This project will support a team of investigators who seek to resolve evolutionary relationships within the fungi. The research will enhance understanding of the ancient evolutionary diversification of the fungi by addressing evolutionary relationships among the major groups of fungi. This study will develop integrated molecular and morphological datasets, which will be freely accessible on the Web. Molecular data will include sequences from a target set of 76 genes that were identified from analyses of known fungal genomes. Morphological data will include characters associated with nuclear and cellular division and the morphological organization of hyphae. In addition the study will develop ontologies for morphological characters to promote further sampling and analytical integration across disparate organisms.
Fungi make up one of the major groups of life, with an estimated diversity of approximately 1.5 million species. These organisms play crucial ecological roles as decomposers, beneficial mutualists, and parasites and pathogens, including pathogens of humans. The economic significance of fungi is almost incalculable as they perform essential ecological functions and impact diverse applied disciplines, including agriculture, medicine, and drug discovery. A better understanding of the early evolutionary history of the Fungi is necessary to expand our knowledge of the history of life of Earth and the evolution of its ecosystems. Phylogenomic analyses and databases for fungi will transform the field of comparative fungal biology and will benefit all fields of fungal biology that rely on an accurate understanding of evolutionary relationships and diversity of Fungi. The bioinformatics tools for managing and analyzing phylogenomic data that will be developed will be broadly applicable across the Tree of Life. Training and outreach activities will include graduate and post-doctoral training, undergraduate training, and outreach to K-12 educators.
Fungi are among the least well known groups of eukaryotes. Only about 100,000 have been described to date, yet Fungi are estimated to encompass more than 1.5 million species. As decomposers, and as mutualists with forest trees and other plants including crops, fungi are an integral component of all ecosystems on earth. Some fungi benefit humans as sources of food, of enzymes for biofuel production, or of secondary compounds with medicinal properties. Others fungi including plant and human pathogens cause direct harm. The main goals of this project were to sequence complete fungal genomes and to use genome-wide DNA sequence data to find the best genes for fungal phylogenetics. In this way, we could reconstruct, with high confidence, the core of the fungal tree of life. We would also provide a basis for comprehensive and efficient discovery of the previously untapped biotechnological resources hidden among diverse fungal genes and proteins. From September 2007 to August 2012, a team of researchers at Duke University, led by Rytas Vilgalys (http://biology.duke.edu/fungi/mycolab), Jolanta Miadlikowska and François Lutzoni (www.lutzonilab.net), and a research group at the University of British Columbia (Canada) led by Mary Berbee (www.botany.ubc.ca/people/mary-berbee) collaborated in the NSF-supported project "AFTOL: Resolving the Evolutionary History of the Fungi". Other collaborators in an additional seven labs also contributed to this project. The Vilgalys and Berbee labs were responsible for obtaining data for the early diverging fungi, while the Lutzoni lab, in addition to be focusing on lichen-forming Ascomycota and allied fungi, tested all potential genes identified through comparative genomics, developed primers, and tested these primers on subset of species representing the global diversity of Fungi. As part of this project several fungal genomes of fungi were sequenced and made available to the public. A total of 49 scientific articles and two book chapters resulted from this project. Two additional major publications are in preparation, which will be reporting findings from this study. New genome-based methodologies to infer the fungal tree of life resulted from this study, which will transform phylogenetic studies of eukaryotes. An unparalleled number of fungal relationships have been resolved, and new lineages of fungi, as old as 450 million years, have been discovered as a result of this project. Transitions between beneficial and detrimental interactions with their hosts were inferred using fungal phylogenies generated by this project. This project supported the training of six postdoctoral researchers and five Ph.D. students, most of whom are actively pursuing careers in biology. Through the NSF RET program, one teacher at a technical college received training in molecular phylogenetics. Thanks in part to this experience, he recently defended his Ph.D. thesis. Three graduate students conducting research in the US, Belgium and France joined this project as visiting scholars. Workshops and forays were organized in the US and abroad to introduce students and amateurs to fungal biology. Vilgalys contributed to a PBS documentary on Fungi. Lutzoni participated in a workshop to help young plant and fungal systematists in Germany to obtain funding for their research and the Lutzoni lab was the subject of a cover article in the journal ScienceNews for their research on lichen symbioses. Berbee introduced culturing and microscopy of fungi to First Nations (=Native American) children during two half-day workshops at the University of British Columbia (UBC), to encourage children to plan a return to UBC for a university education. Berbee also designed exhibits for the new Beaty Biodiversity (public) museum at the University of British Columbia, Vancouver, BC, Canada.
