Rachel J Whitaker

Rachel J Whitaker


3402 Carl Woese Institute for Genomic Biology
Office: (217) 244-8420

Mail to: C222 CLSL
601 S. Goodwin Ave.
Urbana, IL 61801
Lab Page
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Professor of Microbiology

Research Topics

Archaea, Computational Biology, Genetics, Genomics, Host-Pathogen Interactions, Microbial Ecology, Microbial Physiology, Molecular Evolution, Virology

Disease Research Interests

Infectious Diseases


B.A, (Biology, SiSP), Wesleyan University, 1993
Ph.D., (Microbiology), University of California, Berkeley, 1998-2004
Postdoctoral Researcher, (Geomicrobiolgy), University of California, Berkeley, 2004-2006

Microbial Evolution and Ecology Research at Illinois Web Site

Teaching Interests

The Whitaker lab studies the molecular evolution of cellular microorganisms in their natural environmental contexts ranging from hot springs to human infectious disease.

We make use of genetics, genomics, and experimental evolution with wild isolates to follow microbial evolution in natural populations. We are interested in how interactions between gene flow, migration, genetic drift and selection shape the evolutionary trajectory in different model microbial systems. We are extending evolution theory about island dynamics in hot spring islands to human “island” populations integrating ideas of meta-population dynamics and local adaption across a diversity of microbial systems in both Archaeal and the Bacterial Domains. Spanning time from the present to the past, we are interested in how evolution changed with the origin of the cell which led to individuality and increased isolation.

Guided by observations of evolution in action we have recently become focused on developing an evolutionary model in which the emergent properties of organisms result from the symbiotic relationship between the genomes of cellular microbes and their viruses. Viruses possess a dual nature that challenges traditional Darwinian evolutionary theory. An individual virus can act as both a potent pathogen, invading and killing its host, and as an infectious delivery mechanism of novel genetic material that changes the host genotype and phenotype. As semi-autonomous entities, viruses act in the realms of ecology (interactions between species) and evolution (change within species) at the same time, transcending standard models within each discipline. Viruses and their hosts have intimately linked evolutionary trajectories, demographics, transmission dynamics, selection pressures, and sources of variation. We aim to understand how interactions between cells and viruses shape their evolutionary history, fitness and function in complex microbial communities.

Despite their rising important to microbial evolution, the study of viruses today is where microbiology was before the Carl Woese revolutionized the field using 16S rRNA to follow the history of life on earth. This is because viruses have no common molecular marker to link them to cellular life or explore viral diversity. Most of what we know is based on decades of studying few captive viruses in the laboratory and does not scratch the surface of the diversity of virus-host interactions in the natural world. Lucky for us, bacteria and archaea evolved their own molecular surveillance mechanism for their viruses the CRISPR-cas adaptive immunity. Our lab makes use of use sequences recorded in the CRISPR-cas adaptive immune system of Bacteria and Archaea to identify viruses and to track their evolutionary history with their microbial hosts to better understand the impact of viral symbionts on cellular microbial evolution.

Sulfolobus islandicus strain infected by the Sulfolobus spindle shaped virus. (credit Maria A. Bautista)

Schematic of the CRISPR-Cas system. (credit Maria A. Bautista)


Allen Distinguished Investigator
Kavli Fellow National Academy of Sciences
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