Computational infrastructure funded for establishing evolutionary relationships between all organisms

Sept. 17, 2003

AUSTIN, Texas—A team of University of Texas at Austin scientists led by Dr. Tandy Warnow has received $800,000 to participate in a federally funded effort to provide the intellectual and computational know-how needed for reconstructing the evolutionary history of all organisms.

The seven faculty members comprise one of several university teams that will help build the computational infrastructure to support the National Science Foundation’s “Assembling the Tree of Life” program. The $11.6 million project to establish a national resource for phyloinformatics and computational phylogenetics is led by the University of New Mexico, with the three other guiding institutions outside Austin being Florida State University and the University of California at Berkeley and at San Diego. All told, 13 universities will participate in the project directed by Dr. Bernard Moret at the University of New Mexico.

The researchers’ overarching goal is to provide scientists world-wide known as systematists with the right resources to perform computational analyses needed to construct the Tree of Life. The computational backbone to the project will be a large computational platform to assist with international efforts to analyze organisms’ genetic material, high-performance, open-source software for these analyses, and a database of datasets generated by sequencing organisms’ genes. But the real focus will be providing the tools so systematists can take advantage of those resources to understand the evolution of organisms.

“We will develop the necessary theoretical framework and analytical tools for systematists to more rapidly reconstruct the interrelationships of living and extinct organisms on Earth,” Warnow said, noting that the project brings together many internationally renowned computer scientists, biologists and mathematicians.

The effort is needed because molecular biology has enabled scientists to determine the exact blueprint, or DNA sequence, of many organisms. Generic blueprints, or genome sequences, are now known for humans, mice, the bacterium that causes Salmonella poisoning and a host of other organisms, and the completion of other sequences occurs regularly. Tools now are needed to more readily compare the blueprints of different organisms, which can extend billions of genetic “letters” in length.

“Reconstructing the Tree of Life is extremely important, because it will give us a better picture of how life evolved on Earth, a better understanding of where we came from as humans and a sense of where we may be headed, on a long time-scale,” said Dr. Moret. “It will also enormously increase our understanding of the relationships between the genetic code and cell functions, thus accelerating the pace of biomedical discoveries.”

At The University of Texas at Austin, the scientists in the College of Natural Sciences will advance the project by:

  • Developing new software tools for faster phylogenetic (evolutionary reconstruction) analysis of genome sequence data. Dr. Warnow, a computer scientist who is completing a fellowship at the Radcliffe Institute for Advanced Study at Harvard University, and integrative biologist David Hillis will participate in this effort for the Tree of Life project overall.
  • Developing new algorithms (a series of computational steps needed to accomplish a task) and new techniques for constructing evolutionary trees from organisms’ genetic information. Warnow also will lead this Tree of Life effort, which involves University of Texas at Austin computer scientist Warren Hunt.
  • Developing new database technologies for analyzing Tree of Life data. Computer scientist Dan Miranker will lead this overall Tree of Life effort.
  • Comparing organisms’ genome sequences using computer simulation software. Integrative biologists David Hillis and Lauren Ancel Meyers will participate in this effort and will develop complex evolutionary models and test them.

The latter effort will also involve integrative biologists Randy Linder and Bob Jansen. Dr. Linder will study how to incorporate reticulate evolution into the broader family tree. This type of evolution occurs when genetic material is transferred between species such as different types of bacteria, or when distinct species interbreed to create new species, such as occurs in plants. Dr. Jansen will study how to use rare changes in the genome architectures of different species to reconstruct early evolutionary histories.

Dr. Hillis said, “This grant is one important piece of our program at The University of Texas on phylogenetics and the relationships of life. Applications of phylogenetics have become important throughout biology, and this grant will help to build the national infrastructure that is needed to analyze all the data being collected, here and elsewhere.”

For more information contact: Barbra Rodriguez, College of Natural Sciences, 512-232-0675.