Vanessa Hayes and keeper Tim Faulkner with Blackie, a Tasmanian devil. Credit: Children’s Cancer Institute Australia

Researchers are hoping that sequencing the genomes of Tasmanian devils will help to save them from extinction.

Devil facial tumour disease is killing the animals as it spreads across the island of Tasmania. Now, researchers say they have found a genetic 'signature' of resistance to the fatal disease. They want wildlife managers to use gene scans to identify Tasmanian devils with the signature of resistance and breed them during this year's breeding season. The breeding season has just begun and will end by July.

"It would be fabulous if the data that we have generated were used in this year's breeding cycle," says Vanessa Hayes of the Children's Cancer Institute Australia in Sydney.

But scientists with the Australasian Regional Association of Zoological Parks and Aquaria (ARAZPA), which manages the Tasmanian devil captive-breeding programme, say it may be too early to use the gene scans.

"It's not at all clear that there is a practical way to use that information yet," says Paul Andrew of ARAZPA.

Hayes began the Tasmanian devil genome project 15 months ago with Stephan Schuster and Webb Miller of Pennsylvania State University in University Park. Schuster has previously sequenced the genomes of extinct animals, such as the woolly mammoth, using one of a crop of new technologies (see 'Genome sequencing: the third generation') that allow scientists to study genome sequences at ever-faster speeds and lower costs. But these technologies have not yet had much effect on wildlife conservation because they have focused on medicine, agriculture and basic science.

The importance of being Cedric

The devil tumour disease is a contagious cancer that is passed from animal to animal by biting. The devils seem to be vulnerable to the cancer because they are genetically very similar to each other, and to the cancerous cells. This means that most of the animals' immune systems do not recognize the cancer cells as foreign, and so fail to destroy them.

But some animals do fight the cancer, and the Gordon and Betty Moore Foundation of Palo Alto, California, gave the scientists US$1 million to try to understand why, by sequencing the genomes of two devils: Cedric, who resisted the cancer until he was deliberately infected with one strain of it, and Spirit, who died from the disease.

The scientists sequenced about one-third of each animal's genetic code. They then catalogued the places where Cedric and Spirit differed at particular DNA 'letters' called single nucleotide polymorphisms, or SNPs. They then scanned these SNPs in the genomes of 80 more Tasmanian devils. The scientists found that a subset of the SNPs could distinguish between animals from western Tasmania — thought to be more resistant to the cancer — and animals from the vulnerable eastern population. The scan also identified the animals most similar to Cedric or Spirit, the scientists say.

They now hope that officials at ARAZPA will let them run gene scans on all 170 captive Tasmanian devils. The scientists say the scans could help ARAZPA decide which devils are most likely to be resistant to the facial tumour, and are therefore the best animals to breed. "We have enough data to know which devils are similar to the one that succumbed to the disease immediately, and which ones to target at the moment to create maximum diversity," Hayes says.

For instance, the team has already scanned the genomes of devils in one park in the captive-breeding programme, the Australian Reptile Park in New South Wales, and three males there have a genetic profile, or genotype, that closely matches Cedric's, Hayes says: "I want them to try to breed these animals with as many female devils as possible."

The devil you know

ARAZPA is currently reviewing Hayes's request for permission to scan all the devils in the breeding programme. Andrew said that the organization uses a statistical program that pairs up devil mates by matching unrelated animals to preserve genetic diversity. Choosing animals with particular genetic markers might actually diminish overall genetic diversity, he says.

"Everyone thinks, 'Let's look at Cedric's genes, and we'll get a resistant population,'" Andrew says. "But we have to be very careful about retaining just one animal's genes, or we'll lose genetic variation and [they'll] get another cancer in another ten years."

Other scientists welcomed further study of devil genomes, but echoed Andrew's caution. For instance, Jeremy Austin, an evolutionary biologist at the University of Adelaide in South Australia, pointed out that Hayes and her colleagues don't know whether their data pinpoints genes that boost resistance to the cancer.

"You could be maximizing genetic diversity, but you may not be maximizing genetic diversity in the genes of importance," Austin says.

Schuster responds that the project is continuing to add more data about Cedric's and Spirit's genomes and that this information is bound to uncover the most important genes. "There is no way that we would not find the important genes, because we are going to sequence all the genes," Schuster says.

Schuster has also organized a meeting next month that will explore how to use genomic data to study extinct and endangered species — a budding area of research. But already, Hayes, Schuster and Miller argue that their data could provide crucial information that might help save one endangered species if it was incorporated into the current Tasmanian devil breeding programme.

"We would like the pipeline not to end here," Hayes says.