Life - Fossil DNA has clues to surviving rapid climate change

An example of the 26,000-year-old bison bones retrieved from the Yukon region of Canada, from which DNA was extracted (Image: The University of Adelaide)

Surviving the last ice age was more than just a matter of growing a woolly coat. Rapid global temperature swings had to be matched by equally rapid adaptation. Now a remarkable find from Canada's permafrost could help explain how the trick was done, through a process that might offer organisms a way to cope with the dramatic climate change the world is facing.

DNA extracted from the bones of an extinct bison shows that the environment influenced the way the animal's genes worked without altering the genetic code. It is the best evidence yet that such epigenetic changes can be fossilised.

Inheritance doesn't begin and end with genetic mutations. Environmental factors can modify DNA and lead to heritable changes in the way that genes are expressed – even though the genetic code itself is unchanged.

Brief encounter?

The big unanswered question is whether these epigenetic changes influence the long-term evolution and survival of a species, or whether they disappear too quickly to have any lasting impact.

Some evolutionary biologists favour the first option. They say that exposure to an environmental stress could trigger a useful epigenetic change in many members of a population simultaneously. The trait could then be passed down to most of the next generation.

A beneficial genetic mutation, in contrast – the kind we're more familiar with – spreads only through breeding and so takes much longer to become established in the population.

"Epigenetic modification strikes me as an ideal way for animals to respond to environmental change," says Alan Cooper, a palaeobiologist at the University of Adelaide in South Australia.

Frozen perfection

Before that idea can be tested, though, Cooper needed to show that epigenetics is preserved in the fossil record – the best place to study evolutionary processes over a large number of generations.

A prime spot to go looking for ancient epigenetic signals is in permafrost that formed during the last ice age. The frozen soils are already recognised as the best environment on Earth for preserving the ancient DNA in which epigenetic signals might be found.

Cooper and his team extracted DNA from the bones of a 26,000-year-old extinct bison (Bison priscus) preserved in permafrost in the Canadian Arctic. They later analysed the DNA using a technique called bisulfite sequencing to look for evidence of a particular kind of epigenetic change – DNA methylation. Bisulfite sequencing destroys unmethylated cytosine bases in the DNA, so all cytosines that remain must therefore have been methylated.

Convincing stuff

Sure enough, the team found methylated DNA in the ancient sample. Then they went one step further: most of the methylations they found were in exactly the same spots as methylations in the same genes of modern cattle. That is strong evidence that the ancient methylations were not the product of chemical damage occurring after the bison's death (PLoS One, DOI: 10.1371/journal.pone.0030226).

"I'm convinced, and I'm pretty tough that way," says Hendrik Poinar, a palaeogeneticist at McMaster University in Hamilton, Ontario, Canada, who was not a member of Cooper's team.

The next step will be to gather more ancient samples from before and after a major environmental change – the end of a glaciation, for example, or the arrival of humans in the New World – to see whether any epigenetic changes correlate with the environmental transition. If they do, evolutionary biologists will move a step closer to proving that epigenetic changes help species adapt to rapid change.

Neanderthal action

And that applies to more than just extinct bison. Methylation has been found in ancient DNA once before. In 2009, a team led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, uncovered evidence of the process in Neanderthal and mammoth DNA (Nucleic Acids Research, DOI: 10.1093/nar/gkp1163).

Pääbo says he may soon start gathering data on methylation of Neanderthal DNA as part of his work on Neanderthal genomics. Epigenetics is already thought to occur in humans – it has been cited as an explanation for the high incidence of post-traumatic stress disorder among those whose parents survived the holocaust. Epigenetic data spanning a much longer interval in human prehistory could reveal that the process was key to adapting quickly to a wide range of environmental conditions during the Pleistocene.

Tracking ancient epigenetic changes will inevitably be a tough task. For example, although Cooper's team successfully read methylation from a fossil bison specimen, they could not find a signal in five other bison fossils they examined, which suggests that reading ancient epigenetic signatures requires exceptional preservation.

Tall order

Moreover, individual animals – and even particular tissues within an individual – differ in their style of methylation, so researchers may need many samples to tease evolutionarily meaningful differences from all the variability, says Catherine Suter at the University of New South Wales, Sydney, Australia, who co-led the bison research with Cooper.

Even if researchers can pick the signals from the noise, they will then have to work out what the epigenetic changes do, and whether they are in fact adaptive – a tall order given how little we know about interpreting epigenetic signals even in modern DNA.

"It's a very exciting idea, but I think we're very far away from being able to take advantage of it, because we don't know which parts of the genome are important," says Christina Richards, an ecological genomicist at the University of South Florida in Tampa.

Despite these difficulties, the new results open an exciting avenue of further study. "There's been a huge focus on studying ancient DNA from the sequence point of view. I think it's at least as important to look at DNA methylation, and this shows that's possible," says Andrew Feinberg at Johns Hopkins University in Baltimore, Maryland.

Cloning extinct beasts is a mammoth task

The flashiest – and perhaps the most speculative – use of ancient-DNA research might be to clone extinct beasts like the woolly mammoth. Ancient epigenetic signatures could help.
Sequencing ancient DNA is only part of the challenge. To assemble a functional genome, researchers also need to replicate the ancient epigenetic packaging, which influences exactly how the genes are expressed during the development of an embryo.
Now, thanks to Alan Cooper at the University of Adelaide in South Australia and colleagues, we know that some of these epigenetic labels are preserved in ancient DNA, which brings us a small step closer to the cloning goal, says Hendrik Poinar of McMaster University in Hamilton, Ontario, Canada.
Methylation is not the only important epigenetic character, however – and other signatures are less likely to fossilise, says Cooper. Looks like we will have to wait a little longer to resurrect the mammoths.

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