Published online this week in the Proceedings of the National Academy of Sciences, the study is the first to document chromosomal variation in natural populations of a recently formed plant species following whole genome doubling, or polyploidy. Because many agricultural crops are young polyploids, the data may be used to develop plants with higher fertility and yields. Polyploid crops include wheat, corn, coffee, apples, broccoli and some rice species.

“It could be occurring in other polyploids, but this sort of methodology just hasn’t been applied to many plant species,” said study co-author Pam Soltis, distinguished professor and curator of molecular systematics and evolutionary genetics at the Florida Museum of Natural History on the UF campus. “So it may be that lots of polyploids – including our crops – may not be perfect additive combinations of the two parents, but instead have more chromosomes from one parent or the other.”

Researchers analyzed about 70 Tragopogon miscellus plants, a species in the daisy family that originated in the northwestern U.S. about 80 years ago. The new species formed naturally when two plants introduced from Europe mated to produce a hybrid offspring, and hybridization was followed by polyploidy.

Using a technique called “chromosome painting” to observe the plants’ DNA, UF postdoctoral researcher and lead author Michael Chester discovered that while whole genome doubling initially results in a new species containing 12 chromosomes from each parent, numbers subsequently vary among many plants.

The paints are made by attaching different dyes to DNA of the two parent species. Once the dye is applied, there is a match between the DNA of the paint and of the chromosome. Under a microscope, the chromosomes appear in one color or the other (red vs. green) depending on the parent from which they originated. Sometimes chromosomes are a patchwork of both colors because DNA from the two parents has been swapped as a result of chromosomal rearrangements.

“One of the things that makes this so amazing is that where we expected to see 12 chromosomes from each parent (the polyploid has 24 chromosomes), it turns out there aren’t 12 and 12, there are 11 from one parent and 13 from the other, or 10 and 14,” Soltis said. “We’re hoping through some ongoing studies to be able to link these results with the occurrence of another interesting phenomenon – the loss of genes – and also see what effect these changes have on the way the plants grow and perform.”

The polyploid’s two parent species, Tragopogon dubius and Tragopogon pratensis, were introduced to the U.S. in the 1920s. Because its flower only blooms for a few hours in the morning, Tragopogon miscellus is often referred to as “John-go-to-bed-at-noon,” and its common name is goatsbeard. It looks like a daisy except for being yellow in color.

“People have looked at these chromosomes before, but until you could apply these beautiful painting techniques, you couldn’t tell which parent they each came from,” Soltis said.

Of the six populations examined from Washington and Idaho, 69 percent of the plants showed a deviation from the expected 12 and 12 chromosome pattern.

“In order for most plants to be able to interbreed successfully, their chromosomes need to match up,” Chester said. “That doesn’t necessarily happen when you don’t have equal numbers, so there may be some chromosomal barriers to fertility that develop as a result of this sort of chromosomal variation. This mechanism may also explain low fertility in other plants, such as crops. This is something we are looking into with Tragopogon.”

The two-year study was funded by the National Science Foundation. Other co-authors include Doug Soltis, a distinguished professor in UF’s biology department, UF undergraduate biology student Joseph Gallagher and Ana Veruska Cruz da Silva of Embrapa Tabuleiros Costeiros in Brazil and the Florida Museum.

“Among all of the processes that generate biological diversity in the plant kingdom, genome doubling, or polyploidy, is among the most prevalent and important,” said Jonathan Wendel, professor and chairman of the department of ecology, evolution, and organismal biology at Iowa State University, in an email. “This is an area that is receiving international focus and research attention, but the system Pam and Doug Soltis are working on is unique.”

 -30-

Source: Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Michael Chester, 352-392-7924, mchester@ufl.edu
Writer: Danielle Torrent, dtorrent@flmnh.ufl.edu
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

The study, to be published online Sunday in Nature, is the first to identify the occurrence of ancient genome duplication events and show the genomes of seed and flowering plants duplicated before each group of plants diversified. It introduces new factors for further molecular research on the organisms humans depend on for food, clothing and shelter.

Analyses of several hundred genes pinpointed ancient genome duplication events at about 319 million years ago for seed plants and 192 million years ago for flowering plants, making their origins older than previously estimated. Genome duplications result in organisms having twice as much DNA and an extra copy of every gene, allowing for greater genetic variation. For flowering plants, this event is now linked to their rise to success and the more than 300,000 flowering plant species alive today.

