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Tasmanian tiger genome offers clues to its extinction

Geneticists analyse DNA from preserved pup, more than 80 years after the last of its kind died.

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Thylacine in captivity

One of the last captive thylacines, photographed in the 1900s.Credit: Paul Popper/Popperfoto/Getty

The last known thylacine, a marsupial predator that once ranged from New Guinea to Tasmania, died on 7 September 1936 in a zoo in Hobart, Australia. The species’ complete genome, reported on 11 December in Nature Ecology and Evolution, offers clues to its decline and its uncanny resemblance to members of the distantly related dog family1.

“They were this bizarre and singular species. There was nothing else like them in the world at the time,” says Charles Feigin, an evolutionary developmental biologist at the University of Melbourne, Australia, who was involved in the sequencing effort. “They look just like a dog or wolf, but they’re a marsupial.”

People have been nothing but bad news for the thylacine (Thylacinus cynocephalus), commonly known as the Tasmanian tiger. The species’ range throughout Australasia shrivelled as early hunter-gatherers expanded across the region, and the introduction by humans of the dingo (Canis lupus dingo) to Australia several thousand years ago reduced numbers still further, leaving an isolated thylacine population clinging on only in Tasmania. European colonists in the nineteenth century saw the predators as a threat to their sheep, and paid a bounty of £1 per carcass. Thylacines were on the cusp of extinction in the wild when the rewards were ended in 1909, leading zoos to pay handsomely for the last few individuals.

Hundred-year-old pup

Thylacine pup specimen C5757 preserved in jar.

Geneticists sequenced DNA from a thylacine pup preserved in alcohol since it died in 1909.Credit: Benjamin Healley/Museums Victoria

Geneticists had previously sequenced the species' mitochondrial genome — a short stretch of DNA that is maternally inherited — using hairs plucked from a thylacine stored at the Smithsonian Institution in Washington DC2. In the latest study, a team led by developmental geneticist Andrew Pask of the University of Melbourne obtained the much longer nuclear genome, by sampling tissue from a one-month-old thylacine that had been found in its mother's pouch in 1909 and was preserved in alcohol.

The nuclear genome holds information about many more ancestors than a mitochondrial genome. The team saw a steep drop in genetic diversity suggesting that thylacine numbers began dwindling some 70,000–120,000 years ago, well before humans reached Australia. Similar patterns have been seen in the genome of the Tasmanian devil (Sarcophilus harrisii)3. Feigin suspects that a cooling climate shrank the habitats of both species, potentially making them more vulnerable to humans.

Although thylacines are not particularly closely related to the dog family, or canids — the two groups share a common ancestor that lived around 160 million years ago — the shapes of their heads are remarkably similar. This hints that both species may have adapted similarly to their predatory lifestyles.

To test for such convergent evolution, Feigin and Pask’s team identified 81 protein-coding genes in which both canids and thylacines had acquired similar DNA changes, including some with roles in skull development. But none of the genes in which these changes occurred seemed to be evolving under natural selection in both lineages, so it's unlikely that they were responsible for the species’ shared traits.

Instead, the researchers propose that DNA that does not affect protein sequences — but instead influences how they are expressed — underlies the long snouts and other features shared by the two groups.

“That’s a reasonable inference, given what we increasingly understand from development and the evolution of development,” says Sean B. Carroll, an evolutionary developmental biologist at the University of Wisconsin–Madison. New physical traits tend to arise when the expression of developmental pathways shared across animals is tweaked. Identifying the specific pathways and regulatory DNA sequences that shaped the thylacine’s skull will be difficult, Carroll says, because it requires identifying suspect thylacine DNA sequences and inserting them into another organism, such as a mouse or related marsupial, to see their effects.

Back from the dead

Michael Archer, a palaeontologist at the University of New South Wales in Sydney, sees the genome-sequencing effort as important progress towards his long-time vision of bringing the marsupial back from extinction. Advances in genome editing and reproductive biology, such as artificial wombs, provide a viable path to de-extinction, Archer says. “What they have done is provided the wherewithal to take the next giant step.”

But Beth Shapiro, an evolutionary geneticist at the University of California, Santa Cruz, whose team has sequenced the genomes of extinct animals such as the passenger pigeon, warns that genome projects cannot solve the problem of disappearing species.

“The thylacine is extinct, because we made it so. We cannot bring it back,” Shapiro says. “When I see the videos or images of the last thylacines, these are harsh reminders of the pressing need to develop technologies to stop other species from becoming extinct.”

Nature 552, 156-157 (2017)

doi: 10.1038/d41586-017-08368-1
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References

  1. 1.

    Feigin, C. Y. et al. Nature Ecol. Evol. http://dx.doi.org/10.1038/s41559-017-0417-y (2017).

  2. 2.

    Miller, W. et al. Genome Res. 19, 213–220 (2009).

  3. 3.

    Murchison, E. P. et al. Cell 148, 780–791 (2012).

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