Rapidly evolving genes providing new insights in plant evolution

Flowering plants are the largest group of plants and contain just about all of our food crops. Khidir Hilu’s research using rapidly evolving genes to determine the molecular evolution of flowering plants is providing new insights into plant relationships, according to the cover story article in the recently released December 2003 issue of the American Journal of Botany (Angiosperm phylogeny based on <011>matK sequence information1).

Flowering plants include cereals such as wheat, barley, ryes, and corn; major starch plants such as potatoes and sweet potatoes; legumes such as soybeans, beans, and peanuts; all of our fruit crops, spices, and medicinal plants. Also among the approximately 300,000 species of flowering plants are those that provide almost all our lumber (excluding pines).

“Scientists in the past tried to look at how the plants relate to each other and to classify them by the way they looked, their morphology, anatomy, and chemistry,” Hilu, professor of biology in the College of Science at Virginia Tech, said. “But recently, people started using molecular biology, the sequence of genes, to infer relationships and classification. With this molecular approach, the whole classification has been revised and the pattern of evolution looks different from what we perceived before.”

Using the molecular approach in understanding the angiosperms, or flowering plants, scientists traditionally used slowly evolving genes, or genes that mutate at a very slow rate, to understand the deep relationship between the families and orders of the plants, Hilu said. In fact, the use of slowly evolving genes was the traditional way of understanding deep relationships not only in plants, but also in animals.

However, Hilu and his colleagues have come up with a new approach using rapidly evolving genes to understand deep-level relationships. Those genes mutate at higher rates than the slowly evolving genes. Although evolutionary biologists previously thought rapidly evolving genes would give a misleading picture of deep evolutionary history and were useful only in more recent evolutionary events such as evolution at the species and genus levels, Hilu has demonstrated that as few as 1,200 nuclear-type bases of a rapidly evolving gene such as matK, a gene in the chloroplasty genome, will give a tree of angiosperm that is far more robust than that obtained from 13,400 bases of several slowly evolving genes combined.

With this new approach, Hilu said, scientists will be able to sample many more species, and the process will be much more economical. “This does not mean slowly evolving genes are useless,” Hilu said, “but a combination of the two could give us information at different evolutionary levels.”

Hilu has found that the quality of the signal is better in rapidly evolving genes due to tendencies towards neutrality and lack of as many strong functional constraints as in slowly evolving genes. He also found that rapidly evolving genes provide more characters because they keep mutating more quickly. “Between the quality and the quantity, we were able to obtain more historical signals from rapidly evolving genes,” he said.

Hilu is working now on expanding the use of these fast evolving genes beyond flowering plants to understand the evolutionary relationships among land plants such as conifers, ferns, mosses, and liverworts. He would like to understand relationships in plants that could be important, for instance, to ecologists in their work on animal-plant interaction and the evolution of nectar in pollination, as well as to geneticists and breeders who need to understand the genetics of domestication and breeding of crops that may have an impact on farming. His work is important, too, to molecular biologists who want to understand the pattern of differentiation and origin of genes and gene families. These goals could have an effect on assessments of biodiversity in plants by allowing scientists to understand their classification, patterns of variation, and placement of endangered species.

Hilu’s work has resulted in collaborations with some of the top laboratories around the world. The paper in the American Journal of Botany (90: 1758-1776) is based on molecular information mostly from Hilu’s collaboration with the University of Bonn as well as other laboratories in the United States, Germany, France, and England. Hilu is the principal investigator and first author on the paper. Co-authors are Thomas Borsch and Kai Müller, Botanisches Institut, Friedrich-Wilhelms-Universität Bonn; Douglas E. Soltis, School of Biological Sciences, Washington State University; Pamela S. Soltis, Florida Museum of Natural History and the Genetics Institute, University of Florida; Vincent Savolainen, Mark W. Chase, and Martyn P. Powell, Molecular Systematics Section, Royal Botanic Gardens, Surrey, UK Lawrence A. Alice, Department of Biology, Western Kentucky University, Bowling Green; Rodger Evans, Biology Department, Acadia University, Nova Scotia; Hervé Sauquet, Muséum National d’Histoire Naturelle, Paris; Christoph Neinhuis, Institut für Botanik, Dresden; Tracey A. B. Slotta, Virginia Tech graduate student; Jens G. Rohwer, Institut für Allgemeine Botanik, Universität Hamburg; Christopher S. Campbell, Department of Biological Sciences, University of Maine; and Lars W. Chatrou, National Herbarium of the Netherlands, Utrecht University Branch.

Contact Dr. Hilu at hilukw@vt.edu or 540-231-5407