Can science predict the future of certain organisms? This question is being asked by scientists around the globe as they strive to determine which genes make it possible for populations to adapt to changing environments, rather than become extinct.

A series of synergistic breakthroughs in biochemistry, analytical instrumentation, genetics, and computation has placed genomics (the study of genes) as one of the fastest growing fields in the life sciences. Utah State University biology professor Mike Pfrender’s research on comparative genetics is poised to place Utah State at the forefront of this burgeoning field. Pfrender is opening doors to understanding how organisms, including humans, can cope with long-term environmental change.

As part of the Center for Integrated Biosystems and co-founder of the Daphnia Genome Consortium, Pfrender and colleagues are among the first in the field working towards a breakthrough in another realm of genomics, that of Ecological or Environmental Genomics.

“The Earth is a very complex, diverse ecological community, with millions of organisms that interact with one another,” says Pfrender. “Our study aims to examine how genes in naturally existing populations impact the way in which an organism can adapt to changes in the environment.”

Pfrender’s current research focuses on the genetic basis of adaptation and extinction in Daphnia, a microscopic crustacean that can be found in almost every freshwater ecosystem in North America. Daphnia are considered a ‘keystone’ species and play a central role in freshwater ecology because they are primary grazers of algae and primary forage of fish.

“We have found the Daphnia to be between a rock and hard place,” says Pfrender. “The introduction of fish into their environment has led to a reduction in their pigment in order to be less visible to fish, while on the other hand less pigment has exposed the Daphnia to high levels of UV radiation.”

With global concern for the growing levels of UV radiation and the effect it will have on human health and natural populations, Pfrender’s research has applications to how humans will cope with long-term changes in the environment.

“The dominant theme of our research is how populations of Daphnia deal with high UV light and how UV light damages DNA,” says Pfrender. “This allows us to take a closer look at genes that control pigment and genes that control DNA repair, which will lead to a greater understanding of how other more complex populations will cope with long-term environmental change.”

Pfrender and a team of researchers study Daphnia in a suite of alpine lakes located in the Sierra Nevada Mountains of California, where there are known histories of fish introduction, which has led to increased exposure to UV radiation. This has caused some populations of Daphnia to adapt and other populations of Daphnia to become extinct.

“Daphnia are unique in that their eggs can be hatched from the lake sediment up to a century later, which allows the past products of evolution to be hatched and compared against their current descendants in a controlled setting,” says Pfrender. “Daphnia provide a unique opportunity to gain knowledge about adaptation that cannot be gained any other way.”

Recent efforts have lead Pfrender and colleagues to collaborate with the Department of Energy (DOE), the Joint Genome Institute (JGI), the Environmental Protection Agency (EPA), and the Daphnia Genomics Consortium (DGC), to decipher the complete genome sequence of Daphnia, which is projected to be completed in 2005. This advance will contribute greatly to evolutionary and ecological genetics by providing a model system that will be invaluable to other researchers.

“We need a predictive framework, such as Daphnia, in which we can relate genetic architecture of natural populations to the selective forces challenging these populations,” says Pfrender. “We can then determine the probability of a population adapting rather than becoming extinct.”

Once the entire sequence of Daphnia is completed, a new model system for evolutionary and ecological genetics will be available and will further research into the connection between natural populations and genomics.

“Research into these simple systems helps to open doors to studying more complex systems and ecosystems in the future,” says Pfrender. “Through our study of natural populations and communities, we hope to gain a greater understanding of responses to global climate change, and contribute fundamental changes to evolutionary theory.”

- Rachel von Niederhausern