Sequencing the extinct

Researchers have sequenced the mitochondrial genome of the extinct Tasmanian tiger, or thylacine, using museum-preserved tissue samples collected from some of the last remaining individuals.

The mitochondrial DNA used to complete the analysis, which appears in the latest issue of Genome Research, came from hairs on a thylacine skin that had been stored at room temperature for more than 100 years and from a whole tiger preserved in ethanol since 1893.

Pennsylvania State University geneticist Stephan Schuster led the study, and said that modern sequencing techniques enabled the researchers to harvest sufficient amounts of genetic material from the museum specimens. The researchers generated hundreds of thousands of short reads from the preserved materials using whole-genome shotgun sequencing.

Schuster and his Penn State colleague and coauthor Webb Miller also collaborate on a project to harvest ancient DNA from extinct woolly mammoth bones, which often yield analyzable DNA due to the fact that their tissues are deposited and preserved in permafrost. "We kind of looked at the thylacine as the other end of the spectrum from the mammoth" in terms of the sample's integrity Schuster told The Scientist. "We wanted to show that our method is so robust that we could also do this very difficult sampling."

These findings helped place the thylacine in an improved phylogenetic tree with distantly related, extant marsupials and generated possible markers for geneticists seeking to trace the process of extinction through thylacine DNA. They also open the door to the feasibility of successful molecular analyses in museum specimens--something Schuster has dubbed "museomics"--that might not be as well-preserved as deep-frozen woolly mammoth DNA. "You don't have to start from bone every time," Schuster said. "There are advantages to look in other tissues that might also preserve."

The results also validate ancient DNA sequencing techniques and put the sequencing of the complete thylacine genome and that of other extinct organisms within reach. "It's not a question of whether [sequencing the entire thylacine genome] can be done," Webb said, "it's just about coming up with the resources. Any megafauna that went extinct in the last 100,000 years are within reach."

Related stories:

Trash to treasure [January 2008]

Hair yields ancient DNA [27th September 2007]

Video shows the last known motion picture footage of a living thylacine. Shot at the Hobart Zoo in 1933. Courtesy of The Thylacine Museum