Our lab uses comparative and evolutionary genomics to investigate how fungal genomes change across species, populations, and ecological transitions. We are particularly interested in connecting genomic variation with major evolutionary changes, including host specialization, host jumps, the evolution of pathogenicity, and the production of specialized metabolites. By integrating genomic data with well-characterized fungal collections and experimental systems, we can connect patterns of genome evolution with the ecology and natural history of individual lineages.


Powdery mildews provide a particularly powerful system for studying genome evolution in obligate pathogens. Our ongoing work compares genomes across closely related species and populations that differ in host range and geographic distribution to identify genomic changes associated with adaptation to new hosts. We are also using genome-scale population genetic approaches, including ultraconserved element (UCE) target enrichment, to reconstruct population structure, dispersal, and invasion histories and to examine how fungal populations change following geographic expansion and host shifts. We are developing genomic resources across the Erysiphaceae to examine the evolution of gene families, structural variation, effector repertoires, and other genomic features associated with host specialization and major host jumps.

We also use genome mining to investigate evolutionary patterns within fungal genomes and to identify genetic pathways underlying ecologically important traits. Our previous work has demonstrated extensive intragenomic variation in the nuclear ribosomal DNA array, including variation within the ITS region commonly used for fungal identification and phylogenetics (Bradshaw et al. 2023, iScience). More recently, we have expanded genome mining to biosynthetic gene clusters and other pathways involved in fungal secondary metabolism. By connecting genomic predictions with metabolomic and experimental data, we aim to understand how these pathways evolve, how their products contribute to interactions among organisms, and how genomic diversity ultimately translates into ecological and phenotypic diversity.

Image by Uma Crouch