Research Overview
There are currently four main focus areas, all of which seek to use genome-scale data and phylogenetic methodology to address questions in fungal evolutionary biology.
The Zygomycetes Genealogy of Life (ZyGoLife) - the Conundrum of Kingdom Fungi. In collaboration with Jason Stajich (UC Riverside), Robby Roberson (U of Arizona), Tim James (U of Michigan) and numerous other researchers, we have recently initiated a new interdisciplinary project on evolution of the zygomycetous fungi. This project is funded by the new NSF GOLife (Genealogy of Life) program. Our goal is to resolve the evolutionary relationships of zygomycetous fungi through phylogenetic and phylogenomic analyses that are informed by fossils and subcellular data. In addition we will use these data to advance barcoding and environmental sampling strategies, as well as outreach activities (e.g., EOL pages, protocols for teaching, etc.), for this poorly studied group of fungi. Visit ZyGoLife to learn more.
1000 Fungal Genomes Project. The 1000 Fungal Genomes (1KFG) project, is supported by the Joint Genome Institute of the Departmetn of Energy. The goal of 1KFG is to facilitate the genomic sampling of species from every family-level clade of fungi. We are interested in numerous questions including primary metabolism of the early diverging lineages of Fungi and transitions between major fungal ecologies and nutritional modes (e.g., terrestrial vs. marine, saprobe vs. symbiont, etc.). Visit 1000 Fungal Genomes to learn more.
Phylogenomics of Hypocreales. For the better part of 20 years, our lab has worked on systematics of Cordyceps (Hypocreales, Ascomycota) and related insect pathogenic fungi. For a contemporary view of Cordyceps systematics visit an Electronic Monograph of Cordyceps and Related Fungi. While we continue to be interested in basic systematics of the group, much of our recent focus is on phylogenomics of Hypocreales and evolution of ecologies and nutritional modes. The order is unique among Fungi in that it includes plant pathogens, symbionts and saprobes, insect pathogens and symbionts, and mycoparasites. We are seeking to understand patterns and processes of genomic evolution that have facilitated and that have resulted from these transitions.
Systematics and Population Biology/Ecology of Rhizopogon. Rhizopogon (Boletales) is genus of basidiomycete truffles that are ectomycorrhizal with trees of Pinaceae. Species of the genus are common and ecologically important in the forests of the Pacific Northwest (PNW). Our lab has researched phylogenetics and population biology of the genus. Currently, we are working on systematics and population genomics of R. subgenus Villosuli, which is host specific with Pseudotsuga and shares a Pacific Rim distribution, and contains numerous sympatrically distributed species with different life history characteristics (e.g., clone size, inbreeding patterns, etc.).
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The Zygomycetes Genealogy of Life (ZyGoLife) - the Conundrum of Kingdom Fungi. In collaboration with Jason Stajich (UC Riverside), Robby Roberson (U of Arizona), Tim James (U of Michigan) and numerous other researchers, we have recently initiated a new interdisciplinary project on evolution of the zygomycetous fungi. This project is funded by the new NSF GOLife (Genealogy of Life) program. Our goal is to resolve the evolutionary relationships of zygomycetous fungi through phylogenetic and phylogenomic analyses that are informed by fossils and subcellular data. In addition we will use these data to advance barcoding and environmental sampling strategies, as well as outreach activities (e.g., EOL pages, protocols for teaching, etc.), for this poorly studied group of fungi. Visit ZyGoLife to learn more.
1000 Fungal Genomes Project. The 1000 Fungal Genomes (1KFG) project, is supported by the Joint Genome Institute of the Departmetn of Energy. The goal of 1KFG is to facilitate the genomic sampling of species from every family-level clade of fungi. We are interested in numerous questions including primary metabolism of the early diverging lineages of Fungi and transitions between major fungal ecologies and nutritional modes (e.g., terrestrial vs. marine, saprobe vs. symbiont, etc.). Visit 1000 Fungal Genomes to learn more.
Phylogenomics of Hypocreales. For the better part of 20 years, our lab has worked on systematics of Cordyceps (Hypocreales, Ascomycota) and related insect pathogenic fungi. For a contemporary view of Cordyceps systematics visit an Electronic Monograph of Cordyceps and Related Fungi. While we continue to be interested in basic systematics of the group, much of our recent focus is on phylogenomics of Hypocreales and evolution of ecologies and nutritional modes. The order is unique among Fungi in that it includes plant pathogens, symbionts and saprobes, insect pathogens and symbionts, and mycoparasites. We are seeking to understand patterns and processes of genomic evolution that have facilitated and that have resulted from these transitions.
Systematics and Population Biology/Ecology of Rhizopogon. Rhizopogon (Boletales) is genus of basidiomycete truffles that are ectomycorrhizal with trees of Pinaceae. Species of the genus are common and ecologically important in the forests of the Pacific Northwest (PNW). Our lab has researched phylogenetics and population biology of the genus. Currently, we are working on systematics and population genomics of R. subgenus Villosuli, which is host specific with Pseudotsuga and shares a Pacific Rim distribution, and contains numerous sympatrically distributed species with different life history characteristics (e.g., clone size, inbreeding patterns, etc.).
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