June 27, 2011 | 1
Tasmanian devils (Sarcophilus harrisii) have been besieged by a highly contagious cancer that has been pushing the species ever-closer to extinction. In the past 15 years, Devil Facial Tumor Disease has spread throughout Australia’s Tasmania island, killing most Tasmanian devils that catch it.
In an effort to help save the biggest living carnivorous marsupial, conservationists have been collecting individuals for captive populations until the disease has run out of wild individuals to infect. But such a last-ditch strategy could end up constricting the gene pool of a species with an already-limited genetic diversity.
To better guide these protective efforts—and to help untangle behavior of this curious cancer—a team of researches has sequenced the genome of this animal and its tumors. The findings were published online June 27 in Proceedings of the National Academy of Sciences, and more details of the genome are available at The Tasmanian Devil Genome Project.
The team sequenced the full genomes of two devils: Cedric, a captive-born male from northwestern parents, and Spirit, a wild-caught southeastern female. Because they were from the two opposite ends of the Tasmanian devil’s range, the researchers reasoned, they should show a good slice of the species’ current genetic diversity.
Comparing the devil genome to that of other marsupials is tricky as it is rather far away on the phylogenic tree from its already-sequenced cousins, the opossum and the wallaby. So it helped to have two individual to assess against each other. Doing so, the researchers found that they share about 47 percent of their genetic variability—specifically, they have in common many so-called single nucleotide polymorphisms, which are genetic mutations against which relationships are often assessed. That makes these two animals almost twice as similar genetically as people from Japan and China, the researchers pointed out. And the animal’s genome alone is about 300 million base pairs larger than that of a human (3.3 billion versus about 3 billion, respectively).
The genomes of the two devils might also help researchers figure out secrets of the rare immunity to this cancer. Unlike human and most other known mammalian cancers, Devil Facial Tumor Disease (DFTD) spreads from one individual to another individual through physical contact—from a bite or even a casual touch. "Just imagine a human cancer that spread through a handshake," said study co-author Stephan Schuster in a prepared statement. Schuster, a biochemistry and molecular biology professor at Pennsylvania State University added that such an easy spread of cancer "would eradicate our species very quickly."
Spirit had five tumors—one of which was sequenced—which ended up killing her. Cedric, however, had shown resistance to two different strains of the disease (although he was later infected and killed by a third).
About 70 percent of Spirit’s cancer cells’ nuclear DNA did not line up with her own, reinforcing previous observations that the cancer is transferred directly from a different individual. Pinpointing genetic changes that are particular to the cancer—the current study already found 128 amino acid variants—could help find treatments for the deadly disease.
In the meantime, those interested in saving the species from extinction are left to rely on captive breeding. But an effective captive conservation program is "not just a matter of scooping up a few individuals at random," study co-author and Penn State biology and computer science and engineering professor, Webb Miller said in a prepared statement. Instead, using genetic profiles of potential animals, breeders can assemble a population with a known level of genetic diversity. "You want to develop a pool of diverse, healthy individuals that can fight future maladies or even pathogens that have not yet evolved," Schuster said.
The genomic data, along with new genetic profiles of 87 wild individuals, helped researchers outline distinct population groups on the island, providing a roadmap for curating genetically robust captive populations. Collection should come from the seven population areas of the island—including those where the disease is already endemic. "It might seem you’d want to choose only those individuals that are genetically resistant to the DFTD cancer," Schuster explained. "However that would defeat the purpose of maintaining genetic diversity because, by definition, you’d be selecting a tiny subset of the gene pool. Instead, our model suggests a more balanced approach. You don’t want to put out just the one fire."
And for the little devils, the help can’t come soon enough. Researchers estimate that the cancer will have spread to all of the animal’s wild populations as soon as 2016, "making imminent extinction a real possibility," the authors wrote.
For more on the cancer epidemic in Tasmanian devil populations and whether it could affect humans, read "The Tasmanian Devil’s Cancer" from the June 2011 issue of Scientific American, and see the related online slide show.
Image of zookeeper and breeder Tim Faulkner and Tasmanian devil courtesy of Stephan Schuster/Penn State University