Rachel J Whitaker


Office: (217) 244-8420

Mail to: C222 CLSL
601 S. Goodwin Ave.
Urbana, IL 61801
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Rachel J Whitaker

Associate Professor of Microbiology

Research Topics

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


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

For most current information and news please visit our lab website at www.life.illinois.edu/whitaker/

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 of organisms in the Archaeal domain is reflected in genome architecture and how the CRISPR-Cas immune system functions in microbial populations.

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.

Mutnovsky Volcano, Kamchatka, Russia

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.

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

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

2) The effects of CRISPR immunity on chronic viral infection and co-evolution.

Representative 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 [FULL TEXT]

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.

N.L. Held, A. Herrera, H. Cadillo-Quiroz, R.J. Whitaker. CRISPR associated diversity within a natural population of Sulfolobus islandicus. (2010) PLoS ONE. 5(9): p. e12988.

K. Milferstedt, N. Youngblut and R.J. Whitaker. Spatial scaling and persistence in methanogen populations from humic bog lakes. ISME Journal (2010) 4(6): 764-776. [Abstract]

R.J. Whitaker.  Evolution: spatial scaling of microbial interactions.  Current Biology. (2009) 19 (20). R954-6. [Abstract]

M.L. Reno, N.L. Held, C.J. Fields, P.V. Burke and R.J. Whitaker. Biogeography in the pan-genome of Sulfolobus islandicus. Proceedings of the National Academy of Sciences U.S.A (2009) 106 (21) 8605-8610. [Abstract]

N.L. Held and R.J. Whitaker. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environmental Microbiology (2009) 11:457-466. [Abstract]

J.L. Green, B.J.M. Bohannan and R.J. Whitaker. Microbial Biogeography: Taxonomy to Traits. Science (2008) 320 (5879): 1039-43. [Abstract.]

E.E. Allen, G.W. Tyson, R.J. Whitaker, C. Detter, P. Richardson and J.F. Banfield. Recent evolutionary modes deduced by isolate vs. strain population comparative genomics. Proceedings of the National Academy of Sciences U.S.A. (2007) 104(6): 1883-8. [Abstract]

R.J. Whitaker. Allopatric origins of microbial species. Philosophical Transactions of the Royal Society B (2006) doi:10.1098/rstb.2006.1927. [Abtract]

R.J. Whitaker and J.F. Banfield. Population genomics in natural microbial communities. Trends in Ecology and Evolution (2006) 21(9):508–16. dio:10.10.16/j.tree..2006.07.001. [Abstract]

R.J. Whitaker and J.F. Banfield. Population dynamics through the lens of extreme environments. Molecular Geomicrobiology, Reviews in Minerology, and Geochemistry (2005) 59: 259–277. [Abstract]

R.J. Whitaker, D.W. Grogan and J.W. Taylor. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Molecular Biology and Evolution (2005) 22:2354–61. [Abstract]

R.J. Whitaker, D.W. Grogan and J.W. Taylor. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science (2003) 301: 976–8. [Abstract]

Complete Publications List