Smithsonian Conservation Biology Institute (SCBI)

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environmental science

What’s in a cell? Mason team analyzes genomes to support conservation, cloning project

Mariam Aburdeineh — Thu, 15 Apr 2021 22:05:47 +0000

What’s in a cell? Mason team analyzes genomes to support conservation, cloning project Mariam Aburdeineh Thu, 04/15/2021 - 18:05

Elizabeth Ann, the first cloned black-footed ferret at 48-days old. Credit: USFWS National Black-footed Ferret Conservation Center

Black-footed ferrets were once thought to be extinct, until a small population was discovered in Wyoming in 1981. The species is still endangered, but scientists—including a ��AV researcher and students at the Smithsonian-Mason School of Conservation (SMSC)—are coming to the rescue.

In December 2020, Willa, a black-footed ferret who died in 1988, was cloned using her cells that had been frozen. That clone, Elizabeth Ann, is now the first North American endangered species to be cloned in the United States. Senior Research Scientist Klaus-Peter Koepfli conducted critical research on her genetic cell line.

“As conservation geneticists, we try to understand how much variation there is and inform conservation breeding best practices,” Koepfli said. “This really is a revolution in terms of how we can use new tools to help endangered species.”

Revive and Restore, the organization that spearheaded the cloning project, sequenced and analyzed the genetic material (or genome) of Willa’s cell cultures. The cell cultures serve as a way to grow and study cells outside their native environment, and are used to help scientists better understand the species’ physiology and biochemistry.

Klaus-Peter Koepfli

Recognizing Koepfli’s extensive expertise in applying genomics to conservation, the organization asked him and SMSC to further analyze that data, compare it to the previous genome of Willa’s cells, and to other black-footed ferrets.

“What we found is that Willa is contributing variants that we don’t see in any other black-footed ferrets [through Elizabeth Ann],” Koepfli said. “That’s where the cloning is becoming important—if we can clone other cell lines, we can contribute additional new variation to the black-footed ferret population.”

“This research is everything to me,” said senior biology major Marcus Dooley, who assembled the mitogenome of 49 ferrets to compare genetic differences within their sequences. “Being able to live my childhood dream by helping support an endangered species is priceless.”

In the future, the genomic data could potentially be used for other conservation efforts, Koepfli said, such as understanding and minimizing the presence of damaging genetic mutations, and even reengineering a species’ immune system to become resistant to deadly diseases.

Marcus Dooley. Photo provided.

“That sounds like blue-sky thinking, but with gene-editing technology and the tools we have today, it’s in the realm of possibility,” Koepfli said. “There’s still a lot of research that needs to be done to understand this, and we’re trying to help with our genome analysis program.”

Koepfli said he began working with black-footed ferrets in 2017, and started the genomic analysis program when he worked at the Smithsonian Conservation Biology Institute. He’s since brought the program to SMSC, where students can be part of this research that helps save endangered species.

Dooley, who attended SMSC in Fall 2020, said he plans to pursue a career in conservation. He feels Mason’s program is setting him up for success.

“The best part is how immersive the [SMSC] courses are,” Dooley said. “Everything you learn is applicable to the conservation profession and you are constantly out in the field performing hands-on activities to help prepare you for that line of work.”

He adds: “If you’re passionate about the environment and conservation, and truly want to pursue a career in this field, SMSC is the best option.”

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New research coming out of its shell: Mason, Smithsonian study could help save wood turtles

Mariam Aburdeineh — Tue, 23 Feb 2021 21:19:17 +0000

New research coming out of its shell: Mason, Smithsonian study could help save wood turtles Mariam Aburdeineh Tue, 02/23/2021 - 16:19

Two SMSC research students and a Turtle Conservation Ecology intern surveying for Wood Turtles in Virginia. Photo credit: Jessica Meck

For decades, research on wood turtles—a threatened reptile species native to North America—has focused on trying to better understand and protect their populations. But there’s one area of wood turtle research that’s been lacking. This spring, a team from ��AV, the Smithsonian Conservation Biology Institute (SCBI), and the Smithsonian-Mason School of Conservation (SMSC) is heading to the streams to fix that.

