SPRING/SUMMER 2017
New Answers From Old Objects
Technology Powers The Florida Museum’s Second Century
Spring/Summer 2017, Vol. 22, No. 1
The Power of the Object
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On its 100th anniversary, Florida Museum of Natural History researchers are applying new technologies to old specimens
Footprints
Window of Opportunity
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Biodiversity research at UF seeks to connect the dots between all life on Earth
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Terra Incognita
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Mining museums for new knowledge
Night Vision
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Got Frogs?
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Technology opens UF’s collection of amphibians and reptiles to the world
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The McGuire Center for Lepidoptera and Biodiversity expands knowledge of butterflies and moths
Botany Abuzz
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Evolutionary Hot Button A huge temperature spike 56 million years ago provides insights into modern climate change
With their first steps, humans change landscapes and leave evidence behind
Untangling Florida’s botanical family tree
Montbrook
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Fossil finds reveal clues to an ancient Florida era
About the cover: Modern technologies like computed tomography enable Florida Museum scientists to “interrogate” objects like this 50 million-year-old Notharctus tenebrosus skull for new insights.
Dr. Kent Fuchs President Dr. David Norton Vice President for Research Board of Trustees James W. Heavener, Chair David L. Brandon Mori Hosseini Leonard H. Johnson Smith Meyers Rahul Patel Marsha D. Powers Jason J. Rosenberg Steven M. Scott Nicole Stedman Robert G. Stern David M. Thomas Anita G. Zucker Explore is published by the UF Office of Research. Opinions expressed do not reflect the official views of the university. Use of trade names implies no endorsement by the University of Florida. Š 2017 University of Florida. explore.research.ufl.edu Editor: Joseph M. Kays joekays@ufl.edu Art Director: Katherine Kinsley-Momberger Design and Illustration: Katherine Kinsley-Momberger Ivan Ramos Writer: Cindy Spence Photography: Kristen Grace Jeff Gage Bernard Brzezinski Web Editor: Jewel Midelis Copy Editor: Bruce Mastron Printing: StorterChilds Printing, Gainesville Member of the University Research Magazine Association www.urma.org
The Power of the
OB J EC T Atlas moth
Tesuque Pueblo figurine, late 19th - early 20th c.
Photography by Kristen Grace
American crocodile
Arboreal salamander – Aneides lugubris
Caribbean pottery vessel used for drinking manioc beer
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Heliaster sea star
On its 100th anniversary, Florida Museum of Natural History researchers are applying new technologies to old specimens
By Cindy Spence
F
lorida Museum Director Doug Jones draws endless inspiration from objects in the collection. As a paleontologist, he is particularly drawn to fossils like the Heliaster sea star. Unlike an ordinary starfish with five arms, the Heliaster had 30 in a sunburst arrangement that gives it the common name, sun star. The fossil is about 2.5 million years old and is the first appearance of this family of sea stars in the fossil record. Even more intriguing, this one was found in Florida where they are extinct; its ancestors only found today in the eastern Pacific. Its discovery was a fluke because fragile sea stars usually decay before they become fossils. In this slab, several were caught together at the moment of death. “They all died in a mass mortality, stacked on top of one another, during some crisis in the past when conditions were not favorable any longer,” says Jones, director of the museum since 1997. “They’re so different from anything that lives here today. I marvel at their beauty and the story they tell about past connections on Earth.” Jones knows the sea star is only one story: There are 40 million objects in the museum’s collections, each with a powerful story to tell about life on Earth. “These objects are a library of life,” says Jones of the collections in the museum, one of the top three universitybased natural history museums in the nation. “If we can tell the stories of the animals and plants that inhabit the Earth, we can inspire people to want to learn and enjoy the secrets of life.”
Some of the objects are rare, or very old, or they vouch for a plant’s or animal’s existence in a certain place in a certain time, and the museum has protected them throughout its 100-year history. In recent years, their power has grown as scientists use new technologies to interrogate the objects, getting them to reveal new information. And that information can now be shared with scientists worldwide. Jones says the 19th century stereotype of a museum scientist as someone who puts a name on something, puts it under glass and walks away, is changing. UF is the lead on the National Science Foundation’s Integrated Digitized Biocollections project — or iDigBio — a collaborative effort by 283 institutions in all 50 states to digitize information from museum collections and put the information online so scientists worldwide can use it. Other technologies allow scientists to see inside specimens without destroying them, or use fragments of genetic material to assemble evolutionary Doug Jones holds a Cretaceous-era ammonite, an ancient relative of the chambered nautilus that exists today.
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the space more than it wanted the mollusks. But a huge chunk of Vokes’ collection fit nicely with UF’s (the other portion found a home at the Paleontological Research Institution). “Bless y’all,” Vokes says. “What you have is a resource beyond belief.” Jones says he arrived at UF when many curators and collection managers were retiring, but it was clear to him that the old guard had made decisions as young scientists that charted a vigorous course for the museum’s collections, even without knowing how technological advances would increase their value. In the museum’s first annual report, the founding director, Thompson Van Hyning — hired from Iowa and blown away by Florida’s biodiversity — suggested the state museum could be one of the “greatest museums the world has known.” Florida’s rapidly disappearing biodiversity may have been a catalyst for collecting, too. “It’s a sad story, but the rapid population growth, the destruction of the natural environment, the disappearance of species, likely helped our forefathers recognize we’d better hold on to these specimens; that they were going extinct at an alarming rate, and these may be the only specimens we ever have to remember what lived here,” Jones says. Museum Milestones, 2016 Museum collections • Described 195 new species were center stage in • Conducted research in 24 countries • Published 187 peer-reviewed articles the historic 1972 ban • Catalogued 383,962 new objects on DDT, a chemical • Took in over $8 million in federal grants that caused human • Received state funding of $10 million and environmental • Had an economic impact on Florida of $74 million harm. To determine
relationships or process data with powerful computing. “We are at a new frontier of questions we’re going to be able to answer that were really unanswerable just years ago,” Jones says. At a time when some natural history museums are in a holding pattern or even closing, the Florida Museum is one of the nation’s largest and fastest-growing museums, according to the Official Museum Directory. Jones says UF has absorbed collections from the University of Miami and the Florida Geological Survey, and even the collection of retiring paleontologist Emily Vokes of Tulane University. Vokes and her husband, Harold, spent four decades collecting fossil mollusks from New Jersey to Argentina and around the Gulf Coast. As her retirement approached she began to worry about the Lane cabinets lining the hallways, up one side and down the other, outside her Tulane office. Lane cabinets — the size of a small freezer — hold scientific specimens. The cabinets are outfitted with shallow drawers, and for small specimens, one drawer can hold thousands of specimens. Vokes had 100 Lane cabinets. “I realized all of this, literally my life’s work, was going in the dump the minute I was out the door,” Vokes says from her home in New Orleans. Her department’s research priorities had shifted, and the university wanted
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whether DDT might be a culprit in thinning shells of bird eggs, scientists turned to UF’s well-known egg collection to measure changes in eggshells over time. “The eggs from 100 years before, the eggs from 50 years before were important,” Jones says. “We knew how thick the shells were supposed to be because we had those eggs, and could demonstrate that the eggs postDDT were thinner and less viable.” Like Van Hyning, Jones cannot predict how the science of the future may draw on the collections. “We don’t know what the technology of the future is going to be, we don’t know what new information can come from these specimens,” Jones says. “Protecting them is kind of a sacred responsibility.” Jones says the objects connect people to the planet, to life in the past, present and future. “If you and I have a conversation about biodiversity, we might have a meeting of the minds or a difference of opinion, but it will be a pleasant, informed conversation,” Jones says. “But if I bring in an ivory-billed woodpecker that’s gone extinct, or the skull of a saber cat, that conversation changes. “This saber cat lived here in Florida, that’s the skull of a once-living animal that inhabited Florida when Florida was very different,” Jones says. “You can imagine that Florida. “Extinction isn’t just a word, it’s here, in this object.” Doug Jones Museum Director dsjones@flmnh.ufl.edu
Florida Museum A Historical Timeline 1917: The Florida Legislature formally establishes the Florida State Museum at the University of Florida. 1932: Charles E. Doe is hired as ornithology curator. His more than 8,000 sets of North American bird eggs were the museum’s first comprehensive collection.
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1940: Museum assumes ownership of Thomas Farm — one of the richest Early Miocene fossil sites in the world. 1963: The museum acquires Leigh Morgan Pearsall Collection of more than 3,000 Native American art objects. 1983: Paleontologist S. David Webb begins underwater excavations in the Aucilla River that push the earliest date of human habitation in Florida back to nearly 14,000 years ago.
1996: The Randell Research Center is established at the site of a Calusa Indian village and shell mounds on Pine Island in Lee County. 2004: The McGuire Center for Lepidoptera and Biodiversity — funded with more than $7 million in gifts — opens with a living Butterfly Rainforest, research laboratories and collection space to house more than 10 million specimens. 2009: A team led by vertebrate paleontologist Jon Bloch discovers the fossils of Titanoboa — the largest snake the world has ever known — which ruled tropical ecosystems 60 million years ago. 2013: Fountain of Youth Archaeological Park donates more than 97,000 historic St. Augustine objects valued at more than $3.5 million.
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1988
1963
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2009
1983
1988: The museum begins curating the International Shark Attack File, a compilation of more than 5,800 shark attacks from the 1500s to the present.