“These two big genome duplication events may have actually spurred really important evolutionary innovations,” said study co-author Pam Soltis, curator of molecular systematics and evolutionary genetics at the Florida Museum of Natural History on the UF campus. “The evolution of life on our planet changed dramatically with the origin of the seed, and then it changed dramatically again with the origin of the flower. The whole terrestrial landscape changed with the evolution of these two different groups, as different animal groups arose and interacted with these plants.”

Researchers analyzed genes from papaya, rice, poplar, grape and cucumber plants, as well as those from the base of the evolutionary tree of flowering plants, including water lily, pine tree and spruce tree; several of the species had completely sequenced genomes.

“One ancient genome duplication event led to all the diversity of flowering plants that you see today,” said study co-author Doug Soltis, a distinguished professor in UF’s biology department and researcher in the UF Genetics Institute. “You’re taking all the genes that you can study in living plants and reconstructing what the genome history was, and you can see that all the genomes were duplicated. This discovery ties genome doubling to why angiosperms (flowering plants) took off and were successful.”

The study helps set the stage for understanding the genome structure of all the seed plants and all the flowering plants, Pam Soltis said. Every seed and flowering plant will have some signature of this duplication event, which will have to be taken into consideration when trying to determine a genome’s major elements.

“By showing the evolutionary history of all these genome duplications, it helps us understand modern genome complexity,” said Jonathan Wendel, professor and chairman of the department of ecology, evolution, and organismal biology at Iowa State University. “This was the first study that really showed the two really ancient duplications in a robust way.”

A duplication event was calculated for each of about 800 genes analyzed in the study, and the results were almost identical in each of those genes, Pam Soltis said. The researchers have been generating sequence data for the project for nearly 10 years.

“It’s difficult to figure out what happened when you’re dealing with things that old – evolution tends to wipe out some footprints, so the signal gets a little messier and harder to distinguish from noise,” Wendel said. “They used some really robust, huge data sets and robust analysis to see through all that noise and find the signal.”

Researchers believe this molecular research creates a more accurate evolutionary time scale for plants and is expected to affect the way scientists map family trees, especially for flowering plants.

“The further we push back the date of when these events happened, the more confidently we can claim that, not most, but all flowering plants are the result of large-scale duplications of genetic code,” said Claude dePamphilis, a professor of biology at The Pennsylvania State University and lead author of the study. “It’s possible that the important polyploidy events we’ve identified were the equivalent of two ‘big bangs’ for flowering plants.”

The study resulted from the Ancestral Angiosperm Genome Project and was funded primarily by the National Science Foundation. Study co-authors include Yuannian Jiao, Norman Wickett, Lena Landherr, Paula Ralph, Lynn Tomsho, Yi Hu, Stephan Schuster and Hong Ma of The Pennsylvania State University, Saravanaray Ayyampalayam and Jim Leebens-Mack of the University of Georgia, Andre Chanderbali of the University of Florida, Haiying Liang of Clemson University, Sandra Clifton of Washington University and Scott Schlarbaum of The University of Tennessee.

- 30 -

Source: Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Doug Soltis, 352-273-1963, dsoltis@botany.ufl.edu
Writer: Danielle Torrent, dtorrent@flmnh.ufl.edu
Media Contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

The study, to be published online Sunday in Nature, is the first to identify the occurrence of ancient genome duplication events and show the genomes of seed and flowering plants duplicated before each group of plants diversified. It introduces new factors for further molecular research on the organisms humans depend on for food, clothing and shelter.

Analyses of several hundred genes pinpointed ancient genome duplication events at about 319 million years ago for seed plants and 192 million years ago for flowering plants, making their origins older than previously estimated. Genome duplications result in organisms having twice as much DNA and an extra copy of every gene, allowing for greater genetic variation. For flowering plants, this event is now linked to their rise to success and the more than 300,000 flowering plant species alive today.

“These two big genome duplication events may have actually spurred really important evolutionary innovations,” said study co-author Pam Soltis, curator of molecular systematics and evolutionary genetics at the Florida Museum of Natural History on the UF campus. “The evolution of life on our planet changed dramatically with the origin of the seed, and then it changed dramatically again with the origin of the flower. The whole terrestrial landscape changed with the evolution of these two different groups, as different animal groups arose and interacted with these plants.”

