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, Anne E 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 journalArticle

494 Citations (Scopus)

Abstract

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
Volume91
Issue number10
DOIs
StatePublished - Oct 2004
Externally publishedYes

Fingerprint

Ribosomal DNA
Fungi
Basidiomycota
Ascomycota
fungus
taxonomy
phylogenetics
loci
fungi
phylogeny
Glomeromycota
Chytridiomycota
Eumycota
Bayes Theorem
Hyphae
Nucleic Acid Databases
complementarity
Zygomycota
molecular systematics
Datasets

Keywords

  • 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

  • Plant Science

Cite this

Lutzoni, F., Kauff, F., Cox, C. J., McLaughlin, D., Celio, G., Dentinger, C., ... Vilgalys, R. (2004). Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits. American Journal of Botany, 91(10), 1446-1480. https://doi.org/10.3732/ajb.91.10.1446

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

In: American Journal of Botany, Vol. 91, No. 10, 10.2004, p. 1446-1480.

Research output: Contribution to journalArticle

Lutzoni, F, Kauff, F, Cox, CJ, McLaughlin, D, Celio, G, Dentinger, C, Padamsee, M, Hibbett, D, James, TY, Baloch, E, Grube, M, Reeb, V, Hofstetter, V, Schoch, C, Arnold, AE, Miadlikowska, J, Spatafora, J, Johnson, D, Hambleton, S, Crockett, M, Shoemaker, R, Sung, GH, Lücking, R, Lumbsch, T, O'Donnell, K, Binder, M, Diederich, P, Ertz, D, Gueidan, C, Hansen, K, Harris, RC, Hosaka, K, Lim, YW, Matheny, B, Nishida, H, Pfister, D, Rogers, J, Rossman, A, Schmitt, I, Sipman, H, Stone, J, Sugiyama, J, Yahr, R & Vilgalys, R 2004, 'Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits', American Journal of Botany, vol. 91, no. 10, pp. 1446-1480. https://doi.org/10.3732/ajb.91.10.1446
Lutzoni, François ; Kauff, Frank ; Cox, Cymon J. ; McLaughlin, David ; Celio, Gail ; Dentinger, Celiobryn ; Padamsee, Mahajabeen ; Hibbett, David ; James, Timothy Y. ; Baloch, Elisabeth ; Grube, Martin ; Reeb, Valérie ; Hofstetter, Valérie ; Schoch, Conrad ; Arnold, Anne E ; Miadlikowska, Jolanta ; Spatafora, Joseph ; Johnson, Desiree ; Hambleton, Sarah ; Crockett, Michael ; Shoemaker, Robert ; Sung, Gi Ho ; Lücking, Robert ; Lumbsch, Thorsten ; O'Donnell, Kerry ; Binder, Manfred ; Diederich, Paul ; Ertz, Damien ; Gueidan, Cécile ; Hansen, Karen ; Harris, Richard C. ; Hosaka, Kentaro ; Lim, Young Woon ; Matheny, Brandon ; Nishida, Hiromi ; Pfister, Don ; Rogers, Jack ; Rossman, Amy ; Schmitt, Imke ; Sipman, Harrie ; Stone, Jeffrey ; Sugiyama, Junta ; Yahr, Rebecca ; Vilgalys, Rytas. / Assembling the fungal tree of life : Progress, classification, and evolution of subcellular traits. In: American Journal of Botany. 2004 ; Vol. 91, No. 10. pp. 1446-1480.
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T2 - Progress, classification, and evolution of subcellular traits

AU - Lutzoni, François

AU - Kauff, Frank

AU - Cox, Cymon J.

AU - McLaughlin, David

AU - Celio, Gail

AU - Dentinger, Celiobryn

AU - Padamsee, Mahajabeen

AU - Hibbett, David

AU - James, Timothy Y.

AU - Baloch, Elisabeth

AU - Grube, Martin

AU - Reeb, Valérie

AU - Hofstetter, Valérie

AU - Schoch, Conrad

AU - Arnold, Anne E

AU - Miadlikowska, Jolanta

AU - Spatafora, Joseph

AU - Johnson, Desiree

AU - Hambleton, Sarah

AU - Crockett, Michael

AU - Shoemaker, Robert

AU - Sung, Gi Ho

AU - Lücking, Robert

AU - Lumbsch, Thorsten

AU - O'Donnell, Kerry

AU - Binder, Manfred

AU - Diederich, Paul

AU - Ertz, Damien

AU - Gueidan, Cécile

AU - Hansen, Karen

AU - Harris, Richard C.

AU - Hosaka, Kentaro

AU - Lim, Young Woon

AU - Matheny, Brandon

AU - Nishida, Hiromi

AU - Pfister, Don

AU - Rogers, Jack

AU - Rossman, Amy

AU - Schmitt, Imke

AU - Sipman, Harrie

AU - Stone, Jeffrey

AU - Sugiyama, Junta

AU - Yahr, Rebecca

AU - Vilgalys, Rytas

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N2 - 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.

AB - 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.

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KW - Fungal phylogenetics

KW - Fungal systematics

KW - Mitochondrial small subunit ribosomal DNA (mitSSU rDNA)

KW - Nuclear small and large subunit ribosomal DNA (nucSSU and nucLSU rDNA)

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