1940
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2004 To learn more about the museum’s history, visit http://www.flmnh.ufl.edu/about-us/overview/brief-history/
Window of Opportunity
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Biodiversity research connects the dots between all life on Earth
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Photography by Kristen Grace
I
When we try to pick out anything by itself, we find it hitched to everything else in the Universe. — John Muir
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By Cindy Spence
n the human history of the Earth, a mere breath for the 4.5 billion-year-old planet, the next 50 years may be the most important. “This is a critical moment we’re living in,” says Doug Soltis, a distinguished professor in the Florida Museum of Natural History. “In terms of our ability to use data and make analyses, we have the power to do amazing things at this point in our history to inform people what the future could look like.” Earth has survived meteors, ice ages and soaring heat, and five mass extinctions. It will survive the era of human influence, the Anthropocene, too. Human survival, however, depends on embracing the opportunity — and the challenge — at hand: to protect the biodiversity that makes life on Earth possible. Biodiversity is about relationships among all plants and animals, including humans, says Pam Soltis, a distinguished professor recently named director of the University of Florida’s Biodiversity Institute, an initiative that grew out of the museum. “People have to realize biodiversity does matter to them, to their survival, and to their children and grandchildren,” she says. “We have one planet.” UF has 128 scientists and counting who work on biodiversity issues, and has married its huge advances in
computing power to that work, making the Biodiversity Institute a collaborative nexus of biodiversity science unlike any other in the world, Pam says. The investment could not come at a better time, the Soltises say. They have watched their own field, plant genetics, advance by leaps and bounds, and they think it is time for biodiversity science to draw on genetics and other disciplines in a new grand challenge: learning about biodiversity on Earth, and what it could mean to human survival, before that biodiversity disappears. In the midst of what many view as the sixth great extinction, scientists think we are losing species at 1,000 times what is normal. The scary part, Doug says, is we often do not know what we are losing. Nature is the best chemist, and plants we have not discovered yet could yield a cure for a disease. Some losses we recognize, an ecosystem, for example, but without realizing we rely on it to scrub pollution from the air we breathe, or filter the water we drink. Some losses may sneak up on us. Our great grandchildren may only know charismatic big mammals — elephants, rhinos, gorillas — as stuffed animals. On a rapidly changing planet, the Soltises say, we need to view biodiversity as a lifeline, and grab it.
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Relationships Matter The connection of one form of life to another is clear to biologists like Doug. But to make it clear to the rest of us, he and dozens of collaborators embarked on a gargantuan task in 2012, to build a Tree of Life, showing all known species. Doug had been told it could not be done, but the idea had been nagging him for three decades, so he jumped at the chance to work on the project, funded by the National Science Foundation. In 2015, the international group published the Tree of Life and put it online for anyone to view or use. The Tree of Life is depicted as a circle with the origin of life in the middle. From there, lines radiate along the circle’s rim, showing clearly, Doug says, that relationships matter. Of 2.3 million species on the tree, only about 5,500 are mammals. Among the mammals, humans are a speck, a single species reliant on all the others for a functioning planet. “We are over here,” Doug says, using an arrow to show a spot otherwise invisible. “This is a very humbling way to think of ourselves; we are no more important than any of the other tips on this tree. We are simply one of these tips, one small branch on the Tree of Life.” Although the tree is an enormous accomplishment, it’s only a
rough draft, meant to be revised as discoveries are made. There is only DNA data, for example, for about 17 percent of the species on the tree, leading an international group of scientists, including Pam, to propose a gigantic sequencing initiative in February. And the species on the tree are just a fraction of life on Earth. Scientists think there are at least 10 million more species out there, a biodiversity challenge of epic proportions. They are chipping away, discovering about 14,000 new species each year, but at that rate it will take 900 years to describe and name what we think still exists, and Doug says 900 years is way too long for a planet experiencing rapid change. “It’s staggering how little we know about the family tree for our own planet,” Doug says. “We should know more.” Doug points out that the cancer drug, Taxol, is based on a compound first found in the Pacific yew. The Pacific yew, however, is not common, so a better source was needed. By looking at the relatives of the Pacific yew, a more common variety was located, and that tree was used as the source of Taxol until the compound could be made synthetically.
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Nature has already invented a lot of the things we are trying to invent. We can use the Tree of Life to target areas where we are most likely to find active chemistry, and then look at the relationships between those plants. — Doug Soltis
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Taxol is just one example of the promise of plant chemistry, and has prompted pharmacologists, including a group at the University of Vienna, to use the Tree of Life as a tool to identify plants potentially useful in drug development. “Nature has already invented a lot of the things we are trying to invent,” Doug says. “We can use the Tree of Life to target areas where we are most likely to find active chemistry, and then look at the relationships between those plants.” Scientists cannot use these plants in the future — for medicines, cures, crop improvement, soil improvement, clean water, clean air or ecosystem management — if they become extinct. “If we don’t protect our biodiversity, we could lose thousands of unknown species and very likely lose organisms that could provide a cure that could have helped our children or grandchildren,” Doug says.
Finishing the tree would take a major investment in biodiversity and more public awareness of the need for biodiversity. “We just don’t have enough people. We need more scientists and more of the public engaged with working with scientists, more citizen scientists, so we can get everything collected, described and entered,” Doug says. “It’s going to take a village.”
Fast and Furious In 2000, the first plant genome, a simple weed, was sequenced. The
Soltises were among the scientists hard at work on Amborella, the duckbilled platypus of flowering plant species, the point from which all flowering plants evolved millions of years ago. Doug says when he heard about the breakthrough, he turned to Pam and said, “I hope before we retire, we’re able to sequence the Amborella genome.” Recently, they checked that goal off the list, thanks to rapid advances. “We published that in 2013,” says Pam, who recalls a time when it was possible to know each base pair in a sequence intimately because
the sequencing process was so slow. Today there is a flood of data, fast and furious. The revolution in DNA was followed closely by technological advances and increases in computational power, creating a wave of new science. Today, the Soltises’ Laboratory of Molecular Systematics and Evolutionary Genetics is busier than ever. The museum’s Genetic Resources Repository archives more than 60,000 tissue samples and DNA and RNA preparations from specimens in all the biological collections in the museum. The biological material is stored at
Tree of Life DNA Data for
17% of SPECIES on Tree of Life
2.3M SPECIES
ORIGIN
on the
Tree of Life APPROXIMATELY
5,500 are Mammals
HUMANS
SCIENTISTS
estimate there are at least more SPECIES on No Genomic Data
Genome Sequence
10M EARTH
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negative 196 degrees Celsius for use in long-term molecular analyses. The repository is one of the largest of its kind in the country. Mastering the computational challenge of the Tree of Life also unleashed a wave of new approaches in biodiversity sciences as biologists saw the power in the new tools, Pam says. At UF, she says, new investments in bioinformatics and in the HiPerGator supercomputer, with 51,000 computing cores and three petabytes of storage, are beginning to pay off. Combining the genetic data, ecological data, and museum specimen data, and then applying technology like remote sensing and computational power allows scientists to integrate data to produce new models, new ways of looking at a problem and perhaps solving it. Species level data are still important, but as Doug points out, scientists who focus on a species realize it has a relationship to other species and to an ecosystem. What happens if you pull just one species, one thread, out of the fabric of life? Its absence will
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As a community, we’re recognizing that these samples can be used for all sorts of unpredicted purposes. Just like we’re now using herbarium specimens that have been in our collection for over 100 years as sources of DNA.
Pam Soltis holds a plant press used to press specimens collected in the field before they are brought back to the herbarium. This plant press has been with Pam since her days as a graduate student.
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— Pam Soltis
have a ripple effect, and that effect is something scientists are beginning to study in new and exciting ways. Even traditional activities, such as collecting trips, have changed, colored by the urgency with which scientists view the future. “Early on,” Pam says, “we collected leaf samples for DNA, then a herbarium voucher,” which documents where a plant was collected and when. “Today, we think very differently about collecting; it’s much more holistic.” On one current project to study Florida trees, the team is collecting the usual vouchers, but also enough leaves to do analyses of DNA, plant chemistry and metabolomics. Other samples are collected to study microscopic creatures in the leaves, such as bacteria. Soil samples are collected from beneath the trees to study soil microbes. Ecologists are part of the group as well. “As a community, we’re recognizing that these samples can be used for all sorts of unpredicted purposes. Just like we’re now using herbarium specimens that have been in our collection for over 100 years as sources of DNA,” Pam says. “Now, we’re thinking, what would somebody in the future possibly want from this collection? As our natural systems become increasingly degraded, the more information we can collect now and house for future experiments, the better. “This forest, for example, may not be here in 20 years, or if it is, it may not be accessible,” Pam says. “So we need to get the samples while we can.” Doug points out that the scientists who collected the 100-year-old plants he has used for DNA analysis, could not have predicted the DNA
revolution. Even 20 years ago, DNA analysis on aging specimens was difficult, the material too degraded. But technology has advanced, and today, he says, he can use mere snippets of DNA for sequencing. “Some specimens that weren’t so useful with older technology, can now be used,” Doug says. “I think our record for DNA is a 125-yearold plant.” The data create models, and the more data, the better the models. Already, the Soltis lab, working with Associate Curator of Informatics Robert Guralnick, is modeling the distributions of plant species in Florida. The models use location information and environmental data, such as temperature, soil type and precipitation. So far, 1,500 of Florida’s 4,200 plant species are modeled, and already some trends are becoming clear. In a changing climate, plants won’t stay put. Some tree varieties, maples and oaks, are moving northward, as are mangroves. Iconic landscapes like salt marshes are on the verge of drastic change. The model, however, needs more input: what are fungi doing, birds, amphibians, mammals? “People think everything is going to react the same way, that the birds that interact with the plants, the butterflies that depend on the plants, will just do similar things in response to a changing climate. But they won’t, and that’s the challenge,” Doug says. “If organisms go in different directions, a plant could lose a pollinator, a bird could lose a prey item it depends on. That’s already happening in some places. This interplay among all these organisms is so crucial.” Florida is ground zero for the impact of change on biodiversity — few states have more biodiversity
Sampling Point
Community Tree
The red branches on this phylogenetic tree of Florida plants indicate those species that occur in a given sampling point. The sum of the evolutionary change along these red branches is summarized as “phylogenetic diversity,” with dark green areas having greater phylogenetic diversity, representing high priorities for conservation.
