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Ancient DNA deciphers our past

Huge advances in the ability to gather and decode ancient DNA from humans and animals have meant a paradigm shift for science, writes Annie Hastwell.

"Why did the chicken cross the Pacific?"

Laughter at the joke ripples around the room of scientists at the weekly research meeting at the Australian Centre of Ancient DNA, where Professor Alan Cooper leads a fast-faced 'show and tell' of current projects.

The atmosphere is electric with interest and the keen crowd of mainly 20 and 30-something researchers betray by their many and varied accents that they've come from all over the world.

They lean forward around the table, intently focused as their colleagues present powerpoints showing their findings about the long ago Pacific meanderings of the ancestral Polynesian chicken.

Along with the friendly banter, Cooper eggs the group on to robustly critique the presentations. Do those colours work on that background? Is there too much information on that one page? Is that complex map really getting the point across?

Sessions like this are vital preparation for taking the latest findings about ancient chickens — and thus humans — to the world.

"Animals leave more of a signal on the landscape, you're more likely to find lots of chicken bones than lots of human bones," explains Cooper, who heads the Centre.

The key, he explains, is that chickens travel with humans, across landscapes and seas, and mapping their movements starts to give clues about which groups were doing what in ancient times.

In just a few years, huge advances in the ability to gather and decode ancient DNA from humans and animals have meant a paradigm shift for the science.

The whole understanding of human evolution has been turned on its head in the last 10 to 15 years, says Cooper.

"What we are finding now is challenging the way we thought evolution happened, challenging our understanding of how, as humans, we got where we are", he says.

His own current project is a world first, looking at the history of human health by examining the calculus or tartar on ancient teeth, and seeing how the origins of many modern chronic diseases can be tracked back to when society moved from Neolithic hunter-gatherer to urbanisation.

Exponential advances in maths, computing and biotechnology, driven by medical technology and the human genome project, have made it possible to extract genetic code out of ever more ancient remains, bringing ancient DNA studies together with archaeology to reconstruct human evolutionary history.

Dr Mike Bunce, from Curtin University's Trace and Environmental DNA Laboratory, is an expert in extracting and amplifying DNA from New Zealand's extinct birds such as the moa, and obtaining DNA profiles from ice and sediment cores.

"Before this next generation sequencing we were reliant on just looking at the morphology of fossils and their ages, but now that biomolecules are coming into play we're getting a more complete picture of what was going on in the ancient past.

"Developments in DNA sequencing technologies have transformed this process — a good analogy is someone replacing your Morse-code machine with a personal computer," says Bunce.

He says the oldest DNA to be recovered so far, taken from the bottom of the Greenland ice core, has been dated at 800,000 years old.

"It's theoretically possible to go back a few million years especially in frozen conditions, and while non-frozen fossils a million years old may have DNA preserved in them, practically you need big enough fragments of DNA to conduct meaningful analyses", he says.

The condition of the DNA and the number and length of strands are important factors, with warm climates less likely to yield good specimens.

Hi-tech sequencing machines in the lab are now able to pump out billions of base pairs of DNA, and then, says Bunce, "we throw it onto a computer and work out where all these pieces of genetic code fit; a bio-thematic jigsaw if you like".

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More questions than answers

That jigsaw is building a picture of who we are as humans and where we came from, but in the flurry of discoveries brought about by the expanded research possibilities it is raising more questions than answers.

Take the recent analysis of a 400,000 year old femur, found in the Pit of Bones in the Atapuerca caves in Northern Spain. Rather than the Neanderthal origins scientists expected to find in the DNA, they found evidence that the most recently identified hominid, the mysterious Denisovan, previously thought to be confined to Siberia and Australasia, had at some stage interbred with the European Neanderthals.

"It's showing us how little we knew about human evolution out of Africa. The hybridising we're finding between species, both human and animal, is challenging our view of what a species is; we used to think it was a group that didn't breed with anything else," says Cooper.

He says advances in DNA research have meant scientists are pushing back into what he calls a 'shady zone'.

"When we get into this Pleistocene period you're finding mixing and matching, and new groups you didn't know about, whereas if you just look at the modern human DNA it's a misleadingly simple picture.

For example we didn't know the Denisovan DNA existed in modern humans until we'd mapped the genome. We had already been looking at it but couldn't identify that those bits came from another species entirely."

The 2003 discovery of another enigmatic ancient human species, Homo Floresiensis, the so-called Hobbits, in Flores, Indonesia, complicates the picture even further. They appear to be a race of tiny archaic humans who survived the Neanderthals and also mysteriously were able to make the dangerous marine crossing over the Wallace Line near Borneo.

More recent evidence has showed the Denisovans probably also making the same crossing and breeding with humans.

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Reconciling the fossil record

The challenge, says Wolfgang Haak, is to reconcile the genetic signatures with the fossil record.

"We have the full Denisovan genome but no skeleton, just a finger bone, and then in Spain we have those fossils that are Neanderthals but genetically they look like the Denisovans but we can't compare because we don't have a Denisovan fossil. Then in Flores we have a perfect Hobbit skeleton but no DNA," says Haak, also from the Australian Centre for DNA.

Haak's description of himself as working in the field of 'human palaeobiology' or 'molecular archaeology' illustrates just how much the new technologies are bringing different scientific disciplines together.

He is working in conjunction with Harvard, analysing both DNA and archaeological remains to reconstruct why, when and how, over 10,000 years, different cultures have changed, moved in, moved on, and interbred to create the Europe we now know.

For him, ancient DNA is the "killer app" that has taken a lot of guesswork out of his job.

"Before if you compared two genomes, say of a European and an Asian person, there's a shared ancestry which tells you those two genomes go back in time and at some stage probably converged but we had no idea when exactly that was.

"The ancient DNA provides a 'time stamp' to identify when that migration or merging event happened. You get a much more precise time estimate and if you do that multiple times you get a very precise picture of human mobility and migration around the globe and admixture with previous hominids".

The project is potentially trail blazing, says Cooper.

"Europe is the ideal starting place because of the number of bones and what we know about the history of that area. If we are able to interpret our genome with that history, working out where your bits come from using modern data and ancient points to tie it together into a completed picture, it will be the first time anyone has ever come up with a genetic history of a continent on this scale."

In the Pacific, the DNA of the humble chicken plays a vital connection to the story of the ancient humans who carted them around in canoes.

Watching Cooper's easy and open communication style as he evaluates his team's research presentations it's clear he has an eye to how these findings will be understood when they do reach the public

"Why chickens?" he suddenly demands of one presenter.

Surprised at first, caught up with maps and facts and figures, the scientist suddenly relaxes and explains: humans have always liked animals as companions, chickens are small and easy to transport, they lay eggs, and they can be eaten if times get tough.

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