Our lab pursues diverse research projects in fungal diversity, evolution, and ecology, with a focus on Agaricomycetes (mushroom-forming Fungi). Many (but not all!) of our projects have used molecular phylogenies, which provide a framework for investigations of species-level relationships, biogeography, and evolution of morphological and ecological attributes. In recent years, our work has expanded to include comparative genomic studies, which provide insight into functional evolution as well as phylogeny. We are rooted in “whole organism” biology, and our laboratory has facilities for culturing and anatomical study, as well as a small herbarium containing specimens that members of the lab have collected locally and overseas. The following paragraphs describe two currently active areas of research in the laboratory, one centered on collections-based taxonomic studies and the other involving genome-based analyses of functional evolution, but they do not describe all of our current projects. To learn more, go to the People pages and also see our list of Publications. Prospective students who would like to understand the kinds of projects that might be conducted here may wish to view an older version of this page that describes prior endeavors.
1. Systematics of Polyporales and Boletales. We are currently conducting research into the taxonomy of two large clades of Agaricomycetes, the Polyporales and Boletales, with support from two NSF grants that began in 2010. The Polyporales project is supported by the PEET (Partnerships for Enhancing Expertise in Taxonomy) program and is being conducted in collaboration with researchers and trainees from the USDA Forest Products Laboratory (Madison, WI) , the University of Helsinki , and the University of Gothenburg , while the Boletales project is supported by the Biodiversity Inventories program and is being conducted in collaboration with Dr. Roy Halling of the New York Botanical Garden and Dr. Manfred Binder, who is a Research Fellow in our laboratory (and a world expert on Boletales). Both of these projects are aimed at resolving species and generic limits and involve fieldwork and taxonomic studies using molecular and morphological characters.
In addition to producing taxonomic revisions, we aim to develop comprehensive large-scale phylogenies for the Polyporales and Boletales and use these to study morphological and ecological evolution in each group. For example, in the Polyporales, which includes wood-decaying taxa, we are particularly interested in reconstructing the pattern of transitions between white rot and brown rot modes of wood decay (see below) as well as shifts between conifer and angiosperm substrates. In the Boletales, which includes ectomycorrhizal as well as wood-decaying species, we seek to reconstruct transitions between saprotrophic and mycorrhizal lifestyles and shifts in host associations. In both groups, we will study the evolution of fruiting body forms. We have addressed these subjects in prior phylogenetic studies, but having much more complete phylogenies should improve our ability to pinpoint evolutionary transitions as well as to estimate models of character evolution (i.e, we will use comparative methods to assess directionality in character state transformations, correlations among characters, and diversification consequences of particular character states). Finally, we will use phylogenies to assess biogeographic relationships, particularly in the Boletales project, which is focused on taxa from Queensland. In short, we are coupling basic studies in fungal taxonomy with phylogenetic analyses that contribute to understanding of the evolutionary dynamics in Polyporales and Boletales and changes in the community compositions of forested ecosystems.
2. Diversity and evolution of the decay apparatus in Agaricomycotina. As noted above, our lab has long been interested in transitions between nutritional modes in Agaricomycetes, including shifts between mycorrhizal and decayer lifestyles, and between white rot and brown rot decay modes (in white rot, lignin is degraded along with cellulose and hemicellulose, whereas in brown rot lignin is modified but remains largely intact after removal of cellulose and hemicellulose). Previously, we addressed these problems by mapping transitions in nutritional modes and decay chemistries onto organismal phylogenies, but in recent years we have begun to study the genes and gene families encoding ecologically important enzymes directly. While some of our work has used PCR methods to amplify individual genes, we are now focusing principally on comparative genomics.
Our work in this area is supported in part by our current NSF Assembling the Fungal Tree of Life grant, and has recently expanded significantly thanks to a project funded by the JGI Community Sequencing Program (the “Saprotrophic Agaricomycotina Project”, SAP, which is supporting whole-genome sequencing of thirty species of saprotrophic Agaricomycetes, divided into two “tiers” of 14 and 16 species. As of this writing, five of the tier 1 SAP genomes have been completed and the rest should be done by January 2011. Working with multiple collaborators, our plan is combine the tier 1 SAP genomes with other available fungal genomes (emphasizing Basidiomycota) and perform analyses that will resolve the backbone of the Agaricomycotina phylogeny and elucidate the diversity and evolution of the decay apparatus. We will focus on a set of approximately 28 gene families encoding diverse carbohydrate-active enzymes and oxidoreductases implicated in wood decay. We will estimate gene phylogenies for each family and reconcile them with organismal phylogenies to estimate patterns of gene duplication and loss. Collectively, these analyses should allow us to estimate the suites of decay enzymes produced by ancestral Agaricomycetes, and place these in the context of land plant evolution. Preparation of materials for the tier 2 genomes has already begun, and we expect to submit DNA and RNA for all thirty species by summer 2011. The SAP taxa include multiple representatives of Polyporales and Boletales, and therefore complement the taxonomic studies described previously.