UF’s Genetic Resources Repository archives more than 60,000 tissue samples and DNA and RNA preparations from specimens.
1,500 of
FLORIDA’s
4,200
PLANT SPECIES
are modeled
— and that makes UF’s 100-year investment in the museum a solid foundation for the new focus on biodiversity sciences, Pam says. In the Biodiversity Institute, she sees computer scientists working alongside biologists — and alongside students and citizen scientists — to create new knowledge. It’s a great opportunity, she says, to do something lasting. Evolution and extinction are part of life, a balancing act. But when extinction speeds up, it demands attention, and she hopes the Biodiversity Institute can focus attention on the future of the Earth, and humans. “This window we’re in now, the next 40 or 50 years, may be the most crucial window in human history,” Doug says.
In a changing climate, plants won’t stay put. Some tree varieties, maples and oaks, are moving northward, as are mangroves.
As the Biodiversity Institute refines its models, Pam says, the goal is to help citizens make decisions. Just as the evolutionary branches on the Tree of Life diverge at certain points in history, human decisions do, too. “We can model scenarios over the next 50 years,” Pam says, “and then ask: Do you like what you see?” Pam Soltis Director, Biodiversity Institute Distinguished Professor and Curator Florida Museum of Natural History psoltis@flmnh.ufl.edu Doug Soltis Distinguished Professor Florida Museum of Natural History and Department of Biology dsoltis@ufl.edu Related website: https://biodiversity.flmnh.ufl.edu/
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TERRA INCOGNITA
Mining museums for new knowledge By Cindy Spence
Photography by Kristen Grace
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n the map of life, of biodiversity on the planet, there are patches that are unknown, as if a hiker spilled coffee and covered up a chunk here and there. A hiker might have trouble using such a map and so does a scientist struggling to understand Earth’s biodiversity even as it declines. Even with more than 600 million biodiversity records virtually available on any smartphone, filling in the patches will require still more data. For a data analytics fan like Robert Guralnick, that’s like an endless dessert bar. As the associate curator of informatics at the Florida Museum of Natural History, Guralnick’s role is to use technology to place the museum’s resources — not just the specimens but the data housed in the cloud or refrigerator-sized mainframe computers — into the hands of those who can use it and position that data within the larger ecosystem of natural history information worldwide. “What do 600 million biodiversity records tell us about what we know about the planet?” asks Guralnick. Mostly, those records tell us how much more there is to know. “We know the spatial distributions of biodiversity in places that are well sampled. But some places on the map are empty; we need more data to tell the story. And it’s an important story.” The 600 million records Guralnick refers to reside in the Map of Life app, developed by Guralnick and a colleague, Walter Jetz at Yale University. Anyone with a smartphone can access it, and use it multiple ways. First, it serves as a field guide. That tattered guide to butterflies,
Robert Guralnick has developed multiple informaticsrelated apps, including Map of Life.
“ Wherever you are on
the planet, you can find out something about the biodiversity there. — Robert Guralnick
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perhaps several volumes worth, can stay on your shelf at home. Just download the app and take your phone along and you can learn about butterflies and biodiversity wherever you happen to be. If an interesting plant or animal stops you in your tracks on a nature walk — or an urban walk — check the app. Want to contribute? Report what you saw and when and where with the GPS on your phone to help track biodiversity around the globe. Guralnick imagines an army of globe-trotting smartphone users adding data as they go. If your curiosity, or a research project, requires it, you can query the entire dataset, all 600 million records, in about a minute and in six languages. For conservation managers who need data for decisionmaking, the data can be confined to a particular area of interest, such as a national park. As a user, you can email your own records to yourself and keep track of what you have seen. It’s a robust tool, whether used casually or scientifically. “There is a lot of simplicity to the app,” says Guralnick, “but at the heart, it’s a very difficult thing to pull off. Intellectually, it’s rigorous and challenging, but Walter and I have always known in our hearts that out of that rigorous science would be something easy for people to understand.” So easy, in fact, that the American Association of School Librarians named it a Best App for Teaching and Learning in 2016. “Wherever you are on the planet, you can find out something about the biodiversity there,” Guralnick says.
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Web to App The sophistication of the Map of Life is a long way from Guralnick’s web roots. Think back, to the computers on your desk in the early 1990s. Chances are, you were transitioning from five-inch floppies to three-inch diskettes, occasionally whacking the boxy machine or jabbing a keyboard repeatedly, unaware of the paradigm shift at hand. But not Guralnick. In 1992, Guralnick was sitting in a lab in Berkeley, a graduate student at the Museum of Paleontology at the University of California, transfixed by the clunky technology that frustrated others. In the electronic box on his desk, and the ether it connected to, he saw a way to give the public access to fossils cloistered away in the collection. He built one of the world’s first 50 web sites, one of only two or three at the time that were searchable. Did he feel like a pioneer? “No question about it. I had a sense in real time of what we were doing. I knew,” Guralnick says. “It was one of the few times in my life where I was sure what I was doing was important.” Not everyone shared the vision. His mentor predicted web sites would be a flash in the pan but let Guralnick geek out. A couple of years later, the mentor allowed that web sites, even museum web sites, might be around to stay. Guralnick, meanwhile, had been giving talks about the web to companies like Disney because there were so few folks with hands-on experience. “We just had hints of what the transformations would be with the new digital technologies. But we recognized we were giving people a
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“ The web democratized
the data, made it widely available. It got our stuff out of boxes and into people’s hands. — Robert Guralnick
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window into discovering content,” Guralnick says. Before the web, a scientist or student searching for a fossil would follow a laborious process, talking to a collection manager, perhaps several at different museums, then arranging a loan of the specimen. Those with grant funding might have the means to travel to view specimens, only to find a particular object was not quite the right specimen. Overnight, Guralnick says, that changed. “The web democratized the data, made it widely available. It got our stuff out of boxes and into people’s hands.” Museums embraced the information revolution because what any collection manager wants most of all is for others to see and value their stuff. Another benefit: In cramped museum collections, space is at a premium, but in the cloud, there’s plenty of room, making it a huge resource for the information ecosystem of natural history museums. Once an object is in the cloud, it emerges into a world of possibility. Only a handful of people may know an object exists in a museum drawer, but a student, scientist or hobbyist might bump into it online. Then they can explore, perhaps learning genomics, or morphology or other information enriched beyond the object in the drawer.
That prospect for discovery and deepening the knowledge held in each object is what Guralnick is after. In that open access model, the museum’s data does not belong just to the museum anymore; it belongs to anyone.
Technological Toolbox Although Guralnick has spent eight years working on the Map of Life, it is just one tool. Guralnick has a hand in several others and an eye out for any new ways on the horizon to leverage technology. Before he arrived, the museum was already knee-deep in iDigBio, leading a 10-year collaborative effort with a $12 million grant from the National Science Foundation to digitize the massive biological collections tucked away at UF and other natural history museums nationwide. In fact, iDigBio was one of the reasons Guralnick was attracted to UF. One area of particular interest is how to get the public involved in the process of digitization. Guralnick and a team of partners created a citizen science platform called Notes from Nature, that asks the public to help with the challenge of digitizing
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critical biodiversity information contained on each imaged specimen. He was part of a team that developed weDigBio, the Worldwide Engagement for Digitizing Biocollections, an annual event in which volunteers transcribe specimen records so they can be placed online. The 2016 event spanned four countries and resulted in 35,000 transcriptions. A 2010 estimate puts natural history collections at two to four billion objects worldwide. Of these, perhaps 5 to 10 percent are available online, making digitizing a critical step in using museum data. Without knowing what’s there, it is not possible to assess human impacts or environmental changes and then use that information to figure out the changes still to come for the planet. “The really awesome thing about the 21st century, about the next 20 years, is we will be able to go beyond the who, what, when and where of our collections,” Guralnick says. “To ask questions about global change, to understand drivers of
To ask questions about global change … we need to assemble a better mousetrap, and that means bringing together very rich, very complex, very heterogeneous types of data. — Robert Guralnick
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change, we need to assemble a better mousetrap, and that means bringing together very rich, very complex, very heterogeneous types of data. We’ve monitored biodiversity for hundreds of years, but our specimens are so much richer, they can tell us so much more.” Heartened by the community of collaborators he found at UF, Guralnick dove in to a diverse set of projects with big data needs, 10 since his arrival in 2015.