Researchers analyzed genes from papaya, rice, poplar, grape and cucumber plants, as well as those from the base of the evolutionary tree of flowering plants, including water lily, pine tree and spruce tree; several of the species had completely sequenced genomes.

“One ancient genome duplication event led to all the diversity of flowering plants that you see today,” said study co-author Doug Soltis, a distinguished professor in UF’s biology department and researcher in the UF Genetics Institute. “You’re taking all the genes that you can study in living plants and reconstructing what the genome history was, and you can see that all the genomes were duplicated. This discovery ties genome doubling to why angiosperms (flowering plants) took off and were successful.”

The study helps set the stage for understanding the genome structure of all the seed plants and all the flowering plants, Pam Soltis said. Every seed and flowering plant will have some signature of this duplication event, which will have to be taken into consideration when trying to determine a genome’s major elements.

“By showing the evolutionary history of all these genome duplications, it helps us understand modern genome complexity,” said Jonathan Wendel, professor and chairman of the department of ecology, evolution, and organismal biology at Iowa State University. “This was the first study that really showed the two really ancient duplications in a robust way.”

A duplication event was calculated for each of about 800 genes analyzed in the study, and the results were almost identical in each of those genes, Pam Soltis said. The researchers have been generating sequence data for the project for nearly 10 years.

“It’s difficult to figure out what happened when you’re dealing with things that old – evolution tends to wipe out some footprints, so the signal gets a little messier and harder to distinguish from noise,” Wendel said. “They used some really robust, huge data sets and robust analysis to see through all that noise and find the signal.”

Researchers believe this molecular research creates a more accurate evolutionary time scale for plants and is expected to affect the way scientists map family trees, especially for flowering plants.

“The further we push back the date of when these events happened, the more confidently we can claim that, not most, but all flowering plants are the result of large-scale duplications of genetic code,” said Claude dePamphilis, a professor of biology at The Pennsylvania State University and lead author of the study. “It’s possible that the important polyploidy events we’ve identified were the equivalent of two ‘big bangs’ for flowering plants.”

The study resulted from the Ancestral Angiosperm Genome Project and was funded primarily by the National Science Foundation. Study co-authors include Yuannian Jiao, Norman Wickett, Lena Landherr, Paula Ralph, Lynn Tomsho, Yi Hu, Stephan Schuster and Hong Ma of The Pennsylvania State University, Saravanaray Ayyampalayam and Jim Leebens-Mack of the University of Georgia, Andre Chanderbali of the University of Florida, Haiying Liang of Clemson University, Sandra Clifton of Washington University and Scott Schlarbaum of The University of Tennessee.

- 30 -

Source: Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Doug Soltis, 352-273-1963, dsoltis@botany.ufl.edu
Writer: Danielle Torrent, dtorrent@flmnh.ufl.edu
Media Contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

The study, scheduled to appear as the cover story in the March 31 issue of the journal Nature, describes the basal eudicot species, Leefructus mirus, which lived during the early Cretaceous period about 125 million years ago. It is most closely related to living plants in the buttercup family. Eudicots, known as “typical dicots,” are one of the largest groups of flowering plants.

“It is one of the oldest, most complete megafossils in the buttercup family,” said study co-author Hongshan Wang, paleobotany collections manager at the Florida Museum of Natural History on the UF campus. “Flowering plants are what we live on, the food we eat, the crops we have, even the furniture we sit on can come from the hardwood of flowering plants – but for the early history of flowering plants, we know very little, especially when we get into the Cretaceous.”

There are about 250,000 known species of angiosperms, or flowering plants, and this early evidence provides a link to understanding their rapid diversification during the Cretaceous period. Eudicots comprise about 75 percent of all angiosperms today, including peaches, apples, peas, sunflowers and roses.

The fossil was recovered from the middle Yixian Formation in Northeast China, which is part of the Jehol Biota, a community that has been extensively studied because of the unique plant and animal fossils found there.

“A lot of fossils have been found from this biota, which include feathered dinosaurs, early birds, mammals, even a gliding lizard,” Wang said. “All sorts of animals have been found in this area, but I always wonder, ‘What did these animals eat?’ ”

When Leefructus mirus lived, the angiosperms had just started to diversify, Wang said. Based on genetic research, flowering plants are thought to have originated from one common ancestor, and one of Darwin’s “abominable mysteries” was how the many species of flowering plants we know today so quickly diversified from the lower Cretaceous until the middle Cretaceous, about 100 million years ago.

