Method for Computing Evolutionary Trees Could Revolutionize Evolutionary Biology

June 18, 2009

AUSTIN, Texas — Detailed, accurate evolutionary trees that reveal the relatedness of living things can now be determined much faster and for thousands of species with a computing method developed by computer scientists and a biologist at The University of Texas at Austin.

They report their new method in the journal Science.

Since Charles Darwin, biologists have constructed evolutionary trees to explain the relatedness of plants, animals and other organisms. The science of figuring out these trees, known as systematics, has progressed significantly in the last two decades largely due to advances in computation, genetics and molecular biology.

However, many of the relationships among the world's 1.5 million described species (the true number could be 10 million or more) remain to be figured out, and surprises still remain. Figuring out these relationships requires analyzing large amounts of molecular data, such as DNA and protein sequences.

Computer scientist Tandy Warnow, biologist Randy Linder and their graduate students have created an automated computing method, called SATé, that can analyze these molecular data from thousands of organisms, simultaneously figuring out how the sequences should be organized and computing their evolutionary relatedness in as little as 24 hours.

Previous simultaneous methods like Warnow and Linder's have been limited to analyzing 20 species or fewer and have taken months to complete.

"SATé could completely change the practice of making evolutionary trees and revolutionize our understanding of evolution," says Warnow, professor of computer science and lead author of the study.

In addition, SATé can accurately analyze DNA sequences that are rapidly evolving. These sequences have been previously avoided due to concern that the resulting trees would be poor.

Before a tree, or phylogeny, can be determined, DNA and protein sequence data must be organized. This process is called alignment. Key to Warnow and Linder's program is its ability to quickly and accurately align these data.

"Our process is novel because it rapidly and simultaneously aligns sequences and looks for the best phylogenies," says Linder, associate professor of integrative biology. "The old way of doing this for a large number of sequences was basically to align the data once, but we can look at many arrangements to find better ones."

This is important because different alignments can lead to significantly different phylogenies, and scientists must find the phylogeny that best represents the evolutionary relationships among the species in question.

For their paper, Warnow, Linder and their students tested SATé using computer-generated data and real biological data. The biological data had been previously aligned manually by other experts.

The new phylogenies closely match those existing, both validating the method's potential, and, in some cases, validating the evolutionary trees themselves.

"Instead of doing things by hand, evolutionary biologists can now trust our automated program," says Warnow. "It will enable the creation of much more accurate trees, especially for the Tree of Life, which deals with hundreds of thousands of gene sequences from the millions of species on Earth."

"Warnow and Linder have created a method that speeds up the process and removes any subjectivity," says Michael Braun, an evolutionary biologist at the Smithsonian Institution not associated with this project. "This is a major step forward for evolutionary biology."

Computer science graduate student Kevin Liu is first author on the paper. Students Sindhu Raghavan and Serita Nelesen also contributed to the project and co-authored the paper.

For more information, contact:  Craig Linder, Department of Integrative Biology, College of Natural Sciences, 512-471-7825;  Tandy Warnow, Department of Computer Science, College of Natural Sciences, 512-471-9724.

5 Comments to "Method for Computing Evolutionary Trees Could Revolutionize Evolutionary Biology"

1.  Darren W said on July 2, 2009

The truth is, the so-called evolutionary trees are mere conjecture. Science reveals no evidence of such relationships, rather science demonstrates clear genetic distinctiveness. Variation within limits, yes. Macroevolution, no. The fossil record is replete with distinct life forms, no intermediate forms. There should literally be millions of transitional forms in the fossil record. This is why thousands of scientists do not accept evolution, and why one day I am confident it will be discarded. The evidence for design is all across nature and science. I hope one day institutional science and education will return to being open-minded and present all the evidence ... after all, that is what science and education are all about - the search for knowledge without prejudice.

2.  Joseph Allen Kozuh, Ph.D. said on July 6, 2009

Evolutionary biologists say that single-cell organisms like bacteria evolved into multi-cell organisms like insects and dogs and cats. However, they can't demonstrate this empirically or even theoretically. I think they should first prove they understand the roots of the Tree before they pretend they can climb through the highest branches of the Tree.

3.  Frank Morris said on July 6, 2009

Intelligent design is also just a conjecture. Just because the scientific approach leads to continual updating and change does not invalidate it. The proof of the pudding lies in the ability to predict, and test. True there are still numerous gaps in the evolutionary description, but intelligent design won't fill them.

4.  Wayne Howard said on July 6, 2009

Darren W. hit the nail on the head! If a Cro Magnon male was groomed and dressed in a business suit and placed on Madison Avenue, New York, or in Paris, he would draw no more attention than the next dude, maybe a little shorter. Since "The Great Extinction Disaster" that essentially destroyed almost all life on land and sea, there should be a "very clear trail" of fossil evidence to support evolution, but it does not exist. But what does exist is the incredibly complex evidence of "design" in every "life form." Life begets life. It does not occur any other way!

5.  s nedunuri said on July 8, 2009

The fossil record is the collection of intermediate or transitional forms you're seeking. It's a continuum. Minute impercetible changes over millenia became slightly less imperceptible changes over tens of millenia, accumulating into larger changes over hundreds of millenia, and millions of years. On that continuum, several individuals' skeletal forms were by chance (because of favorable climate, soil, erosion conditions) preserved as fossils. It's those fossils that are then used as "markers" on the continuum, making it appear that species made some kind of leap from one marker to the next. It's not like one species formed a transition and another was a designed artifact like a house or sofa.