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Rachel Whitaker

Associate Professor of Microbiology
Infection Genomics for One Health Research Theme Leader, Carl R. Woese Institute for Genomic Biology
University of Illinois at Urbana-Champaign

The Whitaker lab focuses on the evolutionary ecology of microbial populations. They combine field sampling of natural populations with culture and non-culture based genetic and genomic analyses. Currently they are working on understanding how the interactions between basic population genetic parameters (mutation, selection, recombination and genetic exchange, neutral genetic drift, and biogeography) shape diversity, promote ecological differentiation, and lead to speciation in the microbial world. Ultimately they will develop a comparative approach, describing natural population dynamics of different species across spatial and temporal scales, with a particular interest in how population structures reflect the unique biology and ecology of organisms in the Archaeal domain.


"CRISPR-Cas Mediated Host-Virus Co-evolution"

"Long before cells were invented, there could have been selective forces that pushed nucleic acid molecules to greater and greater length and complexity in order to solve the selective problems."
Sol Spiegelman

The ongoing adaptive evolution of Spiegelman’s synthetic monster showed how solutions to simple selective problems could be solved by evolution in a test-tube.  With high-throughput genomics, we can now observe the evolution of complexity in real time in naturally evolving populations.  In these data, we find that solutions to nature’s strongest selective forces have resulted in symbiosis among semi-autonomous, highly mobile, nucleic acid molecules (viruses and plasmids), and their stable host chromosomes.  These symbioses, both positive and negative, are modulated by virus-host interactions including for bacteria and archaea the adaptive CRISPR-Cas immune system.  Selective problems can be solved through transient-strongly selected symbioses that have a cost in highly variable environments.  We show examples of these dynamics in two distinct microbial island populations linked by the fundamental evolutionary principles are likely shared across three of Domains life.

Rachel Whitaker