Hunter VanDoren holding a juvenile wood turtle. Photo Credit: Jessica Meck

“The assumption with animals that have a long-life history, like turtles do, is that adult survival is really the most important thing to focus on for conservation,” said J. Hunter VanDoren, a Mason environmental science and policy PhD student and graduate fellow with SCBI. “But you can’t leave out juveniles, and they have largely been left out of the literature.”

VanDoren, a Front Royal native who interned with SCBI before becoming a graduate fellow, is part of a team headed by Mason alumnus and Smithsonian researcher Tom Akre, who’s been developing science for the conservation of threatened turtles for more than 20 years.

Virginia wood turtle habitat consists of both upland protected forest regions and lowland mixed agricultural areas. Surprisingly, Akre’s data showed juvenile recruitment to be low at protected upland sites, despite reproductive rates remaining high and the land being preserved. To understand why, the team’s research will be of particular importance. It will also be a final piece needed to conduct Integrated Population Modeling and inform a Population Viability Analysis.

A juvenile wood turtle. Photo credit: Jessica Meck

To understand the factors involved and how juveniles fare in both habitats, VanDoren will be putting radio transmitters on the young turtles (primarily identifiable by the length of their shell) and tracking them to estimate their known fate (an estimation of survival probability).

Each week, VanDoren will check on the turtles, collecting data on their status, survival, and location, as well as qualitative habitat data. Later, he will analyze the results in the lab.

The goal is to track 30 turtles at each site, but that will depend on how many juveniles can be captured and tracked, VanDoren said, adding that part of the reason juvenile research is limited is because individuals are elusive and difficult to study.

A radio-telemetry antenna used to track wood turtles at a SCBI study site in VA. Photo credit: Jonathan Drescher-Lehman.

“Juveniles are the missing piece of the puzzle when it comes to understanding their life history, how populations are reacting to land use change, and all the threats they face from habitat loss and fragmentation, road mortality, and illegal collection for the pet trade,” said Jessica Meck, Turtle Conservation Ecology project manager. “The pieces already in place are important for conservation of the species…but the missing data on juvenile survival is particularly crucial for informing landscape-scale conservation in Virginia.”

In addition to their hands-on research, Meck and VanDoren have been mentoring an undergraduate SMSC student each semester. These undergraduates learn experientially by supporting the team in the field and lab.

Jessica Meck holding an adult wood turtle. Photo provided.

Teaching the future generation of conservationists is of critical importance, Meck said, adding that the applied conservation experience is rewarding for both mentor and mentee.

As a student, VanDoren agrees.

“Something I didn’t fully grasp as an undergraduate was just how important the experience itself is in comparison to just learning something out of a book,” he said. “It’s the experience that develops you as a scientist and allows you to fully understand what it is you’re doing and why.”

From networking with leading researchers and academics, to the experiential learning, VanDoren said his experience has been unrivaled.

“I’ve had great mentors, I’ve had great courses that I’ve learned a lot from,” he said. “I would strongly encourage anyone who’s interested in looking into Mason to do so—the opportunities are absolutely incredible and it’s been a fantastic experience at Mason and SCBI.”

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When moving conservation classes online, SMSC shows innovation is key

Mariam Aburdeineh — Tue, 23 Jun 2020 00:05:00 +0000

When moving conservation classes online, SMSC shows innovation is key Mariam Aburdeineh Mon, 06/22/2020 - 20:05

Outside their dorms, students at the Smithsonian-Mason School of Conservation (SMSC) have visual access to rare and endangered species. On any given day, you can find them doing field and laboratory work with influential conservation mentors. Midway through the spring semester, the school known for its hands-on conservation training, had to quickly transition their courses online due to COVID-19.

“It was challenging,” said Anneke DeLuycker, associate professor at SMSC who is teaching and coordinating two of their digital offerings for the summer. “I knew something was going to work because at SMSC, we do everything in our power to give students the best education, time, and experience that they could have, whether in-person or virtually.”

��AV students in the “Research in Conservation” course work one-on-one with conservation mentors on specialized projects. Though video chat replaced face-to-face meetings and learning content, the core mission of SMSC remained.

A student at the Smithsonian-Mason School of Conservation records observations in the field. Photo by Robert Barrett.

“The goal of the research course is to give these students experience in contributing new knowledge to advance the field of conservation,” DeLuycker said.

Creative brainstorming from mentors means students can still achieve that goal online, DeLuycker said, and that’s why she’s excited for this summer.

What does a hands-on conservation course look like online?

It varies from project to project, DeLuycker said. This summer, students in the research course are able to choose from projects that include:

Analyzing video footage of endangered species to collect behavioral data that could be used to help reintroduce the species to the wild;
Gathering data on the impact of COVID-related travel restrictions on the movement of wildlife globally, and training computer algorithms to automatically detect wildlife in aerial and satellite images;
Creating an illustrated guide of the distribution and history of bees in the Washington, D.C., metropolitan area, using museum records and data from the U.S. Geological Survey Native Bee Laboratory; and
Using Google Earth Engine and Geographic Information Systems (GIS) to model animal movements which could provide forecasts of changes in biodiversity.

Darryl Carter, an environmental sustainability studies senior, took the research course last spring. Converting to online was difficult at first, he said, but it had unexpected benefits.

“It required me to find solutions to challenges in new ways,” said Carter, who studied elephant behavioral ecology with Smithsonian scientist Shifra Goldenberg. “I was still able to successfully complete my research project and even continue my research beyond the semester.”

For SMSC students who don’t work directly on research projects with mentors, such as those in the “How to Succeed in Conservation” course, they also receive unparalleled networking opportunities, Deluycker said.

This summer, students will hear from speakers such as Francine Madden, executive director of the Center for Conservation Peacebuilding; Ed Maibach, director of Mason’s Center for Climate Change Communication; and Smithsonian scientists who are engaged in current issues of wildlife trafficking, species reintroduction, and conservation of coral reefs.

“One thing I really wanted out of SMSC was to have a networking experience,” Carter said. “I was concerned that I wasn’t going to be able to have that [online], but I was still able to go to the GIS lab meetings and connect with amazing scientists.”

The experience also taught Carter that now is the time for students to make an impact.

“In a crazy and changing world, we are able to find new ways to innovate and problem solve, which is what conservation needs,” he said.

Department of Environmental Science and Policy (ESP)

Five environmental science students receive Cosmos grants to tackle critical conservation research

Mariam Aburdeineh — Thu, 19 Mar 2020 00:05:00 +0000

Five environmental science students receive Cosmos grants to tackle critical conservation research Mariam Aburdeineh Wed, 03/18/2020 - 20:05

Five PhD students in Mason's Department of Environmental Science and Policy received grants from the Cosmos Club Foundation to conduct conservation research. Chase LaDue, one of the grantees, is studying male Asian elephants. Photo provided.

Around the world, environmental crises are making headlines, from the potential extinction of species and ecosystems to climate change. Students in ��AV’s Department of Environmental Science and Policy (ESP) are driven to make a change.

This year five PhD students in the department received grants from the Cosmos Club Foundation to tackle a wide range of conservation efforts.

In any given year, Mason has received one or two Cosmos grants, said Kathryn Agoston, director of Graduate Fellowships. “To earn five is very exciting.”

The role Mason students play in helping the earth is extremely fundamental, said A. Alonso Aguirre, ESP department chair. Mason’s top-tier faculty, R1 research status and unparalleled opportunities in the backyard of the nation’s capital help take their impact to a new level, he said.

“Now more than ever you see the passion of students to work with species and ecosystems that are threatened, mostly by human impact,” Aguirre said. “They are committed to solving actual problems.”

The Cosmos Scholars grant program is open to graduate students in the Washington, D.C., area in all fields of study. Mason’s Office of Graduate Fellowships is also available to help students secure similar funding opportunities.

“The goal is to provide applicants with the support they need to put forward the strongest possible application,” Agoston said, adding that some awards qualify for additional university support including tuition assistance and health insurance. “We have policies in place to help ensure that these costs do not create a barrier to our students accessing prestigious, nationally competitive awards.”

Here is how Mason’s Cosmos Scholars are making an impact:

Cosmos Scholar Meadhbh Molloy. Photo provided.

Meadhbh Molloy:
Exploring Beyond Face Value

In one of her first graduate classes on disease ecology, Meadhbh Molloy read a paper projecting the extinction of Tasmanian devils. An aggressive and highly contagious facial cancer would likely be the cause of termination within a couple decades, the researcher estimated. The species is endangered, but they have not become extinct.

“[The cancer] spreads like crazy and almost always leads to death,” Molloy said. “But [Tasmanian devils] are persisting in the wild, and no one really knows exactly how.”

Since the class, Molloy said she became fascinated by how species co-evolve with diseases.

“When I learned that diseases were in a way caused by pathogens trying to survive, I started to understand their role in ecology and how they’ve shaped the evolution of other life forms,” Molloy said.

Through the Cosmos grant and an award from the American Australian Association, Molloy will spend up to a year in Australia, working in a lab at the University of Sydney, where she will be analyzing devil fecal samples. She will also be potentially looking at the species’ microbiomes and parasite loads to see if there are differences between diseased wild devils and cancer-free wild devils.

“It’s all about making sure they are successful when they’re released into their native habitat,” said Molloy, who first realized she could have a career with endangered species after a field trip and Mason courses at the Smithsonian-Mason School of Conservation.

“I’m looking forward to the challenge,” the Northern Virginia native said. “I’m looking forward to a lot of personal growth and being able to work with the species that I have been thinking about since I first started my masters.”

—Mariam Aburdeineh

Tovah Siegel, pictured here in the Peruvian Amazon, holds a few piranhas she caught for dinner that night. Photo provided.

Tovah Siegel:
Her Own Best Advocate

Tovah Siegel had never met or spoken to Thomas Lovejoy, and knew him only as the world’s preeminent conservation biologist. But that did not stop Siegel from emailing the Mason University Professor to ask if he would be her advisor as she pursued her PhD in environmental science and policy at Mason.

One return email and three or four phone calls later, he agreed.

“You have to advocate for yourself,” said Siegel, who is from Oregon and earned her undergraduate degree in biology from the University of Puget Sound in Washington.

Siegel, who is also a Smithsonian Fellow at the National Museum of Natural History, is studying the interactions of species and how forest fragmentation in the Brazilian Amazon impacts those interactions.

“A lot of research looks at how one species responds individually to fragmentation. But there isn’t a lot of research about how species A impacts species B that relies on species A,” Siegel said. “You can take that information and say we shouldn’t be looking at one species. We should be looking at these ecosystems as a complex array of interactions.”

Siegel, who previously used a Boren Fellowship to take field courses in the Amazon, will continue her research with the help of the Cosmos grant.

—Damian Cristodero

Chase LaDue with an elephant at the Patara Elephant Farm in Chiang Mai, Thailand. Photo provided.

Chase LaDue:
Where the Elephants Are

African elephants have had a time in the spotlight when it comes to research and media, due to the ivory crisis. But a different elephant species doing worse in terms of survival has received far less attention. Chase LaDue is changing that with his research of male Asian elephants in Sri Lanka.

“I study male Asian elephants in particular because they’ve been less studied than African elephants, and male elephants are unique because they go through this period called musth,” said LaDue, a Dallas native. “It’s completely unique, only elephants do it.”

Musth, which means “intoxicated” in Urdu, is similar to rutting season for a deer, LaDue explained. Testosterone levels and aggression are high, but unlike for other animals, there is no predictable musth season.

