Prairie Research Institute

The Race to Save the Little Brown Bat

How genomic research could rescue a species on the brink of extinction

Jordyn Chace is a huge fan of classic murder mysteries. As a geneticist and wildlife biologist, she considers herself an investigator.

But instead of solving human crimes, she uncovers clues that may help contribute to the recovery of a once-common North American mammal: the little brown bat, Myotis lucifugus, a species now on the brink of extinction.

“There are clues hidden in their DNA that show the little brown bats are in trouble,” Chace explains. “We can use genomics to benchmark it and check these clues to see how the species is doing, and ideally prescribe bespoke conservation action best suited to their needs.”

Little brown bats hibernating in a cave. Photo by Ricky Gieser, acoustics field lead for the Illinois Bat Conservation Program.

The population of this bat has plummeted dramatically — by some reports, a loss of more than 90%. This devastation is largely due to the spread of a fungus, Pseudogymnoascus destructans, which causes white-nose syndrome. A deadly disease, white-nose syndrome was first discovered in a New York cave in 2006 and it has since spread westward across North America, infecting many cave-dwelling bats.

bat with white fungus on its snout, held by two blue-gloved hands.

Little brown bat with white-nose syndrome. Photo courtesy of Steve Taylor, retired INHS conservation biologist.

Chace, a Ph.D. candidate, and Jordan Hartman, an Illinois Natural History Survey postdoctoral scholar — both at the University of Illinois Urbana-Champaign — along with Georgia Auteri and Carly Truijilo at Missouri State University, formed the Little Brown Bat Genomic Collaborative. Funded by the U.S. Fish and Wildlife Service, their project aims to understand the species’ genomics across its North American range. The collaborative’s work represents one of the largest genomic analyses in wildlife conservation.

This summer, they’ve been reaching out to researchers across the continent, asking them to collect tissue samples from adult and juvenile little brown bats before the bats hibernate in caves and abandoned mines, called hibernacula, this winter.

“We’re primarily working with researchers who already have bat-handling permits because that process can take years to complete and it’s important these bats are handled with care,” Chace explains. “Once they have a permit, they can apply for amendments that allow them to take wing [biopsy] punches.”

Bat wing. Photo courtesy of Ann Froschauer, USFWS.

Under the leadership of INHS conservation biologist Mark Davis, Chace and Hartman spent last summer recruiting bat researchers to join the collaborative. Currently, the little brown bat is under review for listing as endangered under the U.S. Endangered Species Act, with research documenting the spread of white-nose syndrome indicating that the species is at high risk of extinction.

“The little brown bat is not listed, yet by some metrics, they’re worse off genomically than other listed species,” says Chace. “Even if population numbers can bounce back, these kinds of bottlenecks can be disastrous for the underlying genetic diversity that allows species to truly recover.”

Chace’s journey to this point accelerated after she presented preliminary findings from her dissertation at a regional wildlife conference last year. Following her presentation, she was approached by Rich Geboy, a U.S. Fish and Wildlife biologist who serves as species lead for little brown bat and Midwest white-nose syndrome coordinator. He shared her vision for a comprehensive genomic analysis of populations across the bat’s entire range.

“Meeting Rich was momentous,” Chace recalls.  “As an early career scientist, his vote of confidence made it feel like this work could truly turn into actionable conservation planning.”

Geboy invited her to the 2023 national white-nose syndrome meeting in Palm Springs, where she presented her research to the top bat and disease researchers on the continent, as well as key policymakers. The potential application of this method sparked widespread interest, with researchers across the U.S. and Canada hoping to harness it in their regions. Rather than complete several smaller regional explorations, Chace decided to pursue one cohesive study of the entire range of the species.

With a team, a mission, and secured funding, the race to save the little brown bats through genomic research is on.

Jordan Hartman working in the lab. Photo by Xander Hazel, Prairie Research Institute.

Uncovering genetic clues to save the little brown bat

Chace spent the summer emailing and calling researchers, asking them to join the collaborative and share samples, hoping to uncover new clues to assess the health of the little brown bat’s populations. The project will require tissue samples from across North America to be sent to the lab.

Much like a detective piecing together clues for a digital murder map, Chace logs each collaborator and prepares a kit with the tools needed to uncover hidden genetic evidence about the bats’ past and potential future. These kits include instructions for collecting and preserving tissue samples in microcentrifuge tubes with silica glass beads.

