Projects

The main focus of our lab group is to study evolutionary genetics and genomics of microbes, especially the ability of viruses to adapt (or not) to changes in their biotic and abiotic environments. These studies concern environmental challenges faced by viruses at all levels of biological organization, including effects of changes in molecules, proteins, cells, populations, communities and ecosystems. Our work is highly interdisciplinary, employing microbiology, computational biology, genomics, molecular biology and mathematical-modeling approaches, and especially experimental evolution (‘evolution-in-action’) studies under controlled laboratory conditions. We use a wide variety of RNA and DNA viruses in our studies, including various lytic, temperate and filamentous phages that infect bacteria. Also, we examine arthropod-borne viruses, such as vesicular stomatitis virus, Sindbis virus, dengue virus, and chikungunya virus, grown in lab tissue culture or within live mosquitoes. Many of our projects use basic research to test fundamental ideas, such as theoretical predictions of virus disease emergence and of virus evolvability. Other projects are more applied and concern evolutionary medicine. For example, we use evolution-thinking to develop novel virus-based therapies to treat antibiotic-resistant bacteria and to attack cancer cells.

Genetic trade-offs occur when organisms evolve adaptive traits for one purpose while suffering reduced performance in an unselected trait. Our work shows that viruses often experience evolutionary trade-offs, under various types of selection pressures. We have observed that evolution of increased virus stability generally trades-off with viral reproduction, obeying a classic survival-reproduction life-history trade-off seen in higher organisms. Also, we have...

RNA viruses are especially capable of jumping to new host species and causing emerging virus diseases in humans and other organisms. My work used both phages and viruses of eukaryotes as laboratory models for elucidating evolutionary rules of RNA virus emergence. These studies demonstrated that mutations underlying host shifts could be beneficial on both the novel and current hosts, and that an evolutionary history of multiple host infection fostered future...

Virus biodiversity on Earth is vast, but as in other biological systems the underlying ecological and evolutionary drivers of biodiversity remain largely unknown. Some viruses specialize on relatively few host types (ecological resources), whereas other viruses are capable of generalizing on a wider variety of host types for infection. Our studies examine the evolutionary genetics of specialist vs. generalist traits in viruses, to determine how and why viruses...

Viruses can rapidly degrade in stressful environments, such as exposure to heat shock (elevated temperature). We examine the evolutionary genetics of virus adaptation in stressful environments, to determine the mutations responsible for increased particle stability to tolerate temperature changes (thermotolerance). More generally, these studies test ecological and evolutionary theory on population persistence vs. extinction, when environments change...

Our work concerns the evolutionary consequences of virus co-infection, especially disentangling the fitness advantages and disadvantages to virus genotypes when replicating within the same host cell. These projects are sometimes highly interdisciplinary, harnessing mathematical game theory and experimental evolution studies of viruses in the laboratory, as well as subjecting natural samples of viruses to phylogenetic and genomic analyses to infer effects of co-...

The rise of antibiotic resistance in bacterial pathogens presents an increasing challenge in public health and in agricultural systems. Phage therapy (use of phages to combat bacterial infections) may provide a viable alternative, when phage alone or in combination with traditional antibiotics are used to target multi-drug resistant bacteria. We examine how phage exert selection pressure on pathogenic bacteria, especially phage binding to virulence factors that...