Elephants in musth can also pose an economic burden, he said.

“Elephants will raid farmers’ crops, so that can be dangerous to the people that live around elephants, and a single elephant can wipe out a farmer’s crop for the entire year,” LaDue said.

Through behavioral observations and analyzing hormones in fecal samples, LaDue will examine what environmental and social factors influence musth. Because Asian elephants are classified as endangered by the International Union for Conservation of Nature, the findings could also contribute to understanding how to better conserve their populations.

This year marks the second time LaDue has earned a Cosmos grant. He also received a Fulbright scholarship to go to Sri Lanka in 2019, but had to return to the United States early due to terrorism in the country. Being able to continue his studies is both validating and rewarding, he said.

—Mariam Aburdeineh

Betsy Collins:
Leafing for Answers

Collins standing next to a palo santo tree in the Marañón Valley, Peru. Photo provided.

From churches to yoga studios to individual homes, communities have been burning palo santo—holy wood—for generations. The South American plant similar to frankincense and myrrh is primarily used as incense, and it has been so widely marketed that its populations are declining due to habitat loss. Betsy Collins hopes her research can help save the species.

“It’s really important when you’re planting for reforestation that what you’re planting is genetically diverse,” said Collins, who is from West Palm Beach, Florida. “I’m looking at comparing the genetics of the replanted populations with the natural population to see [whether] they are in line or can be doing better in our reforestation projects.”

A National Geographic grant in 2018 took Collins to Peru, Mexico and Colombia to collect leaf samples and preserve the plants’ DNA. With her Cosmos grant, she will work in Mason’s labs to extract and analyze the DNA from those hundreds of samples, she said.

“No country has unlimited sources for conservation,” Collins said. “I hope that this research can give some ideas as to where are some really unique genetically diverse populations that we should look at protecting.”

—Mariam Aburdeineh

Charles Coddington:
Flocking to the Amazon

Cosmos Scholar Charles Coddington. Photo provided.

Birds of a feather may flock together, but to avoid predators, birds of different species will do the same. Once at their destination, Charles Coddington wants to know how deforestation and habitat fragmentation affect them.

“One of the most critical [threats] to conservation is the loss of diversity,” said Coddington, who graduated from Mason in 2018 with a master’s in evolutionary biology and returned to the university for his PhD. “I hope that my research will help contribute to better restoring biodiversity to fragmented landscapes.”

Mix-species flocks are found on every continent except Antarctica, Coddington said, and they are especially prevalent in the Amazon. Hundreds of birds and dozens of species fly there, he said.

Going into Amazonian forests, Coddington will study how these birds use regenerating forest fragments, and how their nesting behaviors are affected in forests that have developed naturally (primary forests) versus forests recovering from human disturbances (secondary forests).

After finding the nests, Coddington said he will set up camera traps to record what happens when predators are near. He will also set up artificial nests in primary and secondary forests “to see if predation is one of the limiting factors that’s preventing [birds] from successfully breeding in secondary forests.”

The opportunities Coddington has had at Mason, including a fellowship with the Smithsonian-Mason School of Conservation, and the Cosmos grant, have allowed him to foster a community and conduct meaningful research, he said.

“This is the time to get involved in conservation of species and ecosystems as many factors are threating the health of all,” Aguirre said.

—Mariam Aburdeineh

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Red pandas on red alert: Mason student, alumni conduct research to save endangered species

Mariam Aburdeineh — Mon, 02 Dec 2019 15:30:00 +0000

Red pandas on red alert: Mason student, alumni conduct research to save endangered species Mariam Aburdeineh Mon, 12/02/2019 - 10:30

Saving an endangered species is possible, but it takes a village. Conservationists, including three ��AV alumni working at the Smithsonian and a current student, are part of the team at the Smithsonian Conservation Biology Institute (SCBI) and the Smithsonian-Mason School of Conservation (SMSC) working to ensure red pandas move off the endangered list.