“These discoveries are pushing the age of angiosperms, or at least the age of a rapid diversification in angiosperms back in time,” said William Crepet, chairman of the department of plant biology at Cornell University. “This will have significant implications for dating models of all sorts and may shift our investigations of likely fossils to those found in earlier sediments. This is hence an important discovery.”

The fossil was the first eudicot found in the Yixian Formation and the fifth angiosperm found in the Jehol biota, Wang said. Crepet said the study analysis of the fossil eudicot matches estimates projected from studies using molecular genetics data.

“The authors are contributing importantly to our understanding of angiosperm history through their studies of fossils from these early Cretaceous sediments,” Crepet said. “We are making stepwise but significant progress in addressing our understanding of angiosperm history.”

Study co-authors include Ge Sun of Shenyang Normal University and Jilin University in China; David Dilcher of Shenyang Normal University, Jilin University and Indiana University; and Zhiduan Chen of the Chinese Academy of Sciences.

The fossil analyzed in the study is preserved as an impression in yellowish grey siltstone measuring about 16 centimeters from the stem to the tip of the leaves and the fish Lycoptera davidi was preserved on the same slab. The impression showed a major stem bearing leaves, fruit and a vegetative shoot.

Leefructus mirus was named “Lee,” after the collector, Shiming Li, “fructus,” which means fruiting and “mirus,” which comes from the Latin word mira, or beautiful. Some of the features distinguishing eudicots from other angiosperms are typically net-like vascular tissue in the leaves, pollen grains with three openings and floral organs usually occurring in multiples of four or five. Previous studies of fossilized pollen show the first eudicots appeared about 127 million years ago, 2 million years before Leefructus mirus – the current study describes the first evidence of a fossilized eudicot plant.

“By the mid-Cretaceous, the angiosperms were already dominating almost every terrestrial ecosystem,” Wang said. “It’s important for us to understand the history and early evolution of flowering plants.”

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Source: Hongshan Wang, 352-273-2107, hwang@flmnh.ufl.edu
Writer: Danielle Torrent, dtorrent@flmnh.ufl.edu
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

Researchers say the study, to be published March 17 in Current Biology, could lead to a better understanding of how to best grow more stable and higher yielding agricultural crops.

“We caught evolution in the act,” said Doug Soltis, a distinguished professor in UF’s biology department and study co-author. “New and diverse patterns of gene expression may allow the new species to rapidly adapt in new environments.”

The study shows the new plant species had relaxed control of gene expression in its earliest generations. But today, after 80 years of evolution, control has been regained, allowing for the production of different patterns of gene expression in different plants. The new species was remade in UF greenhouses as well as studied in its natural habitat.

Researchers analyzed Tragopogon miscellus, a species in the daisy family that originated naturally through hybridization in the northwest U.S. about 80 years ago. The new species formed when two species introduced from Europe mated to produce a hybrid offspring. The species mated before in Europe, but the hybrids were never successful. However, in America something new happened – the number of chromosomes in the hybrid spontaneously doubled, and at once it became larger than its parents and quickly spread.

“No one had extended this to natural populations and the rapidity at which this can occur, and that’s pretty astonishing,” said Jonathan Wendel, professor and chairman of the department of ecology, evolution, and organismal biology at Iowa State University. “That species is such a beautiful model for that.”

Hybridization with chromosome doubling is a prominent mode of species formation and through this study scientists can better understand how different plant groups originated.

“Understanding the impacts this process has on genome structure may help understand how best to breed crops for high and stable yields,” said study co-author Pat Schnable, director of the Center for Plant Genomics at Iowa State University.

Before discovering their relaxed gene expression, the team had expected the artificial hybrids to exhibit a combination of the parents’ genes, said study co-author Pam Soltis, curator of molecular systematics and evolutionary genetics at the Florida Museum of Natural History on the UF campus.

“What we found was a surprise,” said lead author Richard Buggs of Queen Mary University of London, who worked on the study as a postdoctoral researcher at the Florida Museum. “It’s as if hybridization and chromosome doubling hit a reset button on gene expression, turning them all on – this could allow subsequent generations to experiment by switching off different genes.”