With Akito Kawahara and a $2.5 million NSF grant, Guralnick is developing ButterflyNet, an online database and toolbox for comparative studies of butterflies, with the aim of reconstructing the evolutionary history of about 18,000 butterfly species [see related story, page 34]. A smaller project, CreatureFeatures, will build a toolkit for aggregating and annotating trait data for a variety of organisms. Guralnick admits he may be guilty of collaborating too much, but when someone comes to him with an idea to tap technology for science, it’s hard to resist. The transformative value is not just in the whiz-bang of novel technology; it’s in the knowledge technology sets loose. As an evolutionary biologist, Guralnick says, change is the rule, not an exception, so maybe that’s why he’s right at home with the moving target of technology. People talk a lot about big data, he says, but it will take big data to answer the big questions. “This is our century, for biodiversity and ecosystem scientists,” Guralnick says. “We will be able to pull together the systems and how they are changing, and that can help serve as alarms for the planet. We need to be able to run the clock forward from a period in the past to the present and use that to calibrate the future. “To do that, either you get a time machine, or you go work in a natural history collection.” Robert Guralnick Associate Curator of Informatics rguralnick@flmnh.ufl.edu
Robert Guralnick and Akito Kawahara in the Butterfly Rainforest
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GOT FROGS? By Cindy Spence
Photography by Kristen Grace
Technology opens UF’s collection of amphibians and reptiles to the world
Micro CT scans can be used to produce 3-D models, like this replica of the tuatara’s skull. The models are useful for education and outreach. At left, the tuatara is suspended in its jar, the only one in the herpetology collection marked “not to be opened.”
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erpetologist David Blackburn takes a jar off the shelf in the Herpetology Collection at the Florida Museum of Natural History, home to about 300,000 preserved amphibians and reptiles. Inside, suspended in a clear liquid, is a tuatara, one of the rarest creatures in the world. Blackburn handles the jar carefully — it is the museum’s only intact tuatara — and points to the label: “Not to be opened.” “It’s the only specimen in the collection with that label,” says Blackburn, associate curator of the herpetology collection, the eighth largest in the United States. This unique creature, almost extinct, is the subject of fascination in the herpetology world. It is part of an ancient reptilian order that lived with dinosaurs and is the sister lineage of all living lizard and snake diversity in the world. It once roamed widely but now is only found in islands off New Zealand. When Blackburn arrived at the University of Florida in 2015, the tuatara was among the coolest — yet least-used — specimens. There is only one at UF, so dissecting it was out of the question. It had been in the collection since the 1960s but there was no publication history on it. It was glorious, but obscure. Today, the UF tuatara could well be among the most used specimens of that species in the world, Blackburn says. What changed since August 2015? Blackburn’s arrival at UF coincided with the arrival of a micro CT scanner, and one of the first specimens he popped into the scanner was the tuatara. As the scanner went to work, the internal anatomy of the creature was revealed, and a 3-D image took shape on a computer screen. The images alone increased the research value of the specimen, and anyone with a 3-D printer can make a model, increasing the value for education. Explore 19
“The tuatara scan has been used hundreds of times, on four continents in the last couple of months,” Blackburn says. “Pretty cool for something that has basically never been used.” Postdoctoral researcher Edward Stanley, who moved to UF with Blackburn from the California Academy of Sciences, says the micro CT scanner is taking a time-honored phrase in the scientific lexicon — beyond the scope of this study — and making it less reasonable. “If you can think of a question, you can ask it,” Stanley says, “and if a specimen is digitized, you can ask it from almost anywhere in the world.”
it possible to see brain architecture, muscle anatomy, the shape and volume of internal organs, in short, things long hidden. Blackburn and Stanley scan at a resolution of 10 to 50 microns, likely overkill for today’s research. Tomorrow’s questions? “If the future needs a higher resolution, we’ve already collected it,” Blackburn says. “We are able to do it, so we do, to future-proof the data.” The process has yielded what Blackburn calls natural history bycatch: stomach contents, egg sacs, populations of parasites. “For a lot of species we have a name, we’ve known them for 100 years, but we don’t know the first X-ray Vision thing about their biology,” Blackburn In computed tomography, says. “Pretty much every soft tissue X-ray images can be produced and scan turns up something weird or converted into 3-D images on a shows us something about species monitor. To get soft tissues to show interaction — like the parasites — up, a specimen is soaked in iodine to that had been invisible. provide contrast, making it possible “We can begin to eke out pieces of for the X-rays to produce an image. biology from the anatomy and use it The non-destructive method makes to target field or lab research.” Blackburn, a frog scientist, saw firsthand the power of the scanner to break a scientific logjam. In India, new families of frogs have been described in the last 15 years, but India does not export biological specimens, no matter how long they’ve been dead. The creatures were known only from journal articles. So Blackburn located a micro CT scanner in India, and sent Stanley on a two-pronged mission. He trained Indian scientists on the micro CT scanner, and scanned the newto-science frogs. Back home, Blackburn was like a kid glued The Notharctus tenebrosus was a lemur-like adapito Saturday morning cartoons. form, thought to be a link between primitive and advanced primates. This skull is about 50 million years old and was micro CT scanned to learn more about brain size and function.
“As Ed was CT scanning the stuff, I was getting a live stream of them to my computer,” Blackburn says. “These were families of frogs for which we’ve never had anatomical data, and they are utterly the weirdest possible frogs there are.” The exercise opened the door to collaboration quickly, and today, Blackburn is working with Indian scientists on a project to study how these strange frogs hear, which is a cross between the two ways frogs are known to hear, one much like humans and the other through vibrations. “We could never have begun to ask that question before.”
Opening Doors Blackburn has also been excited by the expanded use of the collection. Often a graduate student or researcher will cross paths with an image online and call to ask if other specimens are available for imaging. A limited number of people can walk through the door of the museum, but online, the world is welcome. The incredible investment in asking a question — a trip across the world to India, for instance — is no longer an obstacle. Before, risky questions did not get asked. Now a question may be a gamble, but it does not cost money to ask. Blackburn says until micro CT scanning came on the scene, knowledge about many creatures amounted to the sum of their skeletal structure. Now that soft tissue can be imaged, more questions about comparative anatomy can be explored even when there is only one representative, like the tuatara. “We’re not going to get another one, so being able to do this
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We are entering the era of paleontology for living amphibian species, describing species as new to science that are already extinct.
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— David Blackburn After a specimen is placed into the micro CT scanner, its X-ray image starts to appear on the computer monitor.
virtually, dissect virtually, we can start eking out a whole new generation of data for testing ideas,” Blackburn says. Micro CT scanning today, he says, is doing for science what the explosion in genetics did a decade or so ago. Genetic data today can quickly be sequenced and shared, and that is beginning to happen with anatomical data collected from scanning. It’s hard to share a frog electronically, Blackburn says, so scans are the next best thing. Amphibians and reptiles are not the only beneficiaries of the micro CT scanner. Just about anything can be scanned, and Blackburn’s excitement has been contagious. Environmental archaeologist Kitty Emery has scanned artifacts, and paleontologist Jon Bloch has scanned fossils, turning to the non-destructive method to get information hidden to view. “Take a skull like this,” Bloch says, holding a 57-million-year-old primate fossil. “With micro CT we can virtually dissect it, and we can learn about the expansion of
the brain that you see in primate evolution. “Micro CT scanning has revolutionized how we study the cranial anatomy of extinct animals.”
Found, and Lost Blackburn has an endless appetite for scanning frogs, but also notes an urgency to the project. While 150 new amphibian species are being described each year, almost all of them frogs, discovery and extinction often go hand in hand. “It’s an age of discovery,” Blackburn says, “but it’s also an age of loss. “We are entering the era of paleontology for living amphibian species, describing species as new to science that are already extinct,” Blackburn says. “Just as our knowledge is increasing, we suddenly realize when we go back to the shelf that these frogs from Colombia from the 1960s are totally different from what we thought. Yet when we go back to the field, they’re not there anymore.” Blackburn has had that experience more than once, including in Africa,
where he does most of his field work. As a graduate student, he located a museum specimen from 1930 that is now one of only two specimens (the other from the 19th century) of what he dubbed the “overlooked squeaker frog,” Arthroleptis kutogundua. Yet colleagues working in that part of Tanzania have never encountered this distinctive frog. “Could it maybe be found? I hope so. It seems to be missing in action,” Blackburn says. “Over the last 10 years, we’ve realized that frogs we’ve been studying to ask all sorts of biological questions are becoming harder and harder to find. We are losing a lot before we have the opportunity to ask the questions.” Between habitat loss and a fungal disease, a third of frog species are threatened by extinction. In this race, Blackburn scans. Soon, anyone with an internet connection can call up a digital depository that will represent all of frog diversity, at least for now. The goal, Blackburn says, is to learn about their biology, including things relevant to humans, before they are gone.
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Web of Biology Blackburn found a welcome mat at UF, not just at the museum, but in other departments. He says he was attracted to UF because of the diversity of sciences related to biology and the potential to find new collaborators with whom he could share a quick cup of coffee by just walking across campus. “I love the fact that the museum is across from biology, across the street from wildlife ecology, and there are all these students in and out of the lab. There’s a web of biology happening all across campus,” Blackburn says, “and at the museum we’re in the nexus of all this amazing science that is happening.” This semester he will revive a course on amphibians and reptiles that has not been taught on campus in a decade. His view that science should be accessible extends to much younger students as well. He has had the experience of explaining one of his projects to 8-year-olds only to have them say, “I know that already.” “That particular bit of science was featured in kids’ books. It’s not cited
David Blackburn holds a goliath frog, the largest frog in the world. This specimen is from Cameroon and was donated in the 1980s. The species is threatened and is hunted for food.
