Archives For Julianne Beck

Unfolding the Mysteries of the Ravines

Undercover Science

Julianne Beck —  March 29, 2015 — Leave a comment

Standing guard along the western shore of Lake Michigan, the ravines are a naturally engineered filtration system from land to water.

Curving up from the flat lands of Illinois and arching alongside the coast into Wisconsin, their hills and valleys are filled with an abundance of foliage, plants, and animal life unlike any other ecosystem in the Chicago Wilderness region. Among other benefits, they help to filter rainwater. Rare plants, migratory birds, remnant woodlands, and fish are a part of this shadowed world that has long been entrenched in mystery for local residents and scientists alike.

As urbanization, erosion, increasingly intense weather events, and invasive plants begin to peel away at the perimeter of the ravines, it has become increasingly urgent for us to unwrap those mysteries and help protect the system that has long protected us.

New volunteers are welcome to dig in this spring and summer. Register to begin by attending a new volunteer workshop.

Volunteers and staff sample vegetation along a bluff transect at Openlands Lakeshore Preserve.

Volunteers and staff sample vegetation along a bluff transect at Openlands Lakeshore Preserve.

“The ravines are one of Illinois’s last natural drainage systems to the lake,” said Rachel Goad, manager of the Chicago Botanic Garden’s Plants of Concern program. “They are delicate landscapes. It can be challenging to get in to them. It can be challenging to move around on the steep slopes.” Those challenges have not deterred Goad and a team of citizen scientists from digging in to look for solutions.

For 15 years, the many contributors to Plants of Concern have been collecting data in the ravines, with a particular focus on the rare plant species that can be found there. The data, now quite valuable due to its longevity, is a treasure chest for land managers and others who are trying to better understand the system and how to save it.

Goad and her team are now in the final stages of testing a vegetation assessment connected to a virtual field guide for the ravines. She hopes it will be completed by the end of this year. Its purpose is to serve as a resource for ravine restoration and management long term. The plant-focused sampling method, called a rapid assessment, is the third piece of a larger ravine-management toolkit that includes a way to evaluate erosion and stream invertebrates considered to be indicator species. The toolkit has been assembled by Plants of Concern and partner organizations in recent years.

“The idea is that a land manager or landowner could pull these tools off of the Internet—there would be data sheets and an explanation for how to use them, and these resources would provide a practical, tangible way for people to better understand the ravines,” explained Goad. She and her volunteers will test the protocol this summer, as they meander through the ravines with their notebooks, cameras, and GPS mapping equipment in hand. What they learn could benefit managers trying to determine whether to focus on vegetation management or restoring the stability of a ravine, for example. The toolkit, according to Goad, “is complementary to restoration and understanding these plant communities.”

The data, however, is only one piece of the solution. Goad believes the connections people make when monitoring the ravines are what will impress upon them the significance and urgency of the issue. Her goals are to create connections between people and their local natural communities, and to engage a more diverse representation of volunteers in the program.

“What Plants of Concern is doing is engaging local citizens, introducing them to ravines, and getting them interested in what’s happening in these mysterious V-shaped valleys around them,” said Goad.

In all, Plants of Concern monitors 288 species across 1170 populations in 15 counties, covering 13 habitat types.

Rachel Goad monitors rare plants in a ravine.

Rachel Goad monitors rare plants in a ravine.

Goad hopes that by growing connections between these ravines and those who live nearby, she can increase the chances that this system will continue to protect rare plant species and one of the largest sources of drinking water in the world. As a recent recipient of a Toyota TogetherGreen Fellowship, administered by Audubon, Goad is intent on better understanding how to build such connections.

“We are working to make connections between monitoring and stewardship,” she said. “Monitoring can be a transformative experience.” Once a volunteer is in the field, navigating the terrain and gaining familiarity, they learn to see existing threats, such as encroachment by invasive species. Documenting these threats is important, but can feel disempowering if they’re not being addressed. Goad wants to show volunteers that there is something that can be done about the problems they encounter, and build a proactive understanding of conservation. “I believe in citizen science, which is the idea that anybody can do science and get involved in research,” she said.

Goad stepped in as manager of Plants of Concern just last year, after earning her master’s degree. It was like returning home in some ways, as she had previously helped to manage natural areas at the Garden.

In part because of that initial experience, “I knew I wanted to work in plant conservation,” she said. “It felt pretty perfect to get to come back and work with Plants of Concern. It’s an amazing experience to live in Chicago and to be able to work in some of the most beautiful natural areas in the region.”

Early spring ephemerals in bloom on a ravine bluff.

Early spring ephemerals bloom on a ravine bluff.

Plants of Concern has been a mainstay at the Garden for 15 years, dispatching committed volunteers to the ravines and other key locations across the Chicago Wilderness region to monitor and collect data on endangered, threatened, and rare species. The mounting data collected by the program is often used as baseline information for shifting or struggling species, and is shared with land managers. Through special projects, such as with one of the Garden’s recent REU interns, they have also contributed to habitat suitability modeling for rare species.


©2015 Chicago Botanic Garden and my.chicagobotanic.org

Mapping the Future of the Wild West

Undercover Science

Julianne Beck —  March 6, 2015 — Leave a comment

Silvery-green sagebrush cascades over the canyons of the Great Plains and Great Basin in numbers that would strike envy into the hearts of most rare and endangered plants. The abundant species keeps the wheels turning in a system where struggling plant and animal species rely on it for life-sustaining benefits.

As the climate changes and brings new rainfall levels and other environmental conditions, will this important species transition to new locations? What are the potential consequences for its current neighbors? These questions concern Shannon Still, Ph.D., postdoctoral research associate at the Chicago Botanic Garden.

PHOTO: Dr. Shannon Still looks over the area of his research.

Dr. Still looks over the area of his research.

“Sagebrush is a very big part of the ecosystem in the West, and we need to see what is going to happen,” said Dr. Still. “It’s a workhorse species that is important for pygmy rabbits, sage grouse, and mice that live around it, and it helps to stabilize soils.”

Still made several trips into states including Colorado, Wyoming, Idaho, and Nevada in 2014 to investigate the likelihood of such a transformation and to help prepare land managers for the potential results. “When a climate changes, species often shift their location within it,” he explained. When that species has already become an integral part in the lives of its neighbors, it can mean a ripple of changes across the entire system.

It’s All About That Brush

PHOTO: Wyoming big sagebrush, the focus of the study.

Wyoming big sagebrush (Artemisia tridentata Nutt. ssp. wyomingensis), the focus of the study

Standing in a thicket of Wyoming big sagebrush (Artemisia tridentata Nutt. ssp. wyomingensis), the focus species of his study, Still reaches into a 3-foot tall plant with his Felco 8 pruners to take a sample. (He’ll later send this sample to his collaborator in Utah who will confirm the subspecies identification through a genetic test.)

Still plots the location of the plant with his GPS unit, which he also uses to track his route through the dusty wilderness in the Garden research vehicle. He snaps a few photos for visual reference and makes notes in his computer tablet before moving on to the next site.

There are millions of plants out there now, Still estimates. So, he strategically collects information from 150 key locations during multiple visits. He then returns to the Garden to add the new information to his database, which also holds data from herbaria records he collected earlier.

At his desk in the Garden, he inputs new data. He then uses a software workflow he built himself to compare a map of the plants with a map of how the climate will look in those locations in future years. He runs models that overlay one map on top of the other to see where climate shifts will occur in the current species range. This allows him to predict where Wyoming big sagebrush will continue to prosper, and where it may disappear due to a lack of rain, too much rain, or temperature shifts, for example.

Staking a Claim

Still is excited about the ability of the software to provide climate-related analysis on sagebrush and other species. In fact, it’s the second study he has run with the program in the last two years since it was developed, using specialized algorithms for each.