The expression of the hybrid plant’s genes in all tissues at all times allowed natural selection to shape what would emerge generations later, Pam Soltis said. With this form of hybridization, there is the opportunity for parental patterns to be equalized, as if the hybrid has a fresh chance to exhibit a wide variety of genetic expressions over time.

Its two parent species, Tragopogon dubius and Tragopogon pratensis, were introduced to the U.S. in the 1920s. The researchers started making the artificial hybrids in 2004 and the plants take about one year to grow from seed to being able to produce seeds, Pam Soltis said.

“Tragopogon miscellus is unique because we actually know when it originated,” Pam Soltis said. “Museum collections tell us when the parent species were introduced, allowing us to infer the age of the hybrid species.”

The researchers studied 144 duplicated gene pairs from the 40-generation-old Tragogogon miscellus, whose common name is goatsbeard. Because the flower of the plant only blooms for a few hours in the morning, it is often referred to as “John-go-to-bed-at-noon.” It looks like a daisy except for being either purple or yellow in color.

“The Soltises are showing at the genetic level how this really important process of genome doubling generates new biological diversity,” Wendel said. “This leads to new questions and the design of new experiments that can help us understand the ecological and evolutionary consequences of the genetic changes they’re observing.”

The study was funded by the National Science Foundation and co-authors include Linjing Zhang of Shanxi Normal University, formerly with UF; Jennifer Tate of Massey University, formerly with UF; Nicholas Miles and Brad Barbazuk of UF; and Lu Gao, Wu Wei and Patrick Schnable of Iowa State University.

- 30 -

Source: Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Doug Soltis, 352-273-1963, dsoltis@botany.ufl.edu
Media Contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu
Writer: Danielle Torrent, dtorrent@flmnh.ufl.edu

GAINESVILLE, Fla. — Flowering plants have evolved at explosive rates throughout history, yet scientists since Charles Darwin have been faced with the great biological mystery of how they originated.

A new University of Florida study to be published online this week in the Proceedings of the National Academy of Sciences presents the deepest insight to the genes that made up the first flower, the common ancestor of all flowering plants, and how those genes have changed over time.

“Our survival depends on products we get from the flower—grains, fruits and many other materials,” said Doug Soltis, UF distinguished professor of biology and project co-investigator. “Crop improvement is so important, but you don’t understand how a flower is put together unless you have a reference point – you can’t modify what you can’t understand.”

After nearly 10 years of research funded by the National Science Foundation, scientists from the Florida Museum of Natural History, the UF department of biology, and the UF Genetics Institute are bringing the study to a close.

“There are 350,000 species of flowering plants (or angiosperms), and they serve as the foundation of nearly all of Earth’s ecosystems, yet we don’t know how the flower originated,” said Pam Soltis, UF distinguished professor, Florida Museum of Natural History curator and project co-investigator. “We now know the origin of many of the genes responsible for making a flower and how those genes have changed during the history of angiosperms.”

A 2009 UF study traced the origin of flowers using genetic data for the avocado (a representative of one of the early lineages of flowering plants) and a well-known plant in genetics research, Arabidopsis thaliana. The new study includes additional comparisons with a water lily, California poppy and cycad (a gymnosperm or non-flowering seed plant) and shows how the first flowers evolved from pre-existing genetic programs in gymnosperm cones.

“We have a much better understanding of the flower than we did 10 years ago and it’s a huge improvement,” Doug Soltis said. “We don’t know every pathway, but we have a much better handle on what makes those parts tick.”

Typical angiosperms have flowers with four organs: sepals (typically green), petals (typically colorful), stamens (male organs, which produce pollen) and carpels (female organs, which produce eggs). But in the earliest flowers, the distinct borders between their floral organs fade to a blur. The flowers of early angiosperms have organs that merge into each other – for example, a stamen of a water lily produces pollen but it may also be petal-like and colorful.

“Our study found that the floral organs of basal angiosperms merge not only in appearance, but also in their underlying genetic pathways,” Pam Soltis said. “During evolution, the timing and location of where these genes act have become restricted, ultimately producing flowers with separate and distinguishable flower parts.”

“These missing links are incredibly important,” Doug Soltis said. “They are our key to the past.”

