Sophisticated Sequencing Techniques Used to Study Ancient Humans

Up to now, studies of this sort on ancestral members of the human species have been hindered by scientists' inability to differentiate the ancient DNA from modern-day human DNA contamination. Now, new research overcomes this hurdle and shows how it is possible to directly analyze DNA from a member of our own species who lived around 30,000 years ago.

DNA is a robust molecule and can persist, conditions permitting, for several tens of thousands of years. Such ancient DNA provides scientists with unique possibilities to directly see into the genetic composition of organisms that have long since vanished from the Earth. Using ancient DNA extracted from bones, the biology of extinct animals as well as of ancient humans, such as the Neanderthals, has been successfully studied in recent years.

This ancient DNA application could not be easily applied to ancient members of the human species. This is because the ancient DNA fragments are multiplied with customized molecular probes that target specific DNA sequences. These probes, however, cannot distinguