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RESEARCH INTERESTS

 

I am an evolutionary population biologist with a wide range of interests, including phylogeography, molecular systematics, ecology and epidemiology. I apply population genetic methods to retrace the natural history of populations or species, to identify the origin of invading plant and animal pathogens and to elucidate the underlying population structure that impacts genome architecture, particularly as it relates to gene clustering, function and adaptation. I am also actively developing a software workbench for managing and deploying a plethora of genetic tools developed by others and myself for analyzing molecular genetic and phenotypic variation in populations. A long-term goal of my work is to apply inferences of evolutionary processes on the population scale to understand patterns of diversity on species and higher taxonomic scales.

 

 

RESEARCH AREAS

 

Evolution of Fungal Secondary Metabolism

 

We are examining the evolution of fungal secondary metabolism focusing on the sterigmatocystin (ST), O-methylsterigmatocystin (OMST) and aflatoxin (AF) biosynthetic pathway in Aspergillus. The genes for ST, OMST, and AF are clustered and these compounds are synthesized as end products by numerous ascomycetes. Although all three metabolites (ST, OMST, and AF) are potent carcinogens in animals, the biological and evolutionary significance of these bioreactive compounds in fungi is unknown. We are combining inferences from macro- and micro-evolutionary analyses to understand the conservation of these metabolites among Aspergillus species and how diversity is generated and maintained within species over long periods of time.

 

A major component of my research program focuses on the evolution of aflatoxigenicity in Aspergillus. Aflatoxin is one of the most carcinogenic compounds known and is responsible for major yield losses in oil seed crops worldwide. The evolutionary processes that maintain or degrade aflatoxin biosynthesis in nature are poorly understood. Currently, we are acquiring basic knowledge on the evolution of the aflatoxin gene cluster in populations of two agriculturally important aflatoxin-producing species, Aspergillus flavus and A. parasiticus. My goal is to apply our knowledge of the evolutionary processes that influence aflatoxigenicity in natural populations of these species to the development of novel biocontrol measures, ultimately fine-tuning these control strategies using our knowledge of the population genetic structure of these fungi.

 

 

Software Tools for Analyzing Population Genetic Data

 

A second component of my research is the development of new software tools to facilitate and enhance our understanding of the underlying evolutionary processes shaping diversity in pathogen populations. The evolutionary toolkit developed in my laboratory (SNAP Workbench) makes population genetic analyses tractable and accessible to the biologist.

 

A key aspect to managing and integrating DNA sequence-based variation with phenotypic data is to recognize the hierarchical nature of DNA sequence variation. This hierarchical organization implies a process driven system that is most accurately captured using evolutionary approaches. We have been developing new methodologies and tools to examine the influence of mutation, recombination, gene flow, selection and demography on the evolution of fungal genomes, populations and species. Our workbench effectively manages and integrates a plethora of new approaches for making inferences on population processes from DNA sequence variation, bringing together simple summary-statistics, nonparametric methods and complex parameter-rich models. A long-term goal is integrating user-interactive tutorials in our workbench for teaching and training on these methods.

 

 

TEACHING RESPONSIBILITIES

 

I am one of three instructors of Plant-Microbe Interactions (PP 707), a required course in the Plant Pathology core curriculum that is offered every Spring. I also teach, in the Fall of alternate years, Applied Evolutionary and Population Genetic Data Analysis (PP 715, formerly PP 610A/810A), an advanced graduate course that focuses on nonparametric and model-based evolutionary methods for biological inference. This is an interdisciplinary course that has attracted students from diverse programs, including Plant Biology, Crop Science, Bioinformatics, Functional Genomics and Computer Science.