The tuatara, a survivor The tuatara is the only living member of the order Rhynchocephalia, and some scientists call it a living fossil. The tuatara is a sister lineage of lizards and snakes, but is not actually a lizard, despite the close resemblance. The tuatara can be traced back 225 million years, and all other members of its lineage became extinct in the late Cretaceous, just after the extinction of the dinosaurs. Museums that have one usually have just one, so are reluctant to loan them out. UF has one preserved whole tuatara and the skull of another tuatara, and there are only about 140 specimens in the U.S. “People would point to it and say this is cool, but no one was using it,” Blackburn says. Tuatara have unusual features, such as a third eye on top of their head that disappears after four to six months, its function unknown. The third eye has a lens and retina but is not used for seeing. Their tooth arrangement, two rows on top that interlock with a single 22 Spring/Summer 2017is not seen in any other reptile. row on bottom,
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very much, but 8-year-olds stop me and tell me about it,” Blackburn says. The micro CT scanner elicits excitement on all fronts, as it lets more people virtually roam the shelves full of preserved lizards and frogs and snakes. It’s a valuable tool, he says. “All museums want this.” But it only works in conjunction with the specimens, some protected and preserved for a century. “People ask, ‘why do you have all this old stuff?’ Well, we use it. It’s irreplaceable, yes, but it’s being used,” Blackburn says. “We don’t have a visitor a day in herpetology, but I bet every day, someone is downloading our data and using it. None of those people walk through our door. “I think that is liberating, and democratizing,” Blackburn says. “Pretty cool.” David Blackburn Associate Curator of Herpetology dblackburn@flmnh.ufl.edu
This African Pig-nosed Frog was CT scanned after soaking in iodine, which allows researchers to visualize the frog’s muscles, organs, glands, and more. The CT scan serves as a digital dissection. The bony armor of this Mexican beaded lizard, one of the only truly venomous lizards, is color-coded to show the most dense (green) to least dense (red) plates in the armor.
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EVOLUTIONARY HOT BUTTON A huge temperature spike 56 million years ago provides insights into modern climate change By Cindy Spence
24  Spring/Summer 2017
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bout 56 million years ago, something weird happened to the planet that has not happened before or since. The temperature spiked by 5 to 8 degrees Celsius, mammal biology went haywire, and primates showed up on the scene. The Paleocene Eocene Thermal Maximum was almost like a hot button for evolution. “There’s this giant hyper-thermal spike in temperature, and then all these mammals were there, and they never went away. They radiated out into the diversity we see today,” says Jonathan Bloch, curator of vertebrate paleontology in the Florida Museum of Natural History. “It was a really dramatic event.” Dinosaurs died out 10 million years before the Paleocene Eocene Thermal Maximum (PETM), and there have been glacial and interglacial cycles — alternating cold and warm periods — since. But the rapid global warming of the PETM was unique, marked by an overall increase in biodiversity, during a time with palm trees and alligator ancestors in the Arctic. During the PETM, Bloch says thousands of petagrams of carbon were released into the seas and air, oceans
“ Exactly coincident with that period of global warming, you get the first primates of modern aspect … ” — Jonathan Bloch acidified and global temperature increased. Scientists know this because no matter where you find rock from that time period — lasting about 170,000 years — the samples contain more enriched carbon than rocks in layers before the PETM and after. Bloch says it’s a carbon signature recognizable in rock records on land and in the ocean floor around the world. The PETM caused a major extinction of tiny sea creatures called foraminifera, but on land, mammals responded differently to the abrupt change in climate. “Exactly coincident with that period of global warming, you get the first primates of modern aspect, the ones that gave rise to lemurs, monkeys, apes, humans. You also get the first horse, and the first ancestor that ultimately gave rise to living pigs, cows, hippos and whales,” Bloch says. “All coincident with that one single climate event.”
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Transition world
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Projected temperature for 2300
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N. Hemisphere ice sheets begin
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The PETM might be just an interesting anomaly if current atmospheric carbon levels and global temperatures were not breaking all the shortterm records humans have. Modern humans have only been on the planet for about 200,000 years, and people have only kept temperature records since 1850, so humans, and human records, are mere blips on the geologic time scale. To find conditions somewhat parallel to today’s, you have to go back in geologic time, and scientists have ways of doing that. By drilling ice cores in Antarctica, they can assess past climate conditions layer by layer, gathering data covering about 800,000 years. Sediment cores drilled from the ocean floor, which contain tiny creatures whose shells absorb carbon, can travel deeper into the past. Modern climate change, it turns out, has some similarities to ancient climate change. On a graph of global temperature since the extinction of the dinosaurs 65 million years ago, Bloch points out the huge spike at 56 million years ago for the PETM and then a peak for
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today’s temperatures. Following the trajectory of the curve up to predicted temperatures for 2100, another spike appears to be in the making. The rate of change is also important. The PETM was sudden, a response to a massive dump of greenhouse gas into the sea and air, the source of the carbon a mystery still, perhaps volcanoes, perhaps methane. The source of modern greenhouse gas is known, but still sudden in its release into the atmosphere. “We are now well beyond the highest CO2 concentration and temperature that the Earth has experienced for the last 800,000
years,” Bloch says. In projecting to 2100, there are times when CO2 and temperature have been that high but “it’s way before humans were on the planet — for example, this hyperthermal spike 56 million years ago.” Paleontological estimates are conservative because the timescales are huge, but the onset of the PETM is so dramatic, Bloch says, that research pegs it closer to human timescale — 5,000 years or even less. The PETM changed Earth forever, and Bloch and his colleagues have spent two decades investigating the ways.
Kristen Grace
The fossil skulls of Notharctus tenebrosus are a link to early primates called adapiforms that lived in the Bighorn Basin when it was tropical, about 50 million years ago. The lower jaw is from Paleonictis wingi, a hyena-like creature that shrank in size during the PETM, then evolved to a larger size when Earth cooled.
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Mini Mammals Bloch’s field work takes him to two very different locations — the dry Badlands of the Bighorn Basin in Wyoming and the tropical forests of Colombia in South America. Both take him back to the time before, during and after the PETM. The Bighorn Basin is the best-known place to find PETM fossils, and from digging there, Bloch says, the museum has built the largest collection documenting what happens to animals during the PETM. In 2003, Bloch and a Smithsonian colleague went on what he calls the Death March, a relentless search all around the southern rim of the basin to find evidence of the PETM and
more excited about “ I’m isolated teeth now than I have ever been. ” — Jonathan Bloch
collect fossils from that time period. “He was talking about how we had no fossils of the forests during the PETM, and I was talking about how little we knew about this strange event when it came to mammal evolution because of very limited known rock that preserved vertebrate fossils from that time,” Bloch says. “We decided we should just look for more of it, just walk into the Badlands until we found it.” They started at a point where the PETM was documented and traced it around the basin as they went, setting in motion the next decade or more of work. Besides the scorching summer heat, the process is more difficult than it might sound. Finding random fossils is nice, but for building the story of a plant or animal, multiple fossils in reasonable condition are needed. In a perfect world, for example, Bloch would find multiple fossils of one animal in the layers of soil before
the PETM, multiple fossils of that same creature in the PETM layer, and multiple fossils in the layers after the PETM. Using those, he could tell a story of how the creature evolved. When he began his career, he looked for whole skeletons, and he has found a few, which he says function as Rosetta stones for fossil identification. More common are teeth, and teeth can say a lot about diet and body size changes over time. “I’m more excited about isolated teeth now than I have ever been,” Bloch says.
The 100-mile-wide Bighorn Basin in Wyoming is famous for its fossils. Jonathan Bloch, holding a Notharctus tenebrosus skull, has focused his research on the PETM layer, highlighted by a red line on this aerial image of the Bighorn Basin.
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Illustration by Jason Bourque
Adding plants to the picture of hyper-thermal life was important, too, and during the Death March the team discovered the first evidence of plants during the PETM. “Why was that exciting? The forests during the climate event were totally different from the ones before or after, and what they looked like were the forests that we find in the Gulf Coast at that time. Forests literally moved about 800 kilometers from where they were into the Rockies, and once the climate event was done, out of the Rockies again, back down to the Gulf Coast,” Bloch says. “The forest was just dancing with climate change.” Mammals, too, were adapting.
“One of the crazy things we’ve documented here is that the mammals get smaller,” Bloch says. The earliest ancestors of horses, he says, were about the size of a dog, and body size turned out to be inversely correlated with temperature: the hotter it got, the smaller the horses. “The horses, just like the plants, are dancing, too, but they’re dancing with body size,” Bloch says. “It looks like one of the universal responses to climate change in mammals; they get smaller as the temperature warms up.” Bloch says one of his questions is still unanswered: Does evolution speed up during extreme climate events? While evidence does show that directional evolution in body size The early ancestors of modern horses were much smaller during the PETM.
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occurs in some mammal lineages, it is harder to know how fast it is happening. That will require a lot more fossils. The PETM, of course, ends, and temperature and carbon go back to something closer to background levels. Somehow, naturally, no one yet knows how, the carbon in the atmosphere is sequestered, pulled out of the atmosphere even faster than the rate at which it was released into the atmosphere. Mammals begin to get larger. The whole event lasts 170,000 years, a timescale almost unimaginable to humans, a pit stop for the Earth.
