Rachel J. Whitaker
Assistant Professor of Microbiology
rwhitaker@life.uiuc.edu
B.A, (Biology, SiSP), Wesleyan University, 1993
Ph.D., (Microbiology), University of California, Berkeley, 1998-2004
Postdoctoral Researcher, (Geomicrobiology), University of California, Berkeley, 2004-2006
Microbial ecology and evolution
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, high-resolution molecular tools are 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 focuses on the evolutionary ecology of microbial populations. We combine field sampling of natural populations with culture and non-culture based genetic and genomic analyses. Currently we are working on understanding how the interactions between basic population genetic parameters (mutation, selection, recombination and genetic exchange, neutral genetic drift, and biogeographic distribution) shape diversity, promote ecological differentiation, and lead to speciation in populations of the hyperthermophilic crenarchaeal species Sulfolobus islandicus. Ultimately we 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.
Typical Sulfolobus habitat Sampling in Lassen National Park
Current projects in population genomics:
To investigate genome dynamics at the population level, we are beginning a comparative analysis between the genomes of 8 closely related Sulfolobus islandicus strains from biogeographically isolated geothermal environments. We will use the data from this US Department of Energy sponsored sequencing project to quantify the rate of lateral gene transfer and other genome level dynamics over geologically-defined time scales. In addition, comparison of sequences derived from Sulfolobus strains from the same environment will allow us to quantify rates of recombination and identify genes under selection. Examples of S.islandicus comparative genomics projects are outlined below.
- Horizontal gene transfer is believed to be a widespread phenomenon important to adaptive microbial evolution in every environment. However, genome sequences of highly divergent species only identify ancient evolutionary events, and say nothing about gene transfer on a more recent timescale. My previous research identified populations of Sulfolobus islandicus that became isolated 700,000 to 2 million years ago. Comparative genomics of strains from geographically isolated populations allows us to quantify rates of horizontal gene transfer on geologic time scales.
- Modeling recombination and selection in microbial populations.The balance between recombination and selective clonal expansion in microbial populations determines population stability and rates of adaptation. We are developing a theoretical model to describe the dynamics of populations that are both clonal and recombining. Model predictions will be tested through experimental evolution and by assessing rates of recombination and evidence of selection from the genomes of closely related Sulfolobus strains.
- Gene flow and local adaptation. Ecological theory predicts that low levels of gene flow between populations lead to local adaptation. I have already described Sulfolobus populations that show evidence of geographic isolation and very low levels of gene flow. We are testing for evidence of local adaptation in these populations through competition assays across a range of laboratory conditions and by identifying genes important for differential adaptation through comparative genome analysis. Evidence of local adaptation has rarely been observed in microbial species, and may have important implications for understanding global patterns of microbial diversity.
Bumpass Hell, Lassen National Park
Interested in joining the Whitaker lab?
I will be accepting 1-2 graduate students in the fall of 2007. I am accepting applications for a postdoctoral researcher interested in genomics and/or computation biology. Please email rwhitaker@life.uiuc.edu for more information.
Rachel J. Whitaker. "Allopatric origins of microbial species." Philosophical Transactions of the Royal Society B. doi:10.1098/rstb.2006.1927
Rachel J. Whitaker and Jillian F. Banfield. "Population genomics in natural microbial communities." Trends in Ecology and Evolution. 21(9):508-516. dio:10.10.16/j.tree..2006.07.001. [Abstract]
Rachel J. Whitaker, Dennis W. Grogan and John W. Taylor. (2005) “Recombination Shapes the Natural Population Structure of the Hyperthermophilic Archaeon Sulfolobus islandicus.” Molecular Biology and Evolution, 22:2354-2361. [Abstract]
Rachel J. Whitaker and Jillian Banfield. (2005) “Population Dynamics Through the Lens of Extreme Environments.” in Molecular Geomicrobiology, Reviews in Minerology and Geochemistry 59: 259-277.
Eric E. Allen, Gene W. Tyson, Rachel J. Whitaker, Chris Detter, Paul Richardson and Jillian F. Banfield. (in review) “Recent evolutionary modes deduced by isolate vs. strain population comparative genomics.”
Rachel J. Whitaker, Dennis W. Grogan and John W. Taylor. (2003) “Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea.” Science 301: 976-978. [Abstract]
View Rachel J. Whitaker's publications at the National Library of Medicine (PubMed)