The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Conrad L. Schoch, Gi Ho Sung, Francesc López-Giráldez, Jeffrey P. Townsend, Jolanta Miadlikowska, Valérie Hofstetter, Barbara Robbertse, P. Brandon Matheny, Frank Kauff, Zheng Wang, Cécile Gueidan, Rachael M. Andrie, Kristin Trippe, Linda M. Ciufetti, Anja Wynns, Emily Fraker, Brendan P. Hodkinson, Gregory Bonito, Johannes Z. Groenewald, Mahdi ArzanlouG. Sybren De Hoog, Pedro W. Crous, David Hewitt, Donald H. Pfister, Kristin Peterson, Marieka Gryzenhout, Michael J. Wingfield, André Aptroot, Sung Oui Suh, Meredith Blackwell, David M. Hillis, Gareth W. Griffith, Lisa A. Castlebury, Amy Y. Rossman, H. Thorsten Lumbsch, Robert Lücking, Burkhard Büdel, Alexandra Rauhut, Paul Diederich, Damien Ertz, David M. Geiser, Kentaro Hosaka, Patrik Inderbitzin, Jan Kohlmeyer, Brigitte Volkmann-Kohlmeyer, Lizel Mostert, Kerry O'Donnell, Harrie Sipman, Jack D. Rogers, Robert A. Shoemaker, Junta Sugiyama, Richard C. Summerbell, Wendy Untereiner, Peter R. Johnston, Soili Stenroos, Alga Zuccaro, Paul S. Dyer, Peter D. Crittenden, Mariette S. Cole, Karen Hansen, James M. Trappe, Rebecca Yahr, Franois Lutzoni, Joseph W. Spatafora

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Abstract

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Original languageEnglish (US)
Pages (from-to)224-239
Number of pages16
JournalSystematic Biology
Volume58
Issue number2
DOIs
StatePublished - Apr 1 2009

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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    Schoch, C. L., Sung, G. H., López-Giráldez, F., Townsend, J. P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P. B., Kauff, F., Wang, Z., Gueidan, C., Andrie, R. M., Trippe, K., Ciufetti, L. M., Wynns, A., Fraker, E., Hodkinson, B. P., Bonito, G., Groenewald, J. Z., ... Spatafora, J. W. (2009). The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology, 58(2), 224-239. https://doi.org/10.1093/sysbio/syp020