Earth & Space
Genomes in the Wild: A Q&A with Professor Joanna Lynne Kelley on Evolution, Extremes, and Hibernating Bears
At UC Santa Cruz’s Coastal Science Campus, Kelley is uncovering how life endures in extreme environments.
Joanna Lynne Kelley. Photo by Jennifer Feitosa.
Growing up in the woods of Santa Cruz, Joanna Lynne Kelley was constantly exposed to the beauty and diversity of nature. Surrounded by the variety of organisms that Santa Cruz harbors and finding a variety of flora and fauna no matter where life took her, Kelley realized diversity exists everywhere — even in the most inhospitable environments on our planet. Inspired by this fact, Kelley has spent the last two decades studying what genes could help organisms adapt to such conditions.
At UC Santa Cruz, the Kelley Lab focuses on answering one big question: How do different groups of animals adapt to Earth’s most inhospitable environments? Using state-of-the-art genomics, her team, based in the Coastal Biology Building at the University of California, Santa Cruz is guided by three main research pillars: the evolution of antifreeze proteins in fish living in polar environments; the adaptation of freshwater fish to toxic hydrogen sulfide; and the study of brown bear hibernation and its potential in aiding their conservation.
The latter project, which began as an effort to understand hibernation as an adaptive trait in brown bears, has since grown into a broader series of studies, many of which are in collaboration with the U.S. Fish and Wildlife Service, the U.S. Geological Survey, UC Riverside, the University of Montana, and the Washington State University Bear Center.
In recognition of her conservation work, Kelley received a National Science Foundation grant in August 2024, for a project investigating the steep decline of brown bear populations in the U.S. over the past 150 years. Her team is exploring the potential of genetic tools for monitoring and managing wildlife living in extreme environments, using samples from both historical museum collections and living bears. We recently spoke with Kelley to talk about how genomics can inform brown bear conservation and to learn more about the wide-ranging research coming out of her lab.
This interview has been edited for length and clarity.
A key part of your project involves developing new, non-invasive genetic tools to rapidly identify individual brown bears. Can you tell us where the samples you’re working with are coming from?
Most of the samples we work with come from collaborations, which are central to all of my projects. I spend most of my time analyzing data and writing, so we’re incredibly fortunate to have strong partnerships with researchers and institutions. One of our key collaborators is the Washington State University Bear Center, which has a research population of brown bears. Many of our tissue and blood samples come from their facility. For our Antarctic and deep-sea species, sample collection is much more challenging. In those cases, we also rely on partnerships and museum collections.
How can studying genomics inform bear conservation?
One of the big questions in conservation is: What scale should we be conserving? Should efforts focus on entire species or more localized populations? Genomics gives us powerful tools to help answer that. It allows us to identify distinct populations, understand how they’re structured across a landscape, and even pinpoint when different groups stopped or started interacting with one another. This information is critical for deciding which populations may need focused conservation efforts, and whether we’re dealing with isolated groups or one large, connected population.
Genomics also helps us detect recent inbreeding and the genetic effects of rapid habitat fragmentation. When landscapes are suddenly split by highways, roads, or other barriers, we can start to see changes in how populations interact — or don’t. These genetic clues help us better understand the impact of human development on wildlife, and guide how we manage and protect species moving forward.
Can you give us a sense of where things currently stand with your NSF-funded project? What progress have you made so far?
We just started. We have sequenced the genomes of 350 brown bears throughout North America and we are currently analyzing the results. We are estimating how much genetic diversity there is in each population and how connected different populations are.
Essentially, the entire project is yet to come. We are so excited about this collaboration between conservation practitioners and academic researchers! We hope that the findings will be valuable for many species, not only brown bears.
When studying brown bear hibernation, which gene expression changes have been the most surprising or significant, and what do they reveal about how bears adapt to months of inactivity?
During hibernation, there are dramatic shifts in gene expression across different tissues, which, when you think about all that a bear’s body has to do to survive months of inactivity, makes a lot of sense. We analyzed three tissues: fat (adipose), muscle, and liver. What stood out most was that fat showed the greatest number of differentially expressed genes between the active season and hibernation, followed by liver, and then far fewer in muscle.
That pattern aligns with what bears need to accomplish physiologically. They’re switching their metabolism from storing fat in the active months to burning it as their primary energy source during hibernation. So it’s no surprise that fat is such a dynamic and central tissue. There’s a phrase we like to use in the lab: “Fat’s where it’s at.”
What’s the weirdest or most surprising thing you’ve learned about brown bears during your research?
One thing that I learnt, from my colleague Beth Shapiro at UCSC, was about polar bear mitochondria—the DNA inherited only from the mother. The polar bear’s mitochondrial genome is most closely related to a specific population of brown bears. Polar bear mitochondria fall within the brown bear mitochondrial family tree. However, when you look at the rest of the genome—the nuclear genome—all polar bears and brown bears are distinct from each other.
This means there was an ancient event where a brown bear’s mitochondrial genome was introduced into polar bears, and now all polar bears carry that mitochondrial DNA. So, there’s a surprising disconnect between the mitochondrial relationship and the rest of the genome between brown bears and polar bears. I think that’s pretty wild.
What’s a widely held myth about bears that you once believed, but that your research later overturned?
A common misconception I once held is that bears sleep all winter — but even during hibernation, they maintain circadian rhythms and cycle between sleep and wakefulness. They do have a very depressed metabolic rate — they’re slow — but they can also respond quickly because they’re not just asleep and immobile. That was a big misconception for me, and it’s one that’s perpetuated in lots of children’s stories, like the idea that baby bears won’t go to sleep. There’s this ongoing narrative about what hibernation is, but hibernation is different from sleep.
For me, that distinction is important because we’re trying to understand how hibernation works at a molecular level — what changes are required to switch from relying on external food to burning fat, and how bears maintain muscle and other tissue functions. When they come out of hibernation, they don’t need to get on a treadmill to get back into shape — they’re ready for the active season.
What is the one big question that you would like to answer in your career?
The biggest question for me is how organisms living in extreme environments manage to survive and thrive. It’s a huge question, and while we focus on a specific group of species, I hope we can get closer to understanding it. Organismal biology is truly fascinating.
What impact do you hope your research will have?
Ten years from now, I hope our current project — creating a model to monitor the long-term impacts of conservation on the genetic diversity of grizzly bear populations — will stand as a strong example of how genomics can be applied to conservation and species management. Using genomics for conservation is an exciting and growing field, and I want our work to highlight its real-world impact.