Fossil DNA Could Save Species

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Australia has the highest rate of terrestrial vertebrate extinction in the last 200 years and many species on the endangered list.
Corbis

THE GIST

- Remnants of long-dead animals and plants may offer clues how to conserve their modern-day descendants.

- Knowing where a species lived in the past can help with decisions about reintroduction to a new area.

- Ancient DNA can also tell us how species could respond to climate change.

For Mike Bunce, the skin, bones and dung of ancient Australian native animals are much more than the sum of their parts -- they are a time machine to the past.

Bunce, who heads the ancient DNA lab at Murdoch University in Western Australia, searches the remnants of long-dead animals and plants for clues about how to conserve their modern-day descendants.

Known as "conservation paleobiology," this emerging field of science relies heavily on fossil and ancient pollen analysis together with carbon dating and, importantly, ancient DNA analysis to answer vital questions about the history of endangered species like discovering where an endangered species lived hundreds of years ago, to how it coped with massive changes in the environment.

As Bunce explains, the field has only recently gained momentum thanks to our growing knowledge about the genetic make-up of modern species, currently available genetic tools and the falling cost of DNA analysis.

"There are a variety of genetic tools now at the disposal of scientists, and these tools have had meaningful impacts in managing modern populations," he says. "It is only natural that this is now spilling over into the past to help us better understand things like biodiversity loss."

And analyzing ancient DNA isn't just a fancy form of fossil analysis.

While the fossil record might show a particular species living in one place for tens of thousands of years, the genetics of those fossils might reveal "entire genetic types disappearing and new populations invading" says Alan Cooper, director of the Australian Centre for Ancient DNA at the University of Adelaide.

"It puts a whole new perspective on the fossil record," he added.

Knowing where a species lived in the past can help with decisions about reintroduction to a new area and interbreeding animals from different modern populations.

"If we're looking at re-establishing an ecosystem to what it formally looked like it's important that we know what used to live there not hundreds of years ago but thousands of years ago," Bunce says.

For example, Bunce's team has found that the woylie, a small marsupial whose numbers have declined rapidly, particularly in the past decade, used to live over the entire south-west of Western Australia.

"We can tell that genetic signatures used to move around the entire south-west area," says Bunce.

There are now only a few isolated woylie populations left. "So we can't really get too precious about interbreeding these populations now because in the past they were definitely connected."

The research also found that the woylie has lost around 90 per cent of its genetic diversity since Europeans arrived with feral animals 200 years ago. But all is not lost.

"Genetic diversity take times to build. You can also use modern genetic tools to make decisions to breed certain animals to facilitate gene flow," says Bunce.

But not all modern populations of animals can be interbred.

Jeremy Austin, deputy director of the Australian Centre for Ancient DNA, was recently involved in research using museum specimens thousands of years old to determine the past geographical range of modern day Victorian and NSW rock wallabies.

Because the two belong to distinct genetic lineages, interbreeding can lead to 'nasty genetic effects', says Austin, so mapping their old ranges means that conservationists now know which type of animal to reintroduce to particular areas.

One of Australia's most beloved animals, the Tasmanian devil, is also in need of a helping hand from ancient DNA.

More than 70 percent of devils have been infected with facial tumor disease, a contagious cancer that can spread between devils because of a lack of genetic diversity.

Recently, scientists have suggested that a population of devils in the northwest of Tasmania may be resistant to the disease because they have a different variant of the "major histocompatibility complex" (MHC) gene family.

The MHC genes code for proteins that ensure the body launches an immune response against foreign tissue. If two animals have the same MHC genes, cancerous tissue passed from one to another won't be rejected, allowing the cancer to take hold.

Austin and his team are using DNA from museum specimens to find out when devils may have lost genetic diversity in their MHC genes and the genetic impact of the disease in the past.

"The important question is have devils had this disease for thousands of years and been surviving until they lost diversity when Europeans arrived? Or is it just an accident that the disease has turned up and taken advantage of the low diversity?" says Austin.

And if devils survive the disease it will be important to know how much of past genetic diversity remains, to assess how much they will be able to adapt to changes in the environment or new diseases, says Austin.

Ancient DNA can also tell us how species could respond to climate change, says Cooper.

Scientists are busy modeling how the climate will change as average temperatures increase, but the impact this will have on animals and plants has received less attention because it's much more difficult to predict how complex ecosystems will respond, he says.

"That's where conservation paleobiology comes into its own," he says. "You're taking information from the past, during, for example, periods of rapid climate change, to look at consequences that you can't gain from looking at the last few hundred years."

Looking at DNA from animals that lived between 18,000 and 10,000 years ago (from just after the last glacial period to the beginning of the Holocene period) allows us to observe a huge 'experiment' as the Earth warmed, he says.

"The most surprising stuff ... is the incredible dynamism of the response of populations to climate: how violent it is; there are extinctions and migrations and replacements -- huge see-sawing of populations. That's the kind of thing we absolutely need to know about if we're trying to predict what are the consequences of temperature change."

But however good researchers become at inferring the future from the past, and however sophisticated technologies become, they will always be constrained by the lottery of past conditions.

Australia is a challenging place to work with ancient DNA, says Bunce. The hot climate means it rarely remains intact.

"Antarctic environments allow for conditions that preserve DNA for up to one million years but the oldest DNA we've managed to get from Australian conditions is about 20,000 years old," says Bunce.

Bunce's team often take sediments from cave sites, such as Western Australia's South-West Caves, for analysis because they tend to be protected from the wildest swings in temperature.

Scientists are always going to be working with tiny fragments of DNA, adds Cooper, and are always going to need specimens to have that unique set of circumstances for the DNA to be preserved.

"That's always going to give you a limited pool of samples to work from," he says.

But the work is essential, says Austin.

Australia has the highest rate of terrestrial vertebrate extinction in the last 200 years and many species on the endangered list.

"For all the wrong reasons we should be at the forefront of using ancient DNA to try and save what's left," he says.

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