TY - JOUR
T1 - Assembling the fungal tree of life
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, A. Elizabeth
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
PY - 2004/10
Y1 - 2004/10
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.
KW - Fungal classification
KW - Fungal morphology and ultrastructure
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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U2 - 10.3732/ajb.91.10.1446
DO - 10.3732/ajb.91.10.1446
M3 - Review article
C2 - 21652303
SN - 0002-9122
VL - 91
SP - 1446
EP - 1480
JO - American journal of botany
JF - American journal of botany
IS - 10
ER -