PHOTO: Chicago Botanic Garden research vehicle parked in the field.

Colorado Rockies in the background; research subjects all around

First, he developed the software workflow to better understand how more than 500 rare species in the same western region might fare in the future if their environmental conditions change as predicted, and to which changes they are most vulnerable. The study results are like a crystal ball for land managers, identifying which species are most urgently in need of their care. The three-year investigation will come to a close in late 2015.

Already, both studies have received attention, with publications in the January issue of Nature Areas Journal authored by Still and his collaborators.

Still’s initial findings reveal that the Wyoming big sagebrush species already appears to be shifting. An anticipated increase in precipitation in the Great Plains and a drier climate in the Great Basin may lead to a contraction of the species into a smaller range, he explained. “By 2050, models show that 39 percent of the current climate for Wyoming big sagebrush will be lost.”

Still hopes that by identifying locations where sagebrush may fail to thrive, land managers can immediately focus on restoring areas that will continue to be suitable for the species long term.

PHOTO: Sagebrush in the canyon.

Sagebrush population in the canyon

“We don’t expect sagebrush to go extinct,” said Still. “But we may lose plants in areas where we don’t want to lose them, or more rapidly than we hoped. That could lead to more erosion or the loss of suitable habitat.”

Always moving forward, Still is continuing to work with the data, now adding details about plant locations such as the slope of the land and the direction they face. With those details, he will run new models in the future.

The wild West once again finds itself at the forefront of exploration and change. If Still has any say in the matter, its mysteries and historic charm will endure.


©2015 Chicago Botanic Garden and my.chicagobotanic.org

Between a Rock and a Future

Undercover Science

Julianne Beck —  January 10, 2015 — Leave a comment

A pretty little iris growing in the mountainous rocky outcrops of Jerusalem is the focus of a research collaboration stretching over 6,000 miles.

Scientists at the Chicago Botanic Garden and Jerusalem Botanical Gardens have combined their strengths to study the natural population structure, or remaining genetic diversity, of the rare Iris vartanii. What they have discovered may save the species, and others like it, into the future.

The finicky wildflower exists in just 66 locations in Israel’s Mediterranean ecosystem—a dangerously low number. New road construction, urban expansion, and even afforestation in the area have reduced the availability of its natural habitat, fueling the crisis. For a plant that is endemic to, or only lives in, one narrow region, that spells trouble.

PHOTO: Iris vartanii ©Dr. Ori Fragman-Sapir

Iris vartanii Photo ©Dr. Ori Fragman-Sapir

“Whenever you have a rare plant, you always have concern that as diversity starts to go down, the plant becomes more and more endangered,” explained Garden volunteer and molecular biologist Eileen Sirkin, Ph.D. “The idea of diversity is that maybe one plant is more drought tolerant, another is more flood tolerant, and another is more wind tolerant, for example, so no matter what the conditions, there will be some survivors. As you narrow that, you are more and more in danger of losing that species.”

Do the existing plants contain adequate genetic diversity? And to sustain the species, how many plants are enough? These are the central questions.

Gaining a Foothold

The scientific partnership between the two gardens was forged when Jerusalem Botanical Gardens’ Head Scientist Ori Fragman-Sapir, Ph.D., who has monitored the species and studied its demography in the field, visited the Chicago Botanic Garden and met with Chief Scientist Greg Mueller, Ph.D. The two quickly saw an opportunity to combine Dr. Fragman-Sapir’s research with the genetic capabilities of the Garden to answer those critical questions.

“Conservation genetics is one of the core strengths of our science program,” said Dr. Mueller.  “There are few other botanical institutions that have this expertise, especially internationally, so we are happy to collaborate on interesting and important plant conservation projects like this one.”