Titanic Reptiles A different dance was going on in the Colombian rainforest in the period leading up to the PETM. Bloch says there are questions about the antiquity of the rainforest, and the Cerrejon Coal Mine, the world’s largest open pit coal mine, began to yield answers when miners dug down into the Paleocene. There, paleontologists have found
geologic record of the planet is “ The essentially a user’s manual for how to use the planet. As geologists and paleontologists, our job is to go through the pages of that user’s manual and read the instructions …
” — Jonathan Bloch
the first evidence, in the form of fossil leaves and pollen, of chocolate, bananas and beans. A barren landscape today, the mine was a tropical jungle in the Paleocene. As the coal was mined, new fossils were uncovered, and Bloch and his colleagues made eight expeditions Titanoboa vertebra vs. modern-day anaconda there from 2004-2011. the rarest find, a skull. Snake skulls “As soon as we got into the mine, often don’t survive to become fossils, we found bones, the first Paleocene Bloch says, because the bones are vertebrates ever found in the tropdelicate. The team agreed that the ics of South America,” Bloch says. fossils belonged to a new species of Among the early finds: a snake vertesnake. They named it Titanoboa, the bra about four times as big as the largest snake to ever live. At 42 feet vertebra of an anaconda, the largest and about 2,500 pounds, Titanoboa snake alive. A vertebra that big had apparently had no problem with the to be from a monster snake, and for warm climate. a snake to be that big, the planet had The ultimate goal for paleontoloto be really, really hot. gists is to figure out past climate and Mammals adapt to extraordinary how plants and animals responded. heat by getting smaller. Reptiles, It would be nice, Bloch says, to have however, get big, really big. Reptiles a bunch of alternate universes where are ectotherms, maintaining body scientists could plug in variables temperature and deriving energy and measure responses to global from their environment. As the climate change in real time. The next planet warmed, the reptiles just kept best thing is to look at Earth’s past growing. experiments. As the group continued to dig, “The geologic record of the planet more vertebrae appeared, and finally,
is essentially a user’s manual for how to use the planet,” Bloch says. “As geologists and paleontologists, our job is to go through the pages of that user’s manual and read the instructions and look at the scenarios.” Bloch says there is evidence that climate models are not all on the money, but they are better than guessing. Finding which responses to climate change are more universal and which are more variable is key. The future, he says, is a new experiment. “We can refine our models, and how do we do that?” Bloch asks. “With science. “What I can say is the last time the Earth experienced such a rapid, large-scale climate event into territory like this, yes, some weird stuff happened,” Bloch says. “But one other thing that also happened is related to the origin of us. We can trace our origins down to that event, for what it’s worth.” Jonathan Bloch Curator of Vertebrate Paleontology jbloch@flmnh.ufl.edu
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FOOTPRINTS With their first steps, humans change landscapes and leave evidence behind By Cindy Spence
30  Spring/Summer 2017
Photography by Bernard Brzezinski and Kristin Grace
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limate change, ruling elites, stressed natural resources, sustainable development. The world of the ancient Maya was complex, with issues much like those today, says Kitty Emery, associate curator of environmental archaeology at the Florida Museum of Natural History. Modern societies have a romantic view of the past, thinking that people in ancient times lived lightly on the land, leaving it unharmed and unchanged. Not necessarily so, says Emery. During 5,000 years of the ancient Mayan civilization millions of people lived in an area of Mexico, Belize and Guatemala that still feels their impact, Emery says. Their human footprint – on the environment, climate and biodiversity – shows up in the evidence excavated from archaeological ruins. Some remains point to sustainable practices, such as terraforming and intensive cropping, but other remains indicate more negative impacts, such as deforestation and soil erosion. Today we call these human-caused effects anthropogenic, and we date the Anthropocene only to the Industrial Revolution. But for environmental archaeologists, the Anthropocene began a very long time ago. “As soon as people arrive on a landscape, they manipulate it both intentionally and unintentionally, to the extent that by the time we have historic records, the landscapes are completely changed and far from pristine,” Emery says. “There are a lot of arguments about when the
Bones are used to answer questions about dog domestication, such as how dogs were used and how early they were bred. The bones here are Canis lupus familiaris from about 300 AD.
Anthropocene starts, and people want to put it at earliest industrialization, but this is absolutely not true.” Knowing what humans have done in the past is important for conservation. Restoring a habitat to a pristine, or more natural, condition requires a definition that is complicated, Emery says. What is pristine? What is natural? If the target time period is in the last several thousand years it might seem humans have had little impact, but the evidence is underfoot that they have. Is pristine before or after a landscape was farmed or burned? Is it before intense hunting pressures — or domestication — that changed the evolution of species in a habitat? Once humans set change in motion in a landscape, the path of evolution changes, everything changes. And environmental archaeologists can trace it through time.
Bags of Bones Environmental archaeology owes its strong roots at the University of Florida to the pioneering work on archaeological animal remains — zooarchaeology — by Curator Emeritus and National Academy of Sciences Scholar Elizabeth Wing, now 80. Wing is known as the grandmother of environmental archaeology and one book traces the discipline’s southeastern roots to Wing’s dissertation, completed at UF in 1962. The zooarchaeology comparative collection she built became the foundation for her own work and the work of generations of students. Explore 31
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Irv Quitmyer
Wing spent summers as a student at the Museum of Comparative Zoology at Harvard and brought that rigorous training with her to UF. She worked hand in hand with archaeologists, who were glad to bring her any animal remains they unearthed. The faunal remains became a rich source of scientific investigation, and her detailed 1981 work on the Mayan diet was seminal to modern studies of the ancient Maya. Early on, Wing says, it was common for archaeologists in search of human artifacts like pottery to set aside animal bones and shells, sometimes examined, sometimes not. Wing says she was content to let the archaeologists do the digging and date the strata, leaving the animal remains to her. She would compare the excavated remains to modern examples in the museum’s collection or the collections of other museums to answer questions about species that co-existed with humans: how they were used and how that use changed over the years. “The archaeologists wanted to work on the pottery, so they put the bags of animal remains on the shelf at the back of the room. Those bags of bones were there to be worked on,” Wing says. “I thought, ‘Well, there’s something to be discovered by working on those,’ so that’s what I proceeded to do. Besides it’s fun to look at them.” Whole skeletons are diagnostic, she says: How large was the animal, how was it butchered? “Was that dog really lazy, or did she work hard,” Wing says. “You can tell from the joints.” In those early days, when Wing received whole animals that needed to be turned into skeletons, she used the roof of the museum to macerate
The archaeologists wanted to work on the pottery, so they put the bags of animal remains on the shelf at the back of the room. Those bags of bones were there to be worked on. — Elizabeth Wing
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Elizabeth Wing built the environmental archaeology program at UF and served as a valued mentor for generations of students.
the flesh, so the odor of rotting flesh That impact also varied between would drift away on the breeze. For coastal areas, which could rely on smaller specimens, she used her yard inland crops and hunting, and on Bivens Arm in south Gainesville, islands, which were more reliant on weighting the body with a large stone fishing. and letting nature take its course. Wing realized that plant remains, Today, such preparations are done in too, were important, to tell a a special off-site facility. complete story of human diet. Animals also reveal information “You can point to when corn was about humans: What did they eat, first used, or other crop materials, and how did their diets change, did they that goes right together with the use of hunt some animals and domestithe animals for meat,” Wing says. cate others, did they use resources Wing’s work with animal remains sustainably? helped paint a more textured picture The sustainability of fisheries is a of human culture. hot topic today, but Wing was among “That’s the purpose of archaeothe early scientists to note stress on logical research,” Wing says. “What fisheries. Human impact on fisheries, were they up to?” she says, is ancient. “She had a lot of this kind of data even before fisheries people began to put out their publications on overharvest of fisheries,” Emery says. “She was using zooarchaeological data to show that not only did the species change over time, but so Alligator gar from the comparative collections. did the size of those These big fish were a common food species species; individual fish for native people of southeastern got smaller and smaller.” North America.