“It is extremely satisfying to build each handmade kit in the lab from recycled pipet boxes and send them out to our collaborators,” explains Jordan Hartman. “We have been waiting patiently until the end of field season when these kits are returned to us, feeling relief and excitement to start the next phase of the project, the genomic analysis.”

So far, the team, which started as two research labs, has expanded to include 17 other contributing organizations and agencies providing samples from 25 states and provinces. Historically, the species range spans most of the United States and Canada.

A map showing the historic range of the little brown bat, covering all U.S. states and Canadian provinces except New Mexico, Arizona, Texas, Louisiana, and Nunavut. The range area is shaded dark blue. Data collection areas are marked in light blue with diagonal lines, covering 25 states and provinces: California, Colorado, Connecticut, Idaho, Illinois, Indiana, Kentucky, Maine, Maryland, Missouri, New Hampshire, New Jersey, New York, North Carolina, Ohio, Ontario, Quebec, Rhode Island, Saskatchewan, South Carolina, Vermont, Virginia, Washington, Wisconsin, and Wyoming. Locations of 19 collaborator organizations are marked with orange bat icons, including agencies and universities such as Colorado Parks & Wildlife, the Illinois Bat Conservation Program, the University of Wyoming, and the US Fish and Wildlife Service. The map has a legend identifying species range, data collection areas, and a numbered list of contributing organizations. It shows state and province boundaries without other geographic features or a scale.

To date, 19 collaborating institutions are contributing samples from 25 states and provinces across North America.

Collaborators are asked to collect tissue samples from bats through methods like mist netting or from carcasses tested for rabies or those struck by wind turbines, dating back to 2018. Tissue samples obtained from small wing biopsies, or “punches” about 2-3 millimeters in diameter, are sent back to the lab and used to extract DNA.

Through a cutting-edge sequencing technology praised for its efficiency and accuracy — restriction site-associated DNA marker analysis, also called RADseq — Chace and her team can study the population genomics of the little brown bat over time and across regions, determining how white-nose syndrome has affected populations at the molecular level.

The worry for Chace is that little brown bats are spiraling toward extinction because they, along with other bats, were hit hard by white-nose syndrome while also struggling against other chronic threats like habitat loss. For the little brown bat, white-nose syndrome has decimated its populations from hundreds of thousands to just thousands in less than a decade. The genetic consequences of this dramatic decline include inbreeding and harmful mutations, pushing the species even closer to extinction.

Despite this grim scenario, Chace remains optimistic. She believes in the possibility of evolutionary rescue, where developed resilience could help the species survive.

“If the individuals most susceptible to white-nose syndrome die, the survivors might have genes for resistance, and it’s that adaptation that gives us some hope,” Chace explains. “We already know that this species has genes that show potential for evolutionary rescue.”

A genomic benchmark is essential to track whether adaptation is occurring that would give the bats a chance to survive white-nose syndrome.

Photo by Ann Froschauer, USFWS.

Building a genomic lifeline, one sample at a time

With summer winding down, Chace and Hartman’s recruitment efforts have begun to pay off, getting them closer to uncovering clues to understand the health of the species. Each tissue sample arriving at the lab is another puzzle piece — another clue in the race to understand whether these bats can escape extinction.

For U.S. Fish and Wildlife and other bat researchers, genomic analyses can also help evaluate the effectiveness of new management strategies aimed at controlling the spread and impact of white-nose syndrome. Techniques such as artificially cooling caves, administering oral vaccines, using aerosol vaccine sprays or UV lights, and increasing bats’ fat reserves before hibernation are some approaches where population genomics can enhance their assessment.

A ruling on the species’ status could be issued amidst the collaborative’s progress. Whether or not the little brown bat is listed as endangered, the need for genomic research remains urgent. It can be a significant indicator of whether current conservation efforts or natural processes are truly making a difference.

“Conservation is a team effort, requiring diverse skills — from fieldwork to bioinformatics,” says Chace. “The success of our project is built on years of collaboration and expertise, with everyone working together to tackle the biodiversity crisis efficiently and creatively.”

The Little Brown Bat Genomic Collaborative is funded by the USFWS White-nose Syndrome Research and Conservation Grant (2023).