The study was a collaboration of researchers at UF, The Pennsylvania State University, the University of Georgia, and the University at Buffalo. The first author on the paper is Andre Chanderbali, a postdoctoral student at the Florida Museum and the UF department of biology.

“Flowers are the defining feature of angiosperms, the dominant vegetation of our world,” said Stanford University biology professor Virginia Walbot. “The new PNAS article by Chanderbali et al. represents a breakthrough in understanding the origin and evolutionary trajectories of the separate male and female floral parts.”

- 30 -

Source:  Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Doug Soltis, 352-273-1963, dsoltis@botany.ufl.edu
Writer: Danielle Torrent, dtorrent@flmnh.ufl.edu
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

GAINESVILLE, Fla. — University of Florida researchers are part of a nationwide team preparing to open a door into better understanding plant evolution by sequencing the genome of the single living sister species to all other flowering plants.

The information on Amborella trichopoda, a large shrub found only on the South Pacific island of New Caledonia, will help researchers understand how flowering plants diversified over time and provide insight into the key processes that have driven the formation of the world’s ecosystems.

A consortium of five universities will share the complex task of unlocking the plant’s genetic secrets as part of the $7.3 million project funded by the National Science Foundation. The work at UF is a collaborative effort among researchers at the Florida Museum of Natural History, the department of biology and the UF Genetics Institute.

“This plant shares a common ancestor with the first flowering plants, which places it in a unique evolutionary position,” said Pam Soltis, project co-investigator and distinguished professor and curator of molecular systematics and evolutionary genetics at UF’s Florida Museum. “The information from the project will allow researchers to determine whether a specific gene or process is unique to a particular plant or goes back to the beginnings of angiosperm evolution. This will enhance efforts to improve agriculture and forestry by giving plant biologists a reference point for understanding all other flowering plant genomes.”

The Pennsylvania State University is the lead institution on the four-year project, which also involves the University of Arizona, the University at Buffalo and the University of Georgia.

Over the relatively short time span of 130 million years, angiosperms, or flowering plants, have diversified into more than 300,000 species, covering nearly all terrestrial habitats and many aquatic ones.

“This genome will tell us about the evolution of angiosperm genomes through time,” said Doug Soltis, UF distinguished professor of biology and project co-investigator.

Brad Barbazuk, also of the department of biology, is the third member of the UF team, which will receive about $1.5 million for its work on the project.

UF researchers will assemble smaller sequences of DNA generated at other institutions into the complete Amborella genome, and also map specific genes on the plant’s chromosomes through a process that uses microscopic fluorescent labels.

“If tracing your ancestors is your hobby, you will love the Amborella project,” said Stanford University biology professor Virginia Walbot. “All future studies of flowering plants will use this catalog of Amborella genes to interpret the changes that have ensued during the natural selection that resulted in the hundreds of thousands of flowering plant species present on our earth today.”

(EDITORS: STORY MAY END HERE)

Pam Soltis said about 10 flowering plant genomes have been completely sequenced and none comes close to Amborella in terms of its place near the base of the evolutionary tree. Plants are more difficult to sequence than animals because their genomes are generally larger and more complex in terms of repeated sequences.

“Amborella is the platypus of the angiosperms,” Doug Soltis said.

The platypus genome has been sequenced for mammals because it occupies the first branch of the mammal evolutionary lineage and is a reference genome for all other mammals. And like Amborella, there is no other genus in its family.

“But the platypus is a sister species to only about 4,500 mammals,” Doug Soltis said. “Amborella, on the other hand, is a sister species to more than 300,000 flowering plant species, so you can see how much more significant a role it could play in helping scientists better understand how the world’s terrestrial ecosystems, dominated by flowering plants, developed over time.”

A majority of genome research funding goes to the biomedical industry, and much of the technology used in plant genomics comes from that.

“A lot of what we’re doing has trickled down from the human genome project,” Pam Soltis said.

- 30 -

Source: Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Doug Soltis, 352-273-1963, dsoltis@botany.ufl.edu
Writer: Bill Kanapaux
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

A study appearing online this week in the Proceedings of the National Academy of Sciences unravels 100 million years of evolution through an extensive analysis of plant genomes. It targets one of the major moments in plant evolution, when the ancestors of most of the world’s flowering plants split into two major groups.

Together the two groups make up nearly 70 percent of all flowering plants and are part of a larger clade known as Pentapetalae, which means five petals. Understanding how these plants are related is a large undertaking that could help ecologists better understand which species are more vulnerable to environmental factors such as climate change.

