New View Of Evolving Genes, Proteins To Aid Bioinformatics

In the March edition of the journal Evolution and Development, research associate Lev Yampolsky and research biologist Arlin Stoltzfus of UMBI's Center for Advanced Research in Biotechnology (CARB) make a case that simple biases in mutation will change the evolutionary process. They use mathematics and computer simulations to explore the role of mutation biases using the classic "Bateson-Dobzhansky-Muller" model.

"Recognizing this kind of bias as an evolutionary cause will increase our ability to explain and predict evolution, and will aid researchers as they seek to understand such things as the amino acid composition of proteins, the appearance of new strains of viruses strains, and the distribution of introns in genes, all of which exhibit components of change that suggest a role of biases in the process of mutation," explains Stoltzfus. (Introns are DNA sequences in genes that don't encode proteins, thus having no defined purpose.)

The CARB study also helps to make more sense of the results of the rapidly growing science of bioinformatics, the data analysis of genomes and proteins. Since the 1970's when the technique of gene sequencing was developed, evidence has been accumulating that mutation biases strongly influence the evolution of genes and proteins, say the authors. The influence has been interpreted as a sign of "neutral evolution", a kind of random noise in the evolutionary process.

But now Yampolsky and Stoltzfus argue that in a more general theory, mutation-biased evolution does not have to be neutral.

In historic perspective, the new paper shows that it is still possible to stake out a new position on an old issue in evolutionary theory. Charles Darwin and other 19th century scientists realized that evolution was based on individual variation, be it in the size of a finch's beak, for example, or in the shape of a plant's leaves. But the early evolutionists didn't understand exactly how variants arose, and how their origination contributed to directionality or non-randomness in evolutionary change.

"Darwin proposed that evolution largely depends on an abundance of minute 'random' variants that arise with no particular direction. Natural selection, in his view, imposed non-randomness on this mass of 'random' variation," explains Stoltzfus, "and this influence of natural selection gives an external or environment-related direction to evolution by preserving or destroying forms according to their adaptedness."

Stoltzfus says that many of Darwin's 20th century followers adopted the view that all non-randomness in evolution comes from natural selection. "What is important, then, is to use population-genetic reasoning to demonstrate that both mutation biases and selection influence the outcome of evolution under simple conditions. Without disputing that natural selection is a prominent 'external' cause of non-randomness in evolution, we maintain that there is also an 'internal' cause arising from biases in variation. It is this kind of 'internal' directionality- disparaged by 20th century Darwinians as 'orthogenesis'- that is needed to fully appreciate modern research in molecular evolution and in evolutionary developmental biology."

As one of UMBI's five research and education centers (http://www.umbi.umd.edu), CARB is designed to open new horizons in the field of protein structure, function, and design. The center is located on the University of Maryland's Shady Grove Campus at the Shady Grove Life Science Center in Rockville, in the heart of Maryland's thriving biotechnology community, and near Maryland's major university research campuses and several government laboratories, including the National Institutes of Health. CARB scientists work closely with researchers of the Biotechnology Division of the Chemical Science and Technology Laboratory of the National Institute of Standards and Technology (NIST). Stoltzfus is one of seven CARB faculty with an appointment in NIST's Biotechnology Division.