“Conservation genetics is one of the core strengths of our science program,” said Dr. Mueller. “There are few other botanical institutions that have this expertise, especially internationally, so we are happy to collaborate on interesting and important plant conservation projects like this one.”

It wasn’t long before Fragman-Sapir began shipping leaf samples to the Garden’s molecular ecologist, Jeremie Fant, Ph.D. Together with his dedicated volunteer Dr. Sirkin, Dr. Fant set to work extracting data from the samples and documenting DNA fingerprints for each plant. Once they had a large enough data set, they compared and contrasted the findings—looking for similarities and differences among the plants’ genetic compositions.

Gaining Altitude

To give scientists a point of comparison, Fragman-Sapir shared tissue samples from five populations (geographically separated clusters of plants) of a more commonly occurring related species, Iris histrio. By also documenting the DNA fingerprints of those plants, which grow in the surrounding area, but unlike Iris vartanii are not rare, Fant was able to determine how much diversity is needed to sustain the species.

PHOTO: Volunteer Dr. Eileen Sirkin

Dr. Eileen Sirkin volunteers in the laboratory.

Although the study subject is far away from the Garden, its challenges hit close to home. In 2013, Fant and Sirkin published findings from a similar study on a rare plant found at Illinois State Beach Park, Cirsium pitcheri. For that initiative, they examined the DNA of plants from a restored site at the beach and compared them to the DNA of naturally occurring plants across the range, measuring diversity.

“We’re always working with rare and endangered species, and we collaborate with different people around the world to answer those questions,” explained Sirkin.

The Summit

After completing a statistical analysis of Iris vartanii’s DNA fingerprints, Fant made several encouraging conclusions but also issued an alert for continued attention.

The rare species’ genetic diversity was similar to that of Iris histrio. “This does tell us that genetic diversity in Iris vartanii is not likely an issue,” said Fant, who was not surprised by the conclusion. “Genetic diversity of any population is determined by the origins of the species, the age of the population, and proximity to the site of origin,” he explained. “As both species likely arose locally [from Jerusalem northward to the Galilee and further on] and have been around for a very long time, they possess similar levels of genetic diversity.”

PHOTO: Dr. Jeremie Fant.

Conservation scientist Dr. Jeremie Fant

Especially encouraging was that each Iris vartanii population had significant differences in their genes, likely a result of their longtime separation. The findings highlight that it is all the more valuable to conserve each population for their potential to contribute unique genes to future plants, according to Fant.

Although many populations showed high diversity and low inbreeding, which is preferred, others showed the reverse, increasing their potential risk of extinction. The latter group, explained Fant, may benefit from extra special monitoring and care.

To conserve the existing populations, attention will need to be given to their surrounding natural areas, explained Sirkin. “If you find a species that people like and you study it and say we need to do all these things to save it, you are not just saving one plant, you are saving an ecosystem, including all the other plants, insects, other invertebrates, lizards, birds, and whatever else is involved in that ecosystem,” she said.

The findings and recommendations give land managers a clear direction for their conservation efforts, all because of one eye-catching plant that told the story of many.


©2015 Chicago Botanic Garden and my.chicagobotanic.org

The Long Road Home

Undercover Science

Julianne Beck —  December 11, 2014 — 1 Comment

Golden paintbrush (Castilleja levisecta) is gaining ground in its native Oregon for the first time in more than 80 years. Recent reintroductions have seen the charismatic species flourish on its historic prairie landscape. To keep the momentum going, scientists are pulling out all the stops to ensure that the new populations are robust enough to endure.

“Genetic variability will be key to the reintroduction success of golden paintbrush,” explained Adrienne Basey, graduate student in the plant biology and conservation program of the Chicago Botanic Garden and Northwestern University.

PHOTO: Golden paintbrush (Castilleja levisecta).

Golden paintbrush (Castilleja levisecta) growing in propagation beds in Oregon. Photo by Tom Kaye

Basey, who previously managed a native plant nursery, is now studying the genetic diversity of golden paintbrush plants before, during, and after they are grown in a nursery prior to reintroduction to the wild.