Shortly after the two groups split apart, they simultaneously embarked upon a rapid burst of new species that lasted 5 million years. This study shows how those species are related and sheds further light on the emergence of flowering plants, an evolutionary phenomenon described by Charles Darwin as an abominable mystery.

“This paper and others show flowering plants as layer after layer of bursts of evolution,” said Doug Soltis, study co-author and UF distinguished professor of biology. “Now it’s falling together into two big groups.”

Pentapetalae has enormous diversity and contains nearly all flowering plants. Its two major groups, superrosids and superasterids, split apart between 111 million and 98 million years ago and now account for more than 200,000 species. The superrosids include such familiar plants as hibiscus, oaks, cotton and roses. The superasterids include mint, azaleas, dogwoods and sunflowers.

Earlier studies were limited by technology and involved only four or five genes. Those studies hinted at the results found in the new study but lacked statistical support, said study co-author Pam Soltis, distinguished professor and Florida Museum of Natural History curator of molecular systematics and evolutionary genetics.

The new study at UF’s Florida Museum of Natural History analyzed 86 complete plastid genome sequences from a wide range of plant species. Plastids are the plant cell component responsible for photosynthesis.

Previous genetic analyses of Pentapetalae failed to untangle the relationships among living species, suggesting that the plants diverged rapidly over 5 million years. Researchers selected genomes to sequence based on their best guess of genetic relationships from the previous sequencing work.

Genome sequencing is more time-consuming for plants than animals because plastid DNA is about 10 times larger than the mitochondrial DNA used in studying animal genomes. But continual improvements in DNA sequencing technology are now allowing researchers to analyze those larger amounts of data more quickly.

The study provides an important framework for further investigating evolutionary relationships by providing a much clearer picture of the deep divergence that led to the split within flowering plants, which then led to speciation in the two separate branches.

Eventually, researchers hope to match these evolutionary bursts with geological and climatic events in the earth’s history. “I think we’re starting to get to a point with a dated tree where we could start looking at what was happening at some of those time frames,” Pam Soltis said.

- 30 -

Source: Pam Soltis, 352-273-1964, psoltis@flmnh.ufl.edu
Doug Soltis, 352-273-1963, dsoltis@ufl.edu
Writer: Bill Kanapaux, bkanapaux@flmnh.ufl.edu
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

GAINESVILLE, Fla. — Nico Cellinese, assistant curator of the Florida Museum of Natural History herbarium and informatics, has received a prestigious $865,000 CAREER Award from the National Science Foundation.

The grant will support Cellinese’s research on genetic diversity in the flowering plant group Campanulaceae, also known as the bellflower family, in the Eastern Mediterranean Basin, especially on islands in the Aegean Sea. The five-year award totals $865,251 and begins March 1, 2010.

The plant sample she will study includes about 200 species confined to extremely localized places, said Cellinese, who is also a University of Florida assistant professor in biology. These endemic species raise interesting questions about their evolutionary origins and why they are found only on islands in the Aegean archipelago.

“I want to find out whether these islands essentially serve as evolutionary laboratories,” Cellinese said. “Either the islands have been generating new species since being separated from the mainland or the species found on the islands are leftover fragments of an older flora that extended to the mainland before going extinct there.”

The answer to that question will have implications for conservation planning, Cellinese said. The Aegean islands have undergone extreme pressure from human activities for thousands of years. Agriculture, grazing and tourism have significantly altered and reduced these species’ habitats. “Many of these species are threatened or endangered and are essentially at risk of extinction,” she said.

The Aegean Sea has nearly 100 islands, the largest of which is Crete. During an event 5.9 million years ago known as the Messinian Salinity Crisis, the Mediterranean Sea dried up as the Strait of Gibraltar closed access to the Atlantic Ocean.

The event greatly affected the region’s composition of plant and animal species. Areas that had been underwater were now open land, allowing for greater exchange of species in places that previously had been isolated. The Mediterranean basin eventually started to flood again about 5.3 million years ago.

Cellinese plans to begin collecting samples of the islands’ endemic species in May. The fieldwork will also involve collecting species found on the mainland of Greece, Turkey and the Balkans. Back in the lab, data collected on the species’ morphology and a set of genetic markers will be used to determine evolutionary relationships among the different lineages.

