Research Overview
There are currently three main focus areas, all of which seek to use genome-scale data and phylogenetic methodology to address questions in fungal evolutionary biology.
Assembling the Fungal Tree of Life (AFTOL) - 1000 Fungal Genomes. For the past 10 years we have been an active laboratory of the AFTOL project. Our initial focus was on multigene phylogenetics of Ascomycota, the largest phylum of Kingdom Fungi. Over the past few years, however, we have developed pipelines and experimental approaches for genome-scale phylogeny reconstruction. This project has morphed into the 1000 Fungal (1000F) Genomes project, which is spearheaded by the Joint Genome Institute of DOE. The goal of 1000F is to facilitate the genomic sampling of two 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.)
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.).
Assembling the Fungal Tree of Life (AFTOL) - 1000 Fungal Genomes. For the past 10 years we have been an active laboratory of the AFTOL project. Our initial focus was on multigene phylogenetics of Ascomycota, the largest phylum of Kingdom Fungi. Over the past few years, however, we have developed pipelines and experimental approaches for genome-scale phylogeny reconstruction. This project has morphed into the 1000 Fungal (1000F) Genomes project, which is spearheaded by the Joint Genome Institute of DOE. The goal of 1000F is to facilitate the genomic sampling of two 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.)
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.).
