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Last Updated: Monday, 19 September 2005, 12:48 GMT 13:48 UK
'Better' DNA out of fossil bones
By Alison Ross
BBC News

Televisual impression of Neanderthal man (BBC)
Neanderthals are thought to have been replaced by modern humans
Improved technologies for extracting genetic material from fossils may help us find out more about our ancient ancestors.

Scientists in Israel have just developed a new technique to retrieve better quality, less contaminated DNA from very old remains, including human bones.

It could aid the study of the evolution and migration of early modern humans, as well as extinct populations such as our close relatives, the Neanderthals.

Many researchers would dearly love to get their hands on DNA samples from hominids further back in time - from those that lived 100,000 years ago or more - to find out how they were related to people alive today.

But fossil studies this far back in time have long been hindered by contamination with foreign genetic material and the problem of recovering long, intact DNA sequences.

The new method provides hope, however.

What's real?

"DNA gets everywhere. So when we're dealing with a sample and you find it's got human DNA in it - is that DNA from the fossil, or is it actually DNA from the person who unearthed it?" says Professor Chris Stringer, the head of human origins at the Natural History Museum in London, UK.

The DNA molecule is held together by chemical components called bases (C, G, T, and A)
The DNA within our cells contains the genetic information that spells out the "code of life"
It is wound up in bundles known as chromosomes that are found in the cell nucleus (nuclear DNA); DNA also lies within mitochondria outside of the nucleus (mtDNA)
mtDNA is inherited only through females via the egg and can be used to trace backwards through evolution; the male sex chromosome (Y) similarly tracks male evolution
DNA breaks down over time making recovery difficult from ancient specimens. Fossils are often contaminated with modern human DNA during handling, and it is difficult to tell this apart from ancient DNA
Also, DNA falls apart over the course of time.

"It breaks up into very small fragments so it is quite technically complicated to put it all back together again," explains Dr Robert Foley, the director of the Leverhulme Centre for Human Evolutionary Studies at the University of Cambridge, UK.

Freezing provides the ideal preservation conditions. The most widely accepted oldest DNA yet isolated comes from 400,000-year-old plants found in ice in Siberia. But most specimens are not excavated from such places.

An improved technique for retrieving DNA from fossil bone, just published in the journal Proceedings of the National Academy of Sciences (PNAS), may help.

Dr Michal Salamon, from the Weizmann Institute of Science in Rehovot, Israel, and colleagues, showed that "crystal aggregates", small mineral pockets formed during fossilisation, can preserve DNA better than the rest of the bone.

They compared DNA extracted from these crystal aggregates with genetic material taken from untreated, whole-bone powder. The samples were taken from eight different modern and fossil bones.

Isolated crystals on the nanometre scale (Salamon/PNAS)
The crystals are so small they can only be seen with an electron microscope
They found better preserved, less contaminated DNA could be recovered from the isolated crystals.

This approach, "significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones", they told PNAS.

Commenting on the latest research, Dr Michael Hofreiter, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who helped decode 40,000-year-old nuclear DNA from a cave bear earlier this year, said: "It's possible; but there need to be more studies on more samples, and they need to show that you don't get human contamination of animal bones.

"Then I would believe that it is a breakthrough for ancient DNA research."

The big split

Scientists are hopeful the new technique will help them get at the DNA in the chromosomes of a cell - the nuclear DNA.

Ancient DNA research has so far mainly focused on mitochondria, the tiny "power-stations" of the cell. These exist outside of the nucleus and have their own DNA. And, although this information is very useful, it is more limited in its scope than that which could be obtained from nuclear DNA.

Reconstruction of a Neanderthal     (Image: BBC)
Neanderthals evolve about 250,000 years ago
Their range extends from Europe to Central Asia and the Middle East
Modern humans leave Africa about 60,000 years ago and arrive in Europe around 40,000 years ago
By 27,000 years ago, the Neanderthals are extinct
Possible reasons include climate change and competition with modern humans
It is partly a question of sensitivity.

"There's about 1,000 times more mitochondrial DNA than nuclear DNA in our cells, so it's much easier to pick up," explains Professor Stringer.

The mitochondrial DNA is inherited only through the egg - through females. This means it is a useful marker for tracing a line back into the past, as it has never been mixed with DNA from males.

"One of the most important discoveries from studying ancient mitochondrial DNA is the estimate of when humans diverged in evolution from the Neanderthals - around half a million years ago," according to Dr Foley.

Professor Stringer adds: "We've now got about 10 Neanderthal specimens of around 40-50,000 years old that have yielded DNA that is clearly distinct from anyone alive today."

This means scientists can be sure that it is ancient, not just modern DNA from contamination.

It has also given them a measure of how different Neanderthals were from modern people.

"Neanderthals are three times as different from us as we all are from each other," says Professor Stringer.

Species debate

But there remains the hotly debated question of whether Neanderthals were a completely separate species to us. Professor Stringer says that they are if that assessment is based on studying their bone anatomy.

However, the evidence from mitochondrial DNA is somewhat ambiguous.

"The mitochondrial DNA on its own can't tell us if we're a distinct species," he explains.

"It depends what mammal you take. There are some species where the difference in mitochondrial DNA between us and Neanderthals would say they were a different species.

"Whereas in chimpanzees, our closest relative, you could contain the variation between us and Neanderthals in a single species alive today in Africa."

Scientists need to recover better DNA from our fossils, especially the nuclear DNA.

"Each gene has a separate evolution so to understand Neanderthals properly we will need different bits of their DNA to see if they're all telling us the same story," he adds.

Population movements

The male sex chromosome (the "Y") is useful for tracking male inheritance, since males inherit their Y chromosome only from their father.

Using both mitochondrial and Y chromosome DNA from people alive today, complex pathways have been mapped for how modern humans got to where they are - but there are problems.

Dr Mim Bower, an ancient DNA researcher at the McDonald Institute for Archaeological Research in Cambridge, UK, gives an example.

"Using modern DNA we see a different pattern of settlement in the Pacific islands between men and women - the mitochondrial DNA patterns show a different migration pattern to the Y chromosome DNA."

Studying the DNA not of modern humans but of their distant ancestors could help answer such questions.

"At the moment we can't follow that into the past as it's very difficult to get nuclear DNA," Dr Bower says.

This is especially problematic for the Y chromosome, which is nuclear.

  • Map shows first migratory routes taken by humans, based on surveys of different types of the male Y chromosome. "Adam" represents the common ancestor from which all Y chromosomes descended
  • Research based on DNA testing of 10,000 people from indigenous populations around the world
    Source: The Genographic Project

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