“Our main focus is breeding, expanding the population and looking at genetics,” said SCBI’s carnivore curator Juan Rodriguez, BS Biology ’09. In the event that something catastrophic happens in the wild, their goal is to have a genetically viable population in captivity to stave off extinction, he said.

Rodriguez and his team help produce red panda and clouded leopard cubs and maned wolf pups, he said. This year, 4-year-old red panda Moonlight gave birth in June.

Moonlight's new cub was born in June. Photo by Jessica Kordell/Smithsonian Conservation Biology Institute.

Since April 2018, Monika Conrad, an environmental science and policy graduate student, has been conducting behavioral research on the red pandas, including Moonlight and her cub, at SCBI and the National Zoo as part of her master’s program.

“The idea is to understand what disturbs red pandas, what changes their behaviors and their physiology, to see what may negatively impact welfare,” said Conrad, who also assists the undergraduate students in their research at SMSC. “If we can give them the best possible welfare, we can improve breeding success.”

Conrad, who came to Mason after learning about Mason School of Integrative Studies professor and Mason alumna Elizabeth Freeman’s red panda research during a Smithsonian internship, spent 14 months observing the animals and logging their behaviors. She also recorded the climate (temperature, humidity and wind speed), noise levels, and zoo visitor numbers to see if and how these environmental factors influence red pandas.

This semester Conrad spends her days in the SCBI endocrine lab, extracting hormones from the red panda’s fecal samples. Later, she’ll analyze the behavioral data with the hormone concentrations to see if there are connections between the two.

Jessica Kordell, who has been an animal keeper at Smithsonian since 2007, helped hand-raise Moonlight when she was a cub, and continues to provide care for SCBI’s red pandas and clouded leopards. The Mason alumna, who earned her master’s in environmental science and policy in 2017 and studied under Professor Freeman, also mentors undergraduate practicum students attending SMSC.

Mason student Monika Conrad (left) and Mason alumna Jessica Kordell. Photo by Evan Cantwell/��AV

Working with the young cubs and educating students are the most rewarding parts of her job, Kordell said.

“The work that we do here, both with the students and with the animals day-to-day, really matters because we are in this stage where if we don’t work hard to save them or save their environment, [the species] could be gone,” Kordell said.

Moonlight's cub. Photo by Evan Cantwell

Kordell said her Mason experience was significant for her career.

From courses on climate change to learning about collecting genetic samples noninvasively, her classes “really helped me understand more about what I do as a professional and how that actually helps save our species.”

The preservation extends beyond the animals, since each species plays a unique role in the ecosystem and in everyone’s survival, Kordell and Rodriguez agreed.

“Students like Monika are excellent for what we do,” Rodriguez said. “It’s really very fulfilling to see that such a younger generation is ready to go out there and preserve these amazing species.”

This semester Conrad spends her days in the SCBI endocrine lab. Photo by Evan Cantwell.

Conrad and undergraduate students at SMSC work directly with scientists who are at the forefront of conservation research. It’s an unparalleled experience, as most students would otherwise learn about these topics from books or videos, Rodriguez said.

“It’s amazing to be here as a student,” Conrad said. Both the Smithsonian scientists and Mason professors are eager to answer questions and inspire the next generation of conservationists, she said.

“[You’re] never going to be able to find another program that can really immerse [you] in conservation like coming to SMSC will,” Conrad said. “I love that I’ve been able to have this opportunity—not just the knowledge, but the opportunities to connect with these researchers and learn more.”

Moonlight and her cub. Photo by Evan Cantwell/��AV

Smithsonian's National Zoo and Conservation Biology Institute

Department of Environmental Science and Policy (ESP)

Jane Goodall inspires the next generation of conservationists

Mariam Aburdeineh — Wed, 16 Oct 2019 13:28:38 +0000

Jane Goodall inspires the next generation of conservationists Mariam Aburdeineh Wed, 10/16/2019 - 09:28

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