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(American Journal of Botany. 2004;91:1446-1480.)
© 2004 Botanical Society of America, Inc.

Invited Special Papers

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits1

François Lutzoni2,21, Frank Kauff2, Cymon J. Cox2, David McLaughlin3, Gail Celio3, Bryn Dentinger3, Mahajabeen Padamsee3, David Hibbett4, Timothy Y. James2, Elisabeth Baloch5, Martin Grube5, Valérie Reeb2, Valérie Hofstetter2, Conrad Schoch6, A. Elizabeth Arnold2, Jolanta Miadlikowska2,7, Joseph Spatafora6, Desiree Johnson6, Sarah Hambleton8, Michael Crockett6, Robert Shoemaker8, Gi-Ho Sung6, Robert Lücking9, Thorsten Lumbsch9, Kerry O'Donnell10, Manfred Binder4, Paul Diederich11, Damien Ertz12, Cécile Gueidan2, Karen Hansen13, Richard C. Harris14, Kentaro Hosaka6, Young-Woon Lim4,15, Brandon Matheny4, Hiromi Nishida16, Don Pfister13, Jack Rogers17, Amy Rossman18, Imke Schmitt9, Harrie Sipman19, Jeffrey Stone6, Junta Sugiyama20, Rebecca Yahr2 and Rytas Vilgalys2

2Department of Biology, Duke University, Durham, North Carolina 27708-0338 USA; 3Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 USA; 4Department of Biology, Clark University, Worcester, Massachusetts 01610 USA; 5Institute of Botany, Karl-Franzens-University Graz, A-8010 Graz, Austria; 6Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-2902 USA; 7Plant Taxonomy and Nature Conservation, Gdansk University, Al. Legionow 9, 80-441 Gdansk, Poland; 8Biodiversity (Mycology and Botany), Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6 Canada; 9Department of Botany, The Field Museum, Chicago, Illinois 60605-2496 USA; 10Microbial Genomics Research Unit, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604-3999 USA; 11National Natural History Museum, 25 rue Munster, L-2160 Luxembourg, Luxembourg; 12Department of Bryophytes-Thallophytes, National Botanic Garden of Belgium, B-1860 Meise, Belgium; 13Harvard University Herbaria, Cambridge, Massachusetts 02138 USA; 14Institute of Systematic Botany, New York Botanical Garden, New York 10458-5126 USA; 15Current address: Department of Wood Science, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada; 16Genomic Sciences Center, The Institute of Physical and Chemical Research (RIKEN), Yokohama 230-0045 Japan; 17Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430 USA; 18Systematic Botany and Mycology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705 USA; 19Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Berlin D-14191 Germany; 20The University of Tokyo, Tokyo 101-0041 Japan

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.

Key Words: 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) • RNA polymerase subunit (RPB2)




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