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Title: ASSEMBLING THE FUNGAL TREE OF LIFE: Progress, CLASSIFication, and EVOLUTION OF SUBCELLULAR TRAITS

Author
item LUTZONI, FRANCOIS - DUKE UNIV, DURHAM NC
item KAUFF, FRANK - DUKE UNIV, DURHAM NC
item COX, CYMON - DUKE UNIV, DURHAM NC
item MCLAUGHLIN, DAVID - DUKE UNIV, DURHAM NC
item CELIO, GAIL - UNIV OF MINN, ST PAUL MN
item DENTINGER, BRYN - UNIV OF MINN, ST PAUL MN
item PADAMSEE, MAHAJABEEN - UNIV OF MINN, ST PAUL MN
item HIBBETT, DAVID - CLARK UNIV, WORCESTER MA
item JAMES, TIMOTHY - DUKE UNIV, DURHAM NC
item BALOCH, ELISABETH - INST OF BOTANY, AUSTRIA
item GRUBE, MARTIN - INST OF BOTANY, AUSTRIA
item REEB, VALERIE - UNIV OF MINN, ST PAUL MN
item HOFSTETTER, VALERIE - UNIV OF MINN, ST PAUL MN
item SCHOCH, CONRAD - OREGON STATE UNIV, OR
item ARNOLD, A. ELIZABETH - DUKE UNIV, DURHAM NC
item MIADLIKOWSKA, JOLANTA - GDANSK UNIV, POLAND
item SPATAFORA, JOSEPH - OREGON STATE UNIV, OR
item JOHNSON, DESIREE - OREGON STATE UNIV, OR
item HAMBLETON, SARAH - AG & AGRI-FOOD, CANADA
item CROCKETT, MICHAEL - OREGON STATE UNIV, OR
item SHOEMAKER, ROBERT - AG & AGRI-FOOD, CANADA
item SUNG, GI-HO - OREGON STATE UNIV, OR
item LUCKING, ROBERT - FIELD MUSEUM, CHICAGO IL
item LUMBSCH, THORSTEN - FIELD MUSEUM, CHICAGO IL
item O Donnell, Kerry
item BINDER, MANFRED - CLARK UNIV, WORCESTER MA
item DIEDERICH, PAUL - LUXEMBOURG
item ERTZ, DAMIEN - BOTANIC GARDEN, BELGIUM
item GUEIDAN, CECILE - DUKE UNIV, DURHAM NC
item HALL, BENJAMIN - UNIV OF WASH, SEATTLE WA
item HANSEN, KAREN - HARVARD UNIV, MA
item HARRIS, RICHARD - INST OF SYS BOTNAY NY
item HOSAKA, KENTARO - OREGON STATE UNIV, OR
item LIM, YOUNG-WOON - UNIV OF BRITISH COLUMBIA
item LIU, YAJUAN - UNIV OF WASH, SEATTLE WA
item MATHENY, BRANDON - CLARK UNIV, WORCESTER MA
item NISHIDA, HIROMI - RIKEN, YOKOHAMA JAPAN
item PFISTER, DON - HARVARD UNIV, MA
item ROGERS, JACK - WASH STATE UNIV, WA
item Rossman, Amy
item SCHMITT, IMKE - FIELD MUSEUM, CHICAGO IL
item SIPMAN, HARRIE - BERLIN, GERMANY
item STONE, JEFFREY - OREGON STATE UNIV, OR
item SUGIYAMA, JUNTA - UNIV OF TOKYO, JAPAN
item YAHR, REBECCA - DUKE UNIV, DURHAM NC
item VILGALYS, RYTAS - DUKE UNIV, DURHAM NC

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2004
Publication Date: 10/1/2004
Citation: Lutzoni, F., Kauff, F., Cox, C.J., Mclaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T.Y., Baloch, E., Grube, M., Reeb, V., Hofstetter, V., Schoch, C., Arnold, A., Miadlikowska, J., Spatafora, J., Johnson, D., Hambleton, S., Crockett, M., Shoemaker, R., Sung, G., Lucking, R., Lumbsch, T., O Donnell, K., Binder, M., Diederich, P., Ertz, D., Gueidan, C., Hall, B., Hansen, K., Harris, R.C., Hosaka, K., Lim, Y., Liu, Y., Matheny, B., Nishida, H., Pfister, D., Rogers, J., Rossman, A.Y., 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. 91(10):1446-1480.

Interpretive Summary: Fungi make up one of the major evolutionary divisions of life. Therefore, a robust fungal phylogeny is necessary for understanding the history of life, including the evolution of ecosystems. Furthermore, knowledge of their evolutionary relationships will also provide resources for applied purposes, including plant pathology, medical mycology, and drug discovery, and will facilitate discovery of the > 90% of fungal species that remain undocumented. The primary goal of the present study was to provide a phylogenetic synthesis for the fungal tree of life, and to analyze all available data for the four most commonly used genes for studying fungal evolution. As such, the present study represents the most comprehensive analysis of evolutionary relationships among the Fungi to date. Analysis of DNA data from four combined genes resolved multiple relationships that were not revealed previously, or that received only weak support in prior studies. The impact of this newly discovered phylogenetic structure on classification of the Fungi is discussed. Together, these findings provide an overview of our present understanding of the structure of, and approaches to, inferring the fungal tree of life.

Technical Abstract: Fungi make up one of the largest and most taxonomically challenging groups of eukaryotes. However, no large-scale multi-locus phylogenetic analysis has been undertaken to reveal deep relationships among Fungi. The goal of this study is to provide a phylogenetic synthesis for the Fungi. We report here the results of four Bayesian analyses with complementary bootstrap assessment of phylogenetic confidence using neighbor joining, maximum parsimony, and Bayesian methods: 1) 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) combined three-locus data set (nucSSU, nucLSU and mitSSU rDNA) with 236 species; 3) combined three-locus data set (nucSSU, nucLSU rDNA and RPB2) with 157 species; and 4) combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously, or that received only weak support values in prior studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed here. Together, these findings provide an overview of our present understanding of the structure of, and approaches to, inferring the fungal tree of life.