Genes and roses: Genetics researchers put flowers to test of time

Anyone who has ever stopped to smell the roses is familiar with the largest group of plants, the angiosperms, also known as the flowering plants.

But deep understanding requires the melding of various scientific disciplines, such as botany, paleontology and genomics. Further, it requires historical sensibilities grafted from Gregor Mendel, the father of genetics, to look 130 million years through time to the Cretaceous era to find the ancestors of the rose. These were days when the tyrannosaurus was king and plants, although they had existed for about 300 million years, were just beginning to develop flowers and fruit.

Working to understand the origin of the flower and to chart the relationships that connect living species are University of Florida Genetics Institute researchers Douglas and Pamela Soltis.

As notable architects of international scientific efforts such as the Floral Genome Project and Deep Time — both about midway through five-year missions — these are not your parents’ historians. Nor are they strictly aligned with traditional Darwinian evolution. As one writer noted after an interview with the Soltises, perhaps Darwin’s “Origin of Species” would be more aptly titled in the plural: “Origins of Species.”

Key to understanding much of the Soltis’ research is the idea that most plants, as well as some vertebrates and insects, have originated not just once, but many times.

“We are studying mechanisms of genome doubling or genomes combining in particular groups of flowering plants,” said Pamela Soltis, Ph.D., curator of the Molecular Systematics and Evolutionary Genetics at the Florida Museum of Natural History. “Say one of the parental species occupied dry sites and the other parental species occupied wetter sites. If you put those traits together and make a new species with extra genes from both of its parents, perhaps it will grow in environments that span the ranges of both of its parents, and maybe it can be more successful than either of its parents.”

The concept, known as “polyploidy,” refers to species that have more than two copies of each of its chromosomes. Wheat, corn and cotton are all polyploid. Because the polyploid plant retains more than the traditional amount of genetic information from its parents, it is able to evolve as a species with characteristics that exceed those of its parents. What’s more, such evolution takes place quickly, with species instantly gaining genetic variability in contrast to the eons it takes for traditional natural selection to occur.

Backyard evolution

The Soltises studied how polyploid evolution occurred in eastern Washington and parts of Idaho while on the faculty at Washington State University. Three species of a plant with the common name of goatsbeard, a relative of the dandelion that has small yellow or purple flowers, were introduced to the United States in the early 1900s. The plants hybridized to form plants with light purple flowers and were transformed into a new species that was visually similar, but genetically different.

“Basically, it was evolution in our backyard. A new species formed in the last 80 years, a species that was not on the Earth before then,” said Douglas Soltis, Ph.D., a professor of botany in the College of Liberal Arts and Sciences. “It was polyploid. The difference between hybrid formation and the chromosome doubling found in polyploids is that the hybrids have 12 chromosomes, while the polyploids have 24. Hybrids are usually sterile — a mule is a hybrid — but when you double the chromosomes, a hybrid becomes a fertile new species that can reproduce on its own.”

The polyploid mechanism has agricultural implications, but there are vast differences in working with a single gene at a time, as most plant breeders do, as opposed to an entire genome.

“If you're a tomato breeder or citrus breeder, you work with a gene for resistance, or a gene for a larger fruit,” Douglas Soltis said. “With polyploids, the whole genome is affected and that’s why it's a very dramatic change. Actually plant breeders have been interested in polyploidy as a process for making better crops, but the fact is, most crops such as corn and wheat are already polyploid. In a sense, nature already beat us to it. It’s a successful avenue, and that's one of the reasons we’re so interested in it.”

Terms as unpedestrian as polyploid hover with the lightness of seeds in the wind at the Soltis lab in the Florida Museum of Natural History. But their ideas about molecular relationships among flowering plants have taken hold across the scientific world, resulting in their winning the 2002 Dahlgren Prize in Botany from the Royal Physiographic Society of Sweden, and their positions among the leaders of two international research studies.

As co-principal investigators with the Floral Genome Project, the husband-wife team has enabled UF to engage in high-level collaboration with Penn State University and Cornell University, with funding from the National Science Foundation. Researchers studying the origins of the flower are capturing thousands of sequences of genes expressed during early flower development. The goal is to build a resource that all scientists may use to generate hypotheses about common gene function in plants.

