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United States Department of Agriculture

Agricultural Research Service

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

Author
item Lutzoni, Francois
item Kauff, Frank
item Cox, Cymon
item Mclaughlin, David
item Celio, Gail
item Dentinger, Bryn
item Padamsee, Mahajabeen
item Hibbett, David
item James, Timothy
item Baloch, Elisabeth
item Grube, Martin
item Reeb, Valerie
item Hofstetter, Valerie
item Schoch, Conrad
item Arnold, A. elizabeth
item Miadlikowska, Jolanta
item Spatafora, Joseph
item Johnson, Desiree
item Hambleton, Sarah
item Crockett, Michael
item Shoemaker, Robert
item Sung, Gi-ho
item Lucking, Robert
item Lumbsch, Thorsten
item O`donnell, Kerry
item Binder, Manfred
item Diederich, Paul
item Ertz, Damien
item Gueidan, Cecile
item Hall, Benjamin
item Hansen, Karen
item Harris, Richard
item Hosaka, Kentaro
item Lim, Young-woon
item Liu, Yajuan
item Matheny, Brandon
item Nishida, Hiromi
item Pfister, Don
item Rogers, Jack
item Vacant, rl,
item Schmitt, Imke
item Sipman, Harrie
item Stone, Jeffrey
item Sugiyama, Junta
item Yahr, Rebecca
item Vilgalys, Rytas

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.

Last Modified: 8/24/2016
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