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Rachel Whitaker

Associate Professor, Microbiology and Institute for Genomic Biology
University of Illinois
601 South Goodwin Avenue M/C 110
Urbana, IL  61801

(217) 244-8420

Biographical Information

  • 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


Bacteria and Archaea represent the vast majority of biodiversity on Earth. In fact, the closer we look at microbial populations, the more diversity we see. For example, microbial environmental genomics, is uncovering patterns of sequence variation (microdiversity) within species that were once assumed to be homogeneous. Making sense of this diversity will require identifying the ways that dynamic ecological and evolutionary processes interact in the natural microbial world. Because microorganisms are integral parts of all ecosystems on earth, understanding these interactions will have great implications across basic and applied biological systems.

My lab combines population genomics with laboratory-based genetic and genomic experimental techniques to study the evolutionary ecology of microbial populations. We take a comparative approach, examining interactions within and between species using wild strains from natural populations isolated across spatial and temporal scales.  Currently we are working on two critical forces that define the evolutionary process in all organisms: host-virus co-evolution and recombinational gene flow. We have a particular interest in how the unique biology organisms in the Archaeal domain are reflected in genome architecture and how the CRISPR-cas immune system functions in microbial populations.

For most current information and news please visit our lab website at :

Current Projects:

Population genomics of Sulfolobus islandicus

Through population genomic analysis we have identified sympatric species of Sulfolobus islandicus coexisting within a single hot spring population in Kamchatka Russia.  Currently we are investigating:

  1. Molecular mechanisms and barriers to gene transfer between sympatric Archaeal species.
  2. Molecular mechanisms that define the genome architecture within the Archaea.

CRISPR-cas mediated host-virus co-evolution

Viruses infect all organisms; bacteria, archaea, eukaryotes and even other viruses.  We are interested in how the newly discovered, CRISPR-cas adaptive immune system in bacteria and archaea affects virus-host coevolution.  In collaboration with Joshua Weitz at the Georgia Institute of Technology we have developed a mathematical model to simulate co-evolutionary dynamics and discovered a new emergent evolutionary dynamic we call distributed immunity stabilizes host populations.  Based on predictions of this model we are investigating:

  1. CRISPR mediated co-evolutionary dynamics in environmental and host associated microbial populations.
  2. The effects of CRISPR immunity on chronic viral infection and coevolution.

Selected Publications

N.L. Held, A. Herrera, R.J. Whitaker. 2013. Reassortment of CRISPR repeat-spacer loci in Sulfolobus islandicus. Environmental Microbiology.  doi: 10.1111/1462-2920.12146

Hinsby Cadillo-Quiroz, Xavier Didelot, Nicole L. Held, Alfa Herrera, Aaron Darling, Michael L. Reno, David J. Krause, Rachel J. Whitaker. 2012. Patterns of Gene Flow Define Species of Thermophilic Archaea. PLoS Biol 10(2): e1001265. doi:10.1371/journal.pbio.1001265…

Lauren Childs, Nicole L. Held, Mark I. Young, Rachel J. Whitaker * and Joshua S. Weitz *. Multi-scale Model of CRISPR-induced Co-evolutionary Dynamics: Diversification at the Interface of Lamarck and Darwin. * co-corresponding authors.  2013.  Evolution. Volume 66, Issue 7, Pages: 2015-2029.  doi: 10.1111/j.1558-5646.2012.01595.x.

Rachel J. Whitaker.  A new age of naturalists. 2011.  Microbe Magazine.

Rachel J. Whitaker.  Crystal Ball-2011: An appreciation for natural variation.  2011.  Environmental Microbiology. Volume 3, Issue 1, Pages: 1–26.