The Devil and the DNA Details

Biology researcher’s genetic analysis expertise helps scientists uncover hope for the cancer-plagued Tasmanian devil

Tasmanian devils are known for their ferocity, but these fuzzy marsupials’ tendency to fight is killing them: Over the past 20 years, tens of thousands of the world’s Tasmanian devils have died of a contagious cancer that spreads when the animals bite each other.

Devil facial tumor disease first appeared in 1996. Over two decades it has spread across Tasmania, devastating the already rare species. Some populations have declined by more than 90 percent from the combination of cancer and reduced reproduction, and the overall number of devils has dropped by 80 percent.

Scientists predicted the disease would drive the Tasmanian devil to extinction — but a new study from the University of Idaho, Washington State University and the University of Tasmania says there’s hope hidden in devil DNA.

Paul Hohenlohe, an assistant professor of biological sciences in the UI College of Science, contributed his expertise in searching for signs of evolutionary change across animal genomes, the full set of genes in an organism’s DNA.

“If a disease comes in and knocks out 90 percent of the individuals, you might predict the 10 percent who survive are somehow genetically different,” Hohenlohe said. “What we were looking for was the parts of the genome that show that difference.”

WSU’s Andrew Storfer, an evolutionary geneticist disease ecologist, began studying the devil’s response to devil facial tumor disease while spending time in Tasmania and invited Hohenlohe to collaborate on the genetic sequencing arm of the research, using UI’s advanced genomic analysis tools.

As the disease moved across the island, Tasmanian university and government researchers took DNA samples from hundreds of animals, from areas where the cancer had spread and from places it hadn’t yet reached.

“It’s really unprecedented to have these sorts of samples,” Hohenlohe said. “It’s rare to actually capture the disease as it’s spreading, to have samples from in front of the wave and then after the wave has passed.”

Tasmanian researchers sent samples from three groups of devils, which live on different parts of the island, to WSU and Hohenlohe to examine. Hohenlohe used technologies in UI’s Genomics Resources Core and Computational Resources Core to scan the genomes of nearly 300 individual animals, comparing close to a million snippets of DNA across each animal.

“It’s a really fine-scale scan across the genome,” he said.

The scan found two pieces of the Tasmanian devil genome that showed signs of evolutionary change in response to the cancer and the force of natural selection it imposed.

Over the course of just a handful of generations, more Tasmanian devils were born with genetic differences at these two gene sites, which are related to immune function and cancer risk in humans and other mammals. This is statistically unlikely to have happened by chance, according to the study.

Adding even stronger evidence for rapid evolutionary change: The devils in all three independent groups showed the same changes.

“It suggests there may be genetic variants in the species that could lead to resistance to the disease,” Hohenlohe said. “It provides hope that Tasmanian devils will evolve in the face of the disease and persist in the wild.”

Storfer added, “The results are exciting insomuch as they inform biology with regard to the potential for rapid evolutionary change in today’s dramatically changing world. Additionally, we are hopeful that our study may help with Tasmanian devil conservation efforts.”

These changes are surprising because Tasmanian devils as a species have little genetic variation due to their low numbers and small habitat range — but the variation they had was enough to allow them to adapt.

“This emphasizes that evolution can be extremely rapid, whether it’s in response to environmental change or disease, if the genetic variation is present to allow it to happen,” Hohenlohe said. “The traditional concept of evolution is a very long-term, gradual process. Even within the scientific community, that’s how it was considered until fairly recently. But there are more and more examples of rapid, observable evolution happening in natural populations.”

Hohenlohe and his colleagues are continuing their Tasmanian devil research, including studying the genomes of a few devils that have contracted the cancer but survived.

Hohenlohe also brings his expertise and UI’s gene sequencing and analyzing power to study multiple other animals around the world: Channel Island foxes that suffer from a unique cancer, reintroduced wolves in the Pacific Northwest, beetles imported to the western U.S. to control invasive tamarisk plants, capybara populations in Brazil, and more.

Article by Tara Roberts, University Communications & Marketing.
Photos courtesy of Menna Jones, University of Tasmania

Core Facilities at UI

The University of Idaho offers state-of-the-art technologies for research in biology and other sciences. The Institute for Bioinformatics and Evolutionary Studies, or IBEST, supports three facilities that house these technologies and experts who help researchers use it: The Computational Resources Core, the Genomics Resources Core and the Optical Imaging Core.

The core facilities are available to any researchers at UI, as well as their collaborators around the world and researchers from other universities who visit UI to take advantage of these powerful resources.