Temperate phages are viruses of bacteria which can switch between two alternative life-styles -- lytic and lysogenic. We typically think of the lytic lifestyle when we envision a viral infection: the virus enters the host cell, takes over host machinery, makes copies of itself, kills the host and releases viral progeny that can then go infect other hosts. The lysogenic lifestyle, on the other hand, is a dormant infection state that involves the integration of the viral genome into that of host. The viral genome then replicates passively when the host cell divides. External and internal cues can cause the phage to "reactivate" and go back into the lytic cycle.

Unlike the lytic cycle, which is characterized by a purely antagonistic relationship between the virus and its host, the lysogenic cycle represents a complicated relationship where the reproductive success of the virus depends on the reproductive success of its host. I study how this complex relationship leads to emergent ecological and evolutionary dynamics.

Emergent evolutionary dynamics of temperate phages in the face of eco-evolutionary feedback and environmental heterogeneity

Since viruses are obligate intracellular parasites, the relative fitness of lytic vs lysogenic strategies depends strongly on the availablity of hosts, nutrients and other factors. In the short-term, high host availability favors lysis while low host availability favors lysogeny. But the long-term evolutionary dynamics of temperate viruses gets complicated due to the feedback between population dynamics and evolutionary pressures (see schematic above): High host availability leads to increase in lytic viral populations, which in turn drive down host abundance, a condition that favors more lysogenic viruses. Dormant infections by lysogenic viruses allow the host population to recover, leading again to conditions that favor lytic viruses.

I build mathematical models that incorporate this endogeneous eco-evolutionary feedback to study the long-term evolutionary dynamics of temperate viral strategies in fluctuating environments. These fluctuations may be periodic (eg. diurnal changes in light), gradual (eg. rising temperatures, diffusion limited nutrient gradients) or stochastic (eg. catastrophic weather events).

Emergence and maintenance of temperate phage diversity in complex virus-host communities

Viruses of bacteria (phages) show immense diversity, outpacing that of their hosts. This diversity contradicts a basic principle of theoretical ecology — the competitive exclusion principle — which states that species (phages) that compete for the same resource (host bacteria) cannot stably co-exist long-term. However, multiple phage species coexist with far fewer host species, enabled by a complex network of host-host, host-phage and phage-phage interactions.

I build mathematical models to investigate what features of these complex phage-host interaction networks lead to the emergence and maintenance of viral diverstiy.