“The systematics of the group needs to be clarified, and in this work we’ll do that,” Cellinese said.

She will use part of the funding to hire one graduate student and one post-doctoral researcher. She also will develop two online courses in Mediterranean biogeography, one for graduate and undergraduate students and the other for K-12 students.

The project also has a technology-development component that would integrate existing analytic tools within a single database management system. This would allow scientists to conduct studies of phylogenetics, population genetics and statistical inferences in a more efficient research environment.

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Source: Nico Cellinese, 352-273-1979, ncellinese@flmnh.ufl.edu
Writer: Bill Kanapaux
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu

GAINESVILLE, Fla. — A team of researchers including a University of Florida paleontologist has used a rich cache of plant fossils discovered in Colombia to provide the first reliable evidence of how Neotropical rainforests looked 58 million years ago.

Researchers from the Smithsonian Institution and UF, among others, found that many of the dominant plant families existing in today’s Neotropical rainforests — including legumes, palms, avocado and banana — have maintained their ecological dominance despite major changes in South America’s climate and geological structure.

The study, which appears this week in the online edition of the Proceedings of the National Academy of Sciences, examined more than 2,000 megafossil specimens, some nearly 10 feet long, from the Cerrejón Formation in northern Colombia. The fossils are from the Paleocene epoch, which occurred in the 5- to 7-million-year period following the massive extinction event responsible for the demise of the dinosaurs.

“Neotropical rainforests have an almost nonexistent fossil record,” said study co-author Fabiany Herrera, a graduate student at the Florida Museum of Natural History on the UF campus. “These specimens allow us to actually test hypotheses about their origins for the first time ever.”

Herrera said the new specimens, discovered in 2003, also provide information for future studies that promise to provide an even stronger understanding of the plants that formed the earliest Neotropical communities.

Many previous assumptions and hypotheses on the earliest rainforests are based on studies of pollen fossils, which did not provide information about climate, forest structure, leaf morphology or insect herbivory.

The new study provides evidence Neotropical rainforests were warmer and wetter in the late Paleocene than today but were composed of the same plant families that now thrive in rainforests. “We have the fossils to prove this,” Herrera said. “It is also intriguing that while the Cerrejón rainforest shows many of the characteristics of modern equivalents, plant diversity is lower.”

The site, one of the world’s largest open-pit coal mines, also yielded the fossil for the giant snake known as Titanoboa, described by UF scientists earlier this year.

“These new plant fossils show us that the forest during the time of Titanoboa, 58 million years ago, was similar in many ways to that of today,” said Florida Museum vertebrate paleontologist Jonathan Bloch, who described Titanoboa but was not part of the rainforest study. “Like Titanoboa, which is clearly related to living boas and anacondas, the ancient forest of northern Colombia had similar families of plants as we see today in that ecosystem. The foundations of the Neotropical rainforests were there 58 million years ago.”

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Megafossils found at the Cerrejón site made it possible to use leaf structure to identify specimens down to the genus level. This resolution allowed the identification of plant genera that still exist in Neotropical rainforests. With pollen fossils, specimens can be categorized only to the family level.

Researchers were surprised by the relative lack of diversity found in the Paleocene rainforest, Herrera said. Statistical analyses showed that the plant communities found in the Cerrejón Formation were 60 percent to 80 percent less diverse than those of modern Neotropical rainforests. Evidence of herbivory also showed a low diversity level among insects.

The study’s authors say the relative lack of diversity indicates either the beginning of rainforest species diversification or the recovery of existing species from the Cretaceous extinction event.

The researchers estimate the Paleocene rainforest received about 126 inches of rainfall annually and had an average annual temperature greater than 86 degrees. The Titanoboa study, which used different methods, estimated an average temperature between 89 and 91 degrees. Today the region’s temperatures average about 81 degrees.

Herrera is now comparing fossils from the Cerrejón site to specimens from other Paleocene sites in Colombia to see how far the early rainforest extended geographically. He is also examining fossils from a Cretaceous site to determine differences in composition before and after the extinction event.

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Source: Fabiany Herrera, Office: 352-273-1934, Cell: 352-222-3897, fherrera@flmnh.ufl.edu
Writer: Bill Kanapaux
Media contact: Paul Ramey, 352-273-2054, pramey@flmnh.ufl.edu