“My work is looking at the DNA, or genetics, of the wild, nursery, and reintroduction populations to see if there is any change through that process,” she said. If there is a change, she will develop recommendations for adjusting the selection and growing process to better preserve diversity. “My goal is to give both researchers and practitioners more information to work with,” she noted.

Building for the Future

The research is unique in the relatively young field of restoration science, according to Basey’s co-advisor and molecular ecologist at the Garden, Jeremie Fant, Ph.D. “Adrienne’s study is awesome because of the fact that it has data and the samples to back it up; it is early on in this game of reintroductions and restorations, and potentially could have a lot of impact, not just for that species but what we tell nurseries in the future,” he said.

PHOTO: Adrienne Basey with herbarium specimens.

Basey works with herbarium specimens

Basey is working with data collected over the past decade by research scientists at the Institute for Applied Ecology in Corvallis, Oregon, and University of Washington herbarium specimens from Washington and Oregon dating as far back as the 1890s, and data she has collected from existing plants during field work. “It’s a perfect partnership,” said Dr. Fant, who noted that the Garden is guiding the molecular aspect of the study while colleagues in Washington and Oregon are providing a large portion of the data and samples.

The availability of all of this information on a single species that is undergoing restoration is very rare, explained Fant. “It’s a very unique scenario that she has there, so we can look at how diversity changes as we go from step to step and hopefully identify any potential issues and where they are occurring in the process.”

The study itself will likely serve as a research model for other species in the future. “There isn’t much research out there to help propagators understand when and where genetic diversity may be lost during the production process,” said Basey’s co-advisor and conservation scientist at the Garden, Andrea Kramer, Ph.D.

Last year, Basey, Fant, and Kramer worked together to write a paper outlining ten rules to maximize and maintain genetic diversity in nursery settings. “My goal is to support reintroduction efforts by informing nursery practices and demonstrate to nurseries on a broader scale how their practices can influence genetic diversity through a single case study,” said Basey.

A Green Light Ahead

Her preliminary research is focused on four golden paintbrush populations. Early evaluations show clear distinctions between a few of them, which is good news. Basey will next compare those genetic patterns to those of plants in reintroduction sites.

According to Fant, earlier studies by other researchers have shown that many restoration efforts for threatened species suffer from low levels of genetic diversity prior to reintroduction, due to a number of causes ranging from a small population size at the outset to issues in propagation. It is critical to work around those issues, he explained, as the more genetic diversity maintained in a population, the better equipped it is to survive environmental changes from drought to temperature shifts.

Basey will also compare the current level of diversity of golden paintbrush to that of its historic populations, to get a better sense of what the base level should be for reintroduction success. She plans to wrap up her lab work well before her summer 2015 graduation date.

PHOTO: A golden paintbrush is visited by its primary pollinator, a bumblebee.

A golden paintbrush is visited by its primary pollinator, a bumblebee.

For now, she is pleased with the level of diversity she sees in the current population. “I think the fact that it has a high genetic diversity means that these reintroductions could be successful,” she said. “But if we are creating a bottleneck, we need to know that so we can mitigate it as quickly as possible.” (A bottleneck is an event that eliminates a large portion of genetic variability in a population.)

Fant is enthusiastic about the timing of the study as the field of restoration is taking off. “We can jump in early as programs are being started,” he noted. “If we all learn together, I think it really does ensure that everyone gets what they need in the end.”

For Basey, it’s about building a bridge between the theoretical and the applied aspects of restoration. “My interest isn’t so much in this single species but more in the communication of science to practitioners. I like to bridge the line between research and the people who are using research,” she said.

Basey, like the golden paintbrush, is looking toward a bright future.

©2014 Chicago Botanic Garden and my.chicagobotanic.org

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.


©2014 Chicago Botanic Garden and my.chicagobotanic.org