Deep Time, another international effort in which the Soltises play a lead role, is an attempt to integrate plant fossils into phylogenetic trees, which basically chart the evolutionary relationships of living things.

“One of the goals of the Floral Genome Project is to try to understand genetic patterns across the flowering plants,” Pamela Soltis said. “Deep Time adds the element of floral morphology, where we try to infer what ancestral floral structures were like based on what's living today. Ultimately, the goal is to develop a database that will have molecular, morphological and fossil information together in one big evolutionary picture.”

A new backyard

In the context of the Soltis’ research, it becomes clear that a rose is not just a rose, but a corridor to a vast tree of life that spans the ages. Generally, the aesthetic appeal of flowering plants often overshadows their importance. But most vegetables, grains, nuts, beans, fruits, herbs and spices come from plants with flowers, as do tea, coffee, chocolate, wine and cola. Without the angiosperms, there would be no cotton or linen, nor would there be over-the-counter medicines such as aspirin, prescribed drugs such as digitalis and atropine, and controlled drugs such as opium, cocaine, marijuana and tobacco.

“I’ve been impressed with how the Soltises have increased the understanding of relationships among the genera and families of flowering plants,” said Steven Manchester, associate curator of paleobotany at the Florida Museum of Natural History and adjunct associate professor of botany and geology. “Beyond that, they’ve enabled UF to have an exchange of students from different labs.

They’re good communicators in the sense that they get people talking in fields of science that have tended to diverge. The Soltises know modern molecular techniques and are able to work out details of modern plants from DNA, whereas paleobotanists understand fossils that don’t have DNA.”

Integrating data from modern and ancient plants is like piecing together a puzzle that ultimately shows how plants are related, Manchester said. But it’s a puzzle no single scientist, or even a single discipline, can solve.

“We’ve really made an effort for the next generation of scientists to integrate paleobotany and plant systematics,” Douglas Soltis said. “I think that’s already happened pretty well, especially when you see a lot of graduate students who are moving easily between the study of living plants and fossil plants. Both are necessary when you’re trying to really figure out what's going on in plant evolution.”

Knowledge of such evolutionary relationships will become increasingly vital, especially in terms of targeting plants to develop new drugs. If connections between plants with medicinal value aren’t recognized, a plant that may have cancer-inhibiting properties, for example, could be overlooked.

“It's very easy now to use DNA to determine how living plants are related,” Douglas Soltis said. “Although we can’t get DNA from the fossils, we can use morphology and try to integrate them in phylogenetic analysis, where you end up with a branching scheme of relationships. You answer the question of where the fossil comes out in the analysis, rather than just saying, ‘well, it kind of looks like so-and-so.’”

Mainly, Deep Time fosters a more rigorous scientific approach to longstanding questions of fossil relationships.

“People are always curious about where structures come from,” Douglas Soltis said. “You go through biology courses, you learn evolutionary explanations to questions — ‘the hoof of a horse, how did that evolve?’ You have to look at the fossils to determine those sorts of things. But usually in the past, it’s been very arm-waving: ‘Here are the fossils, here are the living things, here is the story.’ We’re taking a more modern approach. When you place fossils of plants or animals in a phylogenetic tree, then you can actually see where they fit. You can begin to make suggestions about the course of evolutionary history.”

At this point, hypotheses can be made about the selection pressures, such as climate change, that have given rise to modern plant forms.

“If we have a good understanding of the ancestral changes in form, we can get a better idea of what questions to ask about the genes that have been responsible for some of those changes,” Pamela Soltis said. “It leads to a better understanding of biodiversity.”

It also helps science understand biological pressures. Aside from global projects, collaborators in the Soltis lab are involved in efforts that are specifically in sync with Florida, such as conservation genetics.

“There are a number of projects in Florida that involve endangered species,” Douglas Soltis said. “That’s a big issue in Florida, and it’s also one of the things that makes it nice to have a lab here. Outside of California, Florida has more rare, endangered plants than anywhere in the United States. There are great opportunities here and an abundance of gene pools to look at.”

Considering the Soltises found evolution in their last backyard, the possibilities are infinitely rosy.