Complex Mayans Emery says the museum’s environmental archaeology program is carrying on the thread of Wing’s work and adding to it by looking at social, economic and political patterns and interpreting the past through combined studies of animal and plant remains and soils. The animal bones found in Mayan archaeological ruins, Emery says, reveal a society as stratified as today’s. Animals were a resource, and access to that resource depended on social class. At most sites, the ruling elites had plenty of jaguar skins and exotic species, symbols of their lavish lifestyles and wealth, and plenty to eat. Although there is evidence all classes had access to white-tailed deer, the elite got the best cuts. “Similar to today, there were limited resources,” says Emery, who, in one recent study, worked with doctoral student Ashley Sharpe to examine almost 25,000 bones from the museum’s collection of Central American animal remains, one of the largest outside that region. In that study, the appearance in inland capitals of animal resources available only near rivers indicates the elites were able to compel lower-class inhabitants living near those rivers to provide them. In another study, combining evidence from plant, animal, and soil remains from archaeological sites in Guatemala, Emery and Williams College colleague Antonia Foias have shown that the middle- and lower-status residents provisioned the royal elite not only with corn and other agricultural crops, but with ritually important animals, and the cacao used in most elite political and religious ceremonies. In return, these
residents may have been feted in feasts held by the elite in the plazas of the capital city. The ancient bones also tell a story of decline. The Mayans deforested on a wide scale to build their cities, and overhunted, too, to the point that bones of large game species like whitetailed deer become less and less common in the ancient garbage dumps at certain sites. Emery says she wanted to determine when the society’s decisions started to go bad, and in a large regional study of remains from 25 archaeological sites, found that harvest of large mammals only declined in proximity to large cities with extensive, politically dominant hierarchies. Farmers and hunters of the past understood sustainable practices just as they do today, but they did not use them when pressured by their allegiance to royalty and the need to pay taxes and tithes. At these dominant sites, Emery suggests, resource decisions were being made by politicians, who were removed from the initial environmental impacts. “We still don’t think of early societies as having the same complexities, the same impacts that we have,” Emery says. “Yes, we have bigger machines, putting out stinkier stuff, but the early societies were still forced by the
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As soon as people arrive on a landscape, they manipulate it both intentionally and unintentionally, to the extent that by the time we have historic records, the landscapes are completely changed and far from pristine. — Kitty Emery
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same social conditions, the same needs and considerations that we would recognize when they made decisions that impacted their fauna and their environment.” Kitty Emery Associate Curator of Environmental Archaeology kemery@flmnh.ufl.edu
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Night Vision The McGuire Center for Lepidoptera and Biodiversity expands knowledge of butterflies and moths By Cindy Spence
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hen night falls, it’s time to go to work, says Akito Kawahara. “The night is where it’s at,” says Kawahara, an assistant curator for the McGuire Center for Lepidoptera and Biodiversity in the Florida Museum of Natural History. “As scientists, we try to tackle questions we can answer, and until now, that’s primarily been what we can see. But there’s also the night that we cannot see very well, and so much is happening then.” The scientific bias toward daylight, he says, has left darkness somewhat unexplored. Part of the reason is that the nocturnal world can be challenging for conducting research. It is difficult for humans to see and the sounds that organisms make at night are often at a frequency too high for humans to hear. Studying night life in an ecosystem often required clunky equipment so disruptive that it altered the very behavior of an organism a scientist might want to observe. Much of that equipment — high-powered cameras with night lenses, hypersensitive microphones, and laptops — now fits in a backpack or two, and that has opened up the world of night to scientific inquiry on a scale not seen before, Kawahara says. Kawahara began working in that world on ultrasound, trying to characterize the sounds moths make, and through that process theorized that moths make an “anti-bat” ultrasound. To test the theory, Kawahara
teamed up with Jesse Barber, a bat researcher at Boise State University, and went to Malaysia, Mozambique, Borneo, Ecuador and other locations, trekking into the dark to study the predator-prey interactions of bats and moths. They found that moths are not always an easy dinner for bats. Over millions of years, many moths, hawkmoths among them, have evolved to produce ultrasound to jam the sonar of the attacking bats, an effective escape maneuver. Bats hunt with echolocation, sending out ultrasonic sounds that echo off a target and give a bat enough information to zoom in for the kill. Hawkmoths, it turns out, can jam bat sonar, and they do it by using their genitalia. “Twenty years ago, we never could have discovered this in the way we did,” Kawahara says. “We took our equipment to Borneo, did our experiments in the field, and expanded our organismal, biological knowledge.” Kawahara and Barber have discovered that many different moth families use anti-predator ultrasound as a defense mechanism, leaving the next step in the evolutionary arms race up to bats. “Human beings can’t hear this high frequency, so we often don’t think about it, but the night sky is extremely loud,” Kawahara says. “All kinds of interactions are happening. We’ve known this for a long time, but the technology was not there, so we couldn’t study it well. Technology and knowledge are coming together.” Hawkmoth
Photography by Kristen Grace
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Butterfly Net The McGuire Center holds one of the world’s largest butterfly collections. With a strong research emphasis, the center has collaborators on nearly every continent. Recently, the National Science Foundation funded two grants. In one project, Kawahara and museum informatics curator Robert Guralnick are using a $2.5 million grant to create ButterflyNet to study the evolution of nearly all butterfly species by sequencing their DNA and collecting trait data. The goal, Kawahara says, is to build an extensive database of butterfly knowledge for each of the approximately 18,000 species: host plants, distribution, conservation status, and
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If we don’t have a family tree to know which species are closely related, we don’t have good ways of conserving a species that is endangered. — Akito Kawahara
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especially DNA. In the other project, with Associate Curator Jaret Daniels, a $3.3 million grant is supporting the digitization of nearly all North American butterfly and moth specimens in the McGuire Center to capture specimen label data for studies on how butterflies and moths are influenced by changing climate. One of the fundamental things scientists still don’t understand is how butterfly species are all related. Getting DNA from each species and using it to construct a family tree can paint a picture of evolution and help with butterfly conservation. “If we don’t have a family tree to know which species are closely related, we don’t have good ways of conserving a species that is endangered,” Kawahara says. A family tree can be useful, for example, if a species is endangered and its host plant is unknown. In that case, a researcher can look at the closest relatives to find likely candidates for host plants. Knowing genetic relationships can also help in cases where a species has not been collected in a long time; knowing close relatives can help target the habitat to search. Kawahara says butterflies and moths are also very sensitive to change, making them important early indicators of disrupted habitats. Some
species, he says, are used to assess the condition of forests, for example. “Some species are acutely sensitive to temperature, and if butterflies and moths start to decline, they can serve as indicators of an impact on a landscape or climate change,” Kawahara says. “We regularly see many examples of butterflies changing their distributions in response to climate change. Butterflies from warmer climates are moving northward,” Kawahara says. Butterfly collections document habitats where nothing has been built and nothing has changed – national parks, for instance – but the butterflies are vanishing. “The one thing that has changed, fairly significantly, is the temperature on mountaintops,” Kawahara says, “and the butterflies are disappearing.”
Moths Matter Kawahara’s relationship with butterflies goes back to childhood trips in Japan with his father. He caught his first butterfly, a snout butterfly, at the age of 4. Soon after, his father bought him a butterfly net, which focused his attention keenly on each butterfly. “That net was a big deal. Whatever falls into the net, you end up
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Everybody that studies butterflies in the world knows about this place. There’s no other place like this. — Akito Kawahara
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Sphinx Moths
looking at. We need to get our kids to use butterfly nets to study the nature around them,” Kawahara says. A couple of years later, his father walked into a shop in Tokyo and bought a field guide on butterflies, complete with dissections and diagrams in the back, sophisticated perhaps, but perfect for the 7-year-old lepidopterist in the making. “That book is really important to me,” Kawahara says. “I carried it everywhere. It opened the door to all this diversity. It wasn’t just this snout butterfly or the white butterflies in the garden, there were hundreds, thousands out there that I didn’t know about. “It opened the world of natural history,” says Kawahara, whose undergraduate thesis was on the snout butterfly. Kawahara describes college as “four years of just amazing, being around all these students all talking science,” and says it was there that he realized he could have more scientific impact studying the poorly understood moth than charismatic butterflies. Today in McGuire Hall, the newest museum building, there is room to grow, and Kawahara gets calls almost weekly from people who want to donate collections.
Collectors, he says, don’t want their specimens to disappear into a museum drawer; they want them to be used by students and researchers, and the McGuire Center’s collection fits the bill as the most used butterfly collection in the world. “Everybody that studies butterflies in the world knows about this place. There’s no other place like this,” Kawahara says. The collection is next door to the Butterfly Rainforest, a 6,400-squarefoot screened exhibit with 1,000 butterflies and moths at any one time. Sometimes, when he needs peace to write, Kawahara sets up his laptop on one of the benches. At dusk in the Butterfly Rainforest, the butterflies retire for the evening and the moths take the night shift. More moths pollinate flowers than butterflies, Kawahara says, and pollination has its own pattern, with some moths flying from 10 to 11 p.m. and others from 3 to 5 a.m., according to their own internal clocks. “Now we have the technology to see a world that we could not understand well in the past,” says Kawahara. “There’s a world we don’t know. It becomes night, and
we had often ignored what insects are doing. Some flowers only bloom at night. Why? Because the moths that fly at night are the ones pollinating them. It’s not bees, it’s not butterflies, it’s moths.” Science, in the night. Akito Kawahara Assistant Curator, McGuire Center for Lepidoptera and Biodiversity kawahara@flmnh.ufl.edu Related website: https://www.flmnh.ufl.edu/mcguire/home/
Luna Moth
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BBotany otany Abuzz Abuzz
Untangling Florida’s botanical family tree By Cindy Spence
Photography by Kristen Grace
A
rose is a rose is a rose. But is an Aster an Aster? Well, it depends. Globally, the plant world is in a tizzy, and that’s a good thing, says Kent Perkins, collections manager for the University of Florida Herbarium in the Florida Museum of Natural History. Plant evolution is robust just now; botanists are busy. This botanical bustle was touched off in the last decade or so by two developments: genetic sequencing of plant specimens and digitizing herbarium specimen images and data and putting that information online. Genetic testing jolted the orderly world of herbaria internationally. With DNA, it turns out that some species weren’t what they were thought to be at all. An Aster is an Aster perhaps only until the genome is sequenced, reclassifying the plant into 10 separate genera. Digital databases have amplified this effect. Put up a photo of a plant, an orchid, for instance, and suddenly experts begin debating: Is it what it appears to be? Does it belong on this branch of the family tree or another? Is there an evolutionary detour in the shape of the flower? Does it need a new name? Perkins goes to a cabinet and pulls out a specimen, carefully mounted on archival paper, its collection data meticulously recorded. First one name appears, then another, and another. For one orchid, Spiranthes x ichetuckneensis, there are a half dozen annotations, its name changing six times.
“Names are very unstable in a lot of plant groups,” Perkins says. “We’ve had things identified as one thing, and someone runs a DNA sequence and checks GenBank and finds it doesn’t match this plant, it matches that other plant.” Such experiences are so commonplace that many plant genera will take years to sort out — even as many others have not been described at all — but that makes collections like UF’s, at 470,000 specimens and counting, all the more important, Perkins says. “The changes in names reflect how vital botany is,” says Marc Frank, a Florida Cooperative Extension Service botanist and associate collection manager at the herbarium. “A lot of research is going on that is refining our knowledge of the relationship between all these different plants and their evolution.” Herbarium Keeper Norris Williams says his own specialty, orchids, demonstrates just what a vast Explore 39
undertaking plant taxonomy can be. The orchid family has more species than mammals, birds, reptiles and amphibians combined, with 28,000 orchids worldwide.
Science from the Specimens Florida is botanically rich — only two states have more species — and the herbarium is the repository of that richness. The herbarium has vouchers that document that a particular plant — or plant fossil or seed — existed in a particular place at a particular time. Using the vouchers, a scientist can study habitat, chemical composition, seasonal variation, morphology. A voucher can also be tied to DNA, for studies of plant evolution. Type specimens are important, too, because they serve as the standard for recognizing each plant species. The herbarium processes about 3,000 specimens into its collection each year, and just as plants are variable, so are collection data. Collecting a plant is more than just plucking it The collection of Civil War Gen. Edmund Kirby from a landscape. For the specimen to Smith, below, dates to the 1800s. It was donated be useful, the collector needs to note to the UF School of Pharmacy in 1932 and the location as precisely as possible, turned over to the Herbarium in 1972, when work began on restoring, preparing and catawhen it was collected, and as many loguing the collection. Much work remains on details as possible about the environthe mosses and lichens. ment: was it disturbed, what else was growing nearby? Sometimes a researcher who is just after molecular information is less attuned to label data, perhaps relying on GPS. “More than once I’ve typed the GPS coordinates into Google Earth only to find them in the middle of a lake,” Frank says. “There’s no way a pasture weed was growing in the middle of a lake; obviously, the GPS 40 Spring/Summer 2017
isn’t properly calibrated. GPS alone is not enough. You need descriptors, or intersections or landmarks, to allow someone to relocate the specimen if they need to.” Williams notes that the most useless location he ever encountered was on a pressed specimen labeled “Amtrop.” The collector might as well have left the specimen in the American tropics. The herbarium recently has been working on incorporating a donated collection from Angus Gholson. Gholson was a 1948 UF forestry graduate who went on to work as a land manager near the Jim Woodruff dam on the Apalachicola River, near Chattahoochee. His collection, about 18,000 specimens, is important because the watershed of the Apalachicola includes many rare and unusual species, some important in erosion control along the riverbanks. The Gholson collection, like all new arrivals, was quarantined for two weeks in a freezer at 0 degrees to be sure it was pest-free before taking its place in the herbarium. Another project, two years of collecting in UF’s Ordway-Swisher Biological Station, likely makes its nearly 10,000 acres among the best-documented chunks of Florida, with the addition of high-resolution field photographs. Ordway-Swisher is not immune to the botanical flux, Perkins notes, and he is braced for the day when a specimen is renamed and all the associated online records have to be changed, too. Getting everything online is a complicated workflow. In SERNEC, the Southeast Regional Network of Expertise and Collection, over 100 herbaria are represented, all with different standards for labels and
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A lot of research is going on that is refining our knowledge of the relationship between all these different plants and their evolution.
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–Marc Frank
data. Digitizing is an important window into collections worldwide and UF’s own, “but it may kill us in the process,” Perkins says wryly.
What is That? Besides research, the herbarium collections are used in a practical way, says Frank, who fields dozens of questions a week about plant identification. With plant names constantly changing, he uses the herbarium to keep up, identifying up to 1,000 plants a year for everyone from a curious homeowner to a professional land manager. “I don’t just know all those plants,” says Frank, noting that about 4,300 plants are native or naturalized in Florida and another 10,000 are cultivated here. “I have the herbarium as my reference.” For land managers, invasive species are a key concern. Frank uses herbarium records to understand the history of a plant’s introduction to Florida and the rate and extent of its spread. On all agricultural fronts in Florida — citrus, pasture, turf grass, ornamentals, aquaculture — invasive plants have a huge impact, Frank says. To find out how quickly an invasive plant is spreading, botanists
From left, Marc Frank, Norris Williams and Kent Perkins.
rely on herbarium voucher specimens and field observations. The herbarium also has digitized Florida’s endangered and threatened plants. The Florida Department of Agriculture and Consumer Services lists 542 Florida native plants as threatened, endangered or commercially exploited (61 are also federally listed). The ability to identify and recognize these plants is the key to discovering them in the landscape and then protecting them. Endangered species can only be collected under permit, so the herbarium specimens become more precious over time. Other collections include insectivorous plants and selected poisonous plants, which prompt a few calls each year, says Frank, who works with Florida Poison Control in his public outreach role. Explore 41
Eric Zamora
Norris Williams moved to Florida and became a world-renowned expert on orchids. He does not grow them; there is beauty enough in their pollination systems.
“A lot of times people want to know if a plant is something they can eat,” Frank says, “but you’d be surprised how often someone calls to find out about a plant after they’ve eaten it or fed it to their family.” Florida’s oleanders, beautiful and poisonous, prompted the strangest request from the public. “Decades ago, we had a woman writing us from California,” Perkins says. “She was in prison for poisoning her husband with oleander and she was trying to get us to help her get off the hook somehow.”
Heading South A chance encounter on a Friday afternoon in graduate school sent Williams to Florida. He was a student at Washington University in St. Louis, sharing a beer with some classmates, when they recommended a tropical ecology class. His interest piqued, Williams took it, and he was smitten, particularly by the orchids. “Orchids were a lot more interesting than what I was working on,” Williams says, “which was algae.” Williams moved to Florida and became a world-renowned expert on orchids. He does not grow them; there is beauty enough in their
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pollination systems. In 1981, he became the keeper of the herbarium. In 1997, when the herbarium moved from Rolfs Hall — out of the bay window on a lift, since there was no elevator — Williams figured the space would last 20 years. “Ten years after we moved, we were nearly full,” Williams says. Initially, the environmental conditions caused issues with beetles, book lice and mold, so a new air conditioning unit was installed just for the herbarium, keeping a constant 68 degrees and 45 percent humidity, perfect for the herbarium but not for every other collection. The unit was so expensive, Williams and Perkins figure they are in place in Dickinson Hall for a while, nipping and tucking to find more space. Even in the cool air, aromas remain. The collection has specimens that date back to 1840, obtained in a trade with the British Museum, and when the older cabinets are opened, the scent of mothballs drifts out, even though mothballs are no longer used for pest control. The mint collection smells sweet, viburnum like dirty socks. “Someone had valerian out the other day, and for a minute I
thought ‘What is that awful smell,’” Perkins says. Wood specimens are part of the collection, too, orderly blocks in rows in drawers. Williams says he knew a UF graduate student who had a piece of charcoal she could not identify, so she sent it to the Smithsonian. The Smithsonian sent it to the U.S. Forest Service’s lab in Madison, Wisc. There, they shipped it back to UF. “They told her they send all charcoal specimens to the University of Florida,” Williams says, noting that UF has the fifth largest wood collection in the U.S. Lesson learned: check the home herbarium first. Botany may be bustling, but the UF herbarium is keeping pace. Norris Williams Keeper of the Herbarium orchid@flmnh.ufl.edu Kent Perkins Collections Manager kperkins@flmnh.ufl.edu Marc Frank Associate Collections Manager and Extension Botanist mfrank@flmnh.ufl.edu
Montbrook
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Fossil finds reveal clues to an ancient Florida era
Photography by Jeff Gage
t’s not uncommon for Florida Museum paleontologists to get calls about fossils. But a call in 2015 from a Levy County landowner about bones discovered on his property led to a bustling dig with valuable finds. Museum paleontologists say the Montbrook dig is the first evidence in North Florida of fossils from the late Hemphillian land mammal age, about 5 million years ago. The site, once an ancient coastal river, has hosted hundreds of volunteers and yielded so many fossils that it is on the verge of a third dig season. Vertebrate paleontology collections manager Richard Hulbert says many of the finds are notable. Among them: • The first known skull of Rhizosmilodon fiteae, the leopard-sized ancestor of the tiger-sized sabertoothed cat of the Ice Age, Smilodon.
• Tens of thousands of fossils of fresh-water reptiles, amphibians, and fish, including multiple skeletons of an early population of Alligator mississippiensis and new species of snapping and soft-shelled turtles. • About 15 individuals of the four-tusked, elephantrelative Rhynchotherium, ranging in age from young babies to old adults. • About 50 fossils of rare bird bones from large swans and condor to a small quail. Like other volunteers, Sheila Lucas says she likes the novelty of working the digs. “When I find a fossil, I’m the first human being to lay eyes on this amazing creature that roamed around millions of years ago.”
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