, Mahajabeen Padamsee, David Hibbett, Timothy Y. James, Elisabeth Baloch, Martin Grube, Valérie Reeb, Valérie Hofstetter, Conrad Schoch, A. Elizabeth Arnold, Jolanta Miadlikowska, Joseph Spatafora, Desiree Johnson, Sarah Hambleton, Michael CrockettRobert Shoemaker, Gi Ho Sung, Robert Lücking, Thorsten Lumbsch, Kerry O'Donnell, Manfred Binder, Paul Diederich, Damien Ertz, Cécile Gueidan, Karen Hansen, Richard C. Harris, Kentaro Hosaka, Young Woon Lim, Brandon Matheny, Hiromi Nishida, Don Pfister, Jack Rogers, Amy Rossman, Imke Schmitt, Harrie Sipman, Jeffrey Stone, Junta Sugiyama, Rebecca Yahr, Rytas Vilgalys

Research output: Contribution to journalReview articlepeer-review

662 Scopus citations


Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

Original languageEnglish (US)
Pages (from-to)1446-1480
Number of pages35
JournalAmerican journal of botany
Issue number10
StatePublished - Oct 2004


  • Fungal classification
  • Fungal morphology and ultrastructure
  • Fungal phylogenetics
  • Fungal systematics
  • Mitochondrial small subunit ribosomal DNA (mitSSU rDNA)
  • Nuclear small and large subunit ribosomal DNA (nucSSU and nucLSU rDNA)

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Plant Science


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