Julianne Beck – Page 6 – My Chicago Botanic Garden

Genomic Discovery Unearths New Theories on Plant Evolution

There’s less mystery in the natural history of aquatic green algae and its relationship to land plants, thanks to research co-led by Chicago Botanic Garden scientist Norm Wickett, Ph.D., published this week in the Proceedings of the National Academy of Sciences and GigaScience.

The study examined how major forms of land plants are related to each other and to aquatic green algae, casting some uncertainty on prior theories while developing tools to make use of advanced DNA sequencing technologies in biodiversity research.

“We have known for quite some time that all plants on land share a common ancestor with green algae, but there has been some debate as to what form of algae is the closest relative, and how some of the major groups of land plants are related to each other,” explained Dr. Wickett, conservation scientist in genomics and bioinformatics.

Over the past four years, he has collaborated with an international team of researchers on the study that gathered an enormous amount of genetic data on 103 plants and developed the computer-based tools needed to process all of that information.

The study is the first piece of the One Thousand Plants (1KP) research partnership initiated by researchers at the University of Alberta and BGI-Shenzhen, with funding provided by many organizations including the iPlant Collaborative at the University of Arizona (through the National Science Foundation), the Texas Advanced Computing Center, Compute-Calcul Canada, and the China National GeneBank. The results released this week were based on an examination of a strategically selected group of the more than 1,000 plants in the initiative.

Researchers dove into the genetic data at a fine level of detail, looking deeply at each plant’s transcriptome (the type of data generated for this study), which represents those pieces of DNA that are responsible for essential biological functions at the cellular level. In all, they selected 852 genes to identify patterns that reflect how species are related.

The study is consistent with ideas and motivations that parallel research Wickett is pursuing in work funded by the National Science Foundation program called “Assembling the Tree of Life.” Both studies seek to better understand how the earliest land plants that first appeared more than 460 million years ago evolved from green algae to yield the diversity of plants we know today.

DIAGRAM: Land plant tree of life. — The “land plant tree of life”

Understanding those lineages, Wickett explained, allows scientists to make better-informed decisions in their research pursuits, and illuminates historical environmental conditions that may have impacted evolution. “Knowing that set of relationships offers a foundation for all evolutionary studies about land plants,” he said.

Using Bioinformatics to Better Understand Our World

Wickett’s expertise in a field of science called bioinformatics allowed him to serve as one of the leaders in the data analysis process, which relied on a set of tools developed by the research team. Using those tools, Wickett helped develop the workflow for a large part of the 1KP study. “The tools we have developed through this project are able to scale up to bigger data sets,” he said. This is significant because “the more data you have, the more power you have to correctly identify those close relatives or relationships.”

By working with a large amount of data, explained Wickett, the team was able to resolve patterns that were previously unsupported. Until recently, the scientific community has largely believed that land plants are more closely related one of two different lineages of algae—the order Charales or the order Coleochaetales, which share complex structures and life cycle characteristics with land plants. However, the study reinforced, with strong statistical support, recent work that has shown that land plants are actually more closely related to a much less complex group of freshwater algae classified as Zygnematophyceae.

A Simpler Ancestor

It may mean that the ancestor of all land plants was an alga with a relatively simple growth form, like the Zygnematophycean algae, according to Wickett. More than 500 million years ago, that ancestral species split into two new species; one became a more complex version that colonized the land, and the other continued on to become the Zygnematophyceae we know today. The unique direction of both species was likely influenced by environmental conditions at the time, and this study may suggest that evolution could have reduced complexity in the ancient group that formed what we now recognize as Zygnematophyceae.

“Our new paper suggests that the order of events of early land plant evolution may have been different than what we thought previously,” said Wickett. “That order of events informs how scientists interpret when and how certain characteristics or processes, like desiccation tolerance, came to be; our results may lead to subtle differences in how scientists group mosses, liverworts, and hornworts, the lineage of plants (bryophytes) that descended from the earliest land plants.”

Wickett can’t help but feel encouraged by the wave of enthusiasm around the release of the publication. “When you get involved in these kinds of projects, it never seems as big as it is—you just get used to the scale. It’s been really great to get the public reaction and to see that people are really excited about it,” he said.

PHOTO: Norman Wickett, Ph.D. — Norman Wickett, Ph.D.

Where We Go from Here

Wickett will convene with the research team in January in San Diego to discuss next steps for 1KP, which will lead to the analysis of some 1,300 species. The team will likely break into subgroups to focus on sets of plants that share characteristics such as whether they produce flowers or cones, or have a high level of drought tolerance.

With the publication of this research, a door to the past has been cast wide open, offering untold access to natural events spanning some 500 million years. After such significant discovery it’s hard to imagine that there could be more in the wings. But with the volume of data generated by the 1KP project, there are certainly exciting results yet to come.

Clicking Through Time

In 1860s New Hampshire, botanical artist Ellen Robbins perched before her canvas, creating wildly popular watercolors of fall leaves. Books of her paintings sold well, landing in the hands of high society members such as fellow artist Gertrude Graves, a cousin of poet Emily Dickinson. Graves presented her copy of one such volume, Autumnal Leaves, to the Massachusetts Horticultural Society in 1923, where it remained until being acquired by the Chicago Botanic Garden in 2002. Today, the historic, storied volume is accessible to us all via a visually crisp, easily navigated online library.

ILLUSTRATION: autumnal leaves. — Selection from *Autumnal Leaves* by Ellen Robbins

Autumnal Leaves is one of the historic books, postcards, and similar materials digitized and conserved by the Garden in recent years and now accessible via the Internet.

“It just opens up the opportunities for more people to see the wonderful pieces that we have,” said Leora Siegel, director of the Garden’s Lenhardt Library, which was established by the Woman’s Board of the Chicago Horticultural Society in 1951.

The Lenhardt Library’s impressive collection includes materials dating from 1483 to 1917, which are now available online to an expanded audience.

“In this age of e-books, these primary resources are something different. They are something really important to our civilization and culture,” said Siegel, who is delighted to help the public, scientists, historians, and artists from around the world access the remarkable materials.

Publications originating in North America are predominant in the collection. Western European books that once resided in the private family libraries of dukes and earls are also included. In some cases, bookplates were traced back to their original owners.

“They were in private libraries and only the family could read them, and now they are on the web and anyone can get to them,” remarked Siegel. The international component of the digitized collection also includes ikebana illustrations from Japan.

These materials were part of a collection of some 2,000 rare books and 2,000 historic periodical titles collected by the Massachusetts Horticultural Society of Boston before being purchased by the Garden in 2002. Since that time, grants including a $172,000 award from the National Endowment for the Humanities in 2011, allowed the Garden to digitize 45 of the books that have traveled time and distance to reach us today.

What did South America’s tropical vegetation look like to illustrator Baron Alexander von Humboldt in the 1850s? How was the Horticultural Building portrayed in Chicago’s 1893 World’s Columbian Exposition?

The answers can be found in the preserved volumes and vintage postcards accessible via the Illinois Digital Archives and the Garden’s new digitized illustrations website, launched in September.

Front of advertising card showing the Horticultural Building at the 1893 Chicago World’s Fair, with inset of company logo.

Front of postcard showing a rowboat on a lake in front of the Horticultural Building at the World's Fair grounds in Chicago, 1934. — Front of postcard showing a rowboat on a lake in front of the Horticultural Building at the World’s Fair grounds in Chicago, 1934.

The new site houses illustrations from a significant number of titles and interpretive notes, and it is continuously updated with material. From books on grafting plants to postcards from flower shows, there is much to discover with cultural and scientific relevance.

ILLUSTRATION: Selection from Water-color Sketched of Plants of North America 1888 to 1910. — Selection from *Water-color Sketches of Plants of North America 1888 to 1910* by Helen Sharp, Volume 08

“The botanical illustrations come close to our herbarium specimens in many cases because you really see the roots and the life cycle of the plant,” noted Siegel.

The majority of materials were digitized offsite by the premier art conservation center in the United States, the Northeast Document Conservation Center. When the processed files arrive at the Garden, metadata is added by Garden librarian Christine Schmidt. She then adds the files to a software program that allows them to be accessed through either website. A volunteer photographer also contributes to the files. In the most recent set of 45 digitized volumes, 18 are currently being processed and prepared for the site.

While the rare books are still available by appointment to those who can make it into the library, many of the books are delicate and will benefit from an increased percentage of online viewing into the future.

ILLUSTRATION: Bookplate from "Physiognomy of Tropical Vegetation in South America" — Selection from *Physiognomy of Tropical Vegetation in South America: a series of views illustrating the primeval forests on the river Magdalena, and in the Andes of New Grenada*

Allowing access to these materials online has yielded many rewards for those who made it possible, from contributing to research around the world to the reproduction of selected images in new book publications, which is done with special permission from the Lenhardt Library.

“People are really blown away,” according to Siegel. Garden exhibitions have benefited from the collection as well, such as the winter Orchid Show exhibition, which was enhanced by complimentary full-text access to some of the rare books from the online portal.

Next, Siegel hopes to digitize the Garden’s collection of an estimated 20,000 pages of manuscripts of scientists’ field notes.

“We have some unique one-of-a-kind manuscripts that no one else has,” she said. “This is just the start.”

Home on the Prairie

A delicate prairie bush clover extends its pink flowers toward the sun, like an early settler attempting to plant a flag on a piece of land to call home. Competition for space is intense where the native herb stands on one of the state’s last remaining prairie landscapes, Nachusa Grasslands, located in north-central Illinois.

The species’ juvenile plants must establish themselves rapidly to avoid being overtaken by dominant native grasses, such as little bluestem. Even if the wispy young herbs live to maturity, they may still struggle to survive the often deadly wake of litter the grass leaves behind.

PHOTO: A view of Nachusa Grasslands taken from Dr. Vitt’s field site. — A view of Nachusa Grasslands taken from Dr. Vitt’s field site. Photo by Pati Vitt.

Chicago Botanic Garden conservation scientist Pati Vitt, Ph.D., has been studying the rivalry between the prairie bush clover and grass species at Nachusa over the past 14 years. Also the curator of the Dixon National Tallgrass Prairie Seed Bank, she has seen the herb species’ population rise and fall.

PHOTO: A tiny, spindly stalk of prairie bush clover in spring. — Prairie bush clover ( *Lespedeza leptostachya*) grows at Nachusa Grasslands.

In Illinois, Nachusa Grasslands is one of the few remaining places where prairie bush clover (Lespedeza leptostachya) can still be found. The issues it faces there are not unusual to the species.

“It is a unique component of this very small subset of North American grasslands that exist nowhere else,” said Dr. Vitt. “Its presence is an indicator of high-quality, well-managed gravel hill prairie. It serves to increase the biodiversity of those types of habitats.”

After years of working to define the ideal environment for the prairie bush clover and getting to know its adversaries, she feels it is time to bring in the big guys.

Bison, 2,000-pound behemoths that are naturally adapted to Midwest weather and vegetation, will soon be arriving to help save the tiny plant. The rust-colored creatures, standing up to 6½ feet tall at the shoulder, are rather particular grazers, explained Vitt. Unlike cows, which graze broadly and without much discretion, bison selectively eat grass. That makes them the perfect friend of the prairie bush clover, which, Vitt has documented, needs a little more room to grow on the limited rocky portion of the 3,000-acre prairie it calls home.

Vitt spent much of her summer at Nachusa, a preserve managed by the Nature Conservancy in Illinois. She was hustling to document the status of prairie bush clover populations there before the arrival of a herd of bison in the fall of 2015.

Little bluestem ( Schizachyrium scoparium ) is a native grass.

Each morning of research she and her team, which included an REU intern, fellow Garden scientist Kay Havens, Ph.D., and additional technicians, were out in the field at daybreak. They worked in teams of two to count and identify all of the plants associated with Lespedeza leptostachya in six plots where it grows. They also took soil samples and did nutrient analysis to measure elements such as nitrogen, phosphorous, and potassium. Lastly, they documented the slope of the land on which the prairie bush clover plants grew, and the aspect—the incline and direction at which they faced the sun. The team spent evenings at their temporary residence inspecting more challenging plants under a microscope to confirm the species identification. All of the data they gathered was recorded into GPS units and later downloaded into a database.

What did they find? Prairie bush clover performs best in soil that has 75 percent versus 82 to 89 percent sand, though all populations grow on soil with low organic matter. It suffers where levels of grass, and especially the litter the grass produces when it dies back each year, are high.

These findings support her research from previous years. Vitt studied the before-and-after status of the species during a one-year trial run with a cow as a grazer. She also investigated the impact of fire as a management tool.

“The more [grass] litter there is, the fewer seeds the [prairie bush clover] plants produce, which is both a function of size and probably nutrient status,” she explained. “Litter may not only serve to suppress the growth of the plant, but because it is carbon heavy it may actually decrease the available nitrogen in the soil.” One of the benefits of prairie bush clover, she theorizes, is that the healthy plants add nitrogen to the soil. That is an asset for surrounding plants.

A research plot where little bluestem is growing over smaller prairie bush clover plants. Photo by Pati Vitt.

When alternated with fire, grazing is a natural and effective management tool, noted Vitt. Fire, she explained, decreases the biomass of grass above soil, resulting in less grass litter. At the same time, it encourages new growth by stimulating meristems in the roots below the soil—areas where new cells are produced. After fire, said Vitt, clumps of grasses such as little bluestem (Schizachyrium scoparium) tend to be larger. However, when they are also grazed, those clumps are less dense, and therefore less discouraging to growth of the prairie bush clover.

Vitt has collected seeds on other prairies in the Midwest where bison have been present. “I’ve seen firsthand how bison graze, and I’ve seen the results of bison grazing versus cattle grazing,” she said. “When they [the Conservancy] decided that they were going to release the bison, for me that was very exciting. It’s kind of an affirmation of the work that I’ve done there, and that’s really great. I can see the benefits of the management and I have every reason to conclude that it’s going to increase the population viability of Lespedeza leptostachya.”

Bison will soon graze the vast prairie. Photo by Pati Vitt.

Vitt is back at the Garden now, sorting through the data she collected this summer and writing about her findings. These data are essential, she said, because she will be back to check on the prairie bush clover after the bison have settled in. She is also planning for future experiments, such as building habitat models for prairie bush clover using remote sensed data.

For a little plant that exists in only four states and is federally threatened, a hero can come in many forms.

The Team Behind the GardenGuide App

The secret is out; visitors to the Chicago Botanic Garden have unprecedented access to plant information, guides, and tours through a groundbreaking smartphone app, called GardenGuide, launched last year. Garden staff and volunteers used their skills and savvy to squeeze interactive maps, audio guides, points of interest, and botanic details on more than 10,000 plants into an application that sits in the palm of your hand. How did they do it, and what keeps the wheels turning?

Dorothy Peck, volunteer team leader at work. — Dorothy Peck, volunteer and team leader, at work

The ability to access this information in real time during a Garden visit is what makes the app so special, according to Boyce Tankersley, the Garden’s director of living plant documentation. He said that people “look down at the app, they see what they need to see, and then they are back to experiencing the Garden, just as we had hoped.” In addition, photos and plant information are frequently being added, so there is always something new to discover.

Before new data and photos were added to the plant collections database, Tankersley and his team upgraded their long-time plant collection’s database to include 37 new information fields that would work well with the app, from soil type to bloom time to sun requirements. Many of the fields were added as check boxes, to make them easier to sort through with the app. It was then that he recruited another 80 volunteers to help gather and enter all of that new information.

As the project progressed, a new team of highly specialized volunteers came together to help build the data that is shared via the app. A group of 20 volunteer photographers captured digital images to accompany each species listed, under the direction of their team leader, Dorothy Peck. A group of 12 volunteers, led by team leader Glenn Kohlmeyer, scanned plant information slides researched by Richard Hawke, the Garden’s plant evaluation manager. Under Tankerley’s watchful eye, another 20 volunteers researched and input key facts about the plants. Perhaps furthest under the radar, was the smallest group of volunteers who handled the intricacies of GIS mapping with guidance from Veronica Harry-Jackson, a Garden GIS specialist. “We wouldn’t be able to pull off a project like this without a lot of dedicated staff and volunteers,” said Tankersley.

“It was a Garden-wide project which was fantastic,”
said Van Deraa

The process to create the app began more than two years ago, when project manager Cheri Van Deraa, the Garden’s director of online marketing, assembled a team including representatives from different areas within the Garden. She led the initial step of researching similar products on the market and incorporating possible features. The list began with the Garden’s plant collections, and grew from there. The planning team considered a growing list of needs that visitors have when they come to the Garden, and included functions to address them. “The visitor needs we documented over time are now being met in this app,” said Tankersley.

Veronica Harry Jackson — Veronica Harry-Jackson with GIS equipment

“We wouldn’t be able to pull off a project like this without a lot of dedicated volunteers.”

“The basis of the app was the plant collections database, but we realized that people like to find other things at the Garden, so we created a new second database for the app. It has points of interest at the Garden, like water fountains, classrooms, sculpture, the location of the Japanese Garden, and more,” said Van Deraa. Once the two databases were polished, they were worked into the architecture and mapping system for the app software.

The GIS, or interactive mapping function, was also a critical component. Both Tankersley and Van Deraa saw tremendous value in offering the ability for a user to go from their Garden location to their desired destination. “We have a large campus and much to see,” said Van Deraa, who uses the app herself. “I just get a thrill every time I want to find a plant,” she said. “There was an iris I wanted to see in the spring, I dialed it in, and I could just walk right up to it. That was so cool.”

For those who are not sure what to look for, there is a feature called What’s in Bloom Highlights. The feature highlights plants in bloom twice each week, with a map that shows the visitor how to walk to them.

Additional functions that were built in include audio tours, walking tours, and Van Deraa’s, favorite—maps leading to ‘secret spots’ such as the quiet bench atop the Waterfall Garden where birds visit early in the morning. “The GardenGuide app was designed to deepen the visitor experience with the Garden,” said Van Deraa.

Gabriela Rocha and Sil Argentin — Gabriela Rocha and volunteer Sil Argentin

GardenGuide has been in use for nearly a year now, and updates are ongoing. In 2014, the app was awarded a Gold Trumpet by the Publicity Club of Chicago for distinguished achievement. Not resting on her laurels, though, Van Deraa has been focused on updating the software necessary to work with a new Android operating system, KitKat, which is now complete. The next version of the GardenGuide 2.0 is in the works.

Volunteers continue to take and add new photos, and research and input new pieces of information. “Because the Garden is constantly adding new plants to the collection, we are always adding new plants to the app,” said Tankersley. “In the long term, in effect this becomes a digital encyclopedia of plants.” Tankersley hopes to eventually add data on another 46,000 plants that have previously lived at the Garden and may one day return.

Users of the GardenGuide app can be assured that the information in the app has been updated with care by a remarkable team of volunteers and professionals working together.

It’s all there, in the palm of your hand, just waiting to be tapped.

This project was made possible in part by the Institute of Museum and Library Services (grant #MA-04-11-0101-11).

Turning the Pages

Historical depth and futuristic innovation meet in the Lenhardt Library and Lenhardt Plant Science Library.

PHOTO: Rare book exhibitions are displayed at the entrance to the library. — Rare book exhibitions are displayed at the entrance to the Lenhardt Library.

Led by director Leora Siegel, the comprehensive library facility houses rare books dating back to the 1400s. The library also serves as a portal to a nearly unlimited amount of scientific information in the digital realm. It’s a resource for staff researchers, students, interns, and citizen scientists alike. Beneath the quiet of the library shelves, there is an ever-present forward movement. “Everything that we do here is about providing information to anyone who needs it,” said Siegel. “Our scientists who are out there in the forefront and publishing have the library behind them to get needed information.”

The library was recently named one of the newest contributors to the Biodiversity Heritage Library, an open-access, digitized collaboration of leading garden and scientific libraries nationwide. The move allows the Chicago Botanic Garden to share digitized materials unique to its collection with the broader research community. Together with other contributing institutions, the Garden is “trying to make biodiversity literature available for everyone around the world, especially in places where they do not have physical libraries,” explained Siegel.

PHOTO: A view into the research and storage shelves at the Plant Conservation Science Center. — Research-specific collections reside in the Plant Science Center.

The Biodiversity Heritage Library collection is a resource long accessed by Garden scientists, in addition to a multitude of books, digitized journals, and databases available through the Lenhardt Library and Lenhardt Plant Science Library. The comprehensive resources allow scientists to dig deeply into subject matter; for example, accessing journal articles from the early days of a publication to the most recent edition. This is critical to their work, according to Siegel, who explained that current research must always reference early work on related material, and build upon subsequent research leading to current theories.

The library facility, which was founded by the Woman’s Board of the Chicago Horticultural Society in 1951, predates the physical structure in which it now sits, the Regenstein Center. The Lenhardt Plant Science Library is a research-specific facility in the Daniel F. and Ada L. Rice Plant Conservation Science Center. It is not open to the public, but is used by Garden scientists.

One of Siegel’s favorite science books is Seeds: Ecology, Biogeography, and Evolution of Dormancy and Germination, which is housed in the Lenhardt Plant Science Library.

Leora Siegel directs the Garden’s libraries.

Siegel has been managing this tremendous resource for more than ten years. To her, it was a natural path from her childhood in New York where her love of plants began. She went on to pursue advanced degrees in biology and library science. “My worlds align in working here,” she reflected. “This is a great institution.”

Perhaps one of her favorite elements is the Rare Book Collection, which can be seen during special tours. “It’s just magical to touch a book from 1483,” she noted. “Sharing it with someone is just a pleasure.” The Rare Book Collection includes original materials published by Carolus Linnaeaus, who changed the way we understand the natural world, and who established binomial nomenclature. A bronze statue of Linnaeus anchors the Heritage Garden near the Regenstein Center.

In summer, Siegel often passes by the statue on her way to her favorite display garden—Evening Island. On cooler days, she enriches her day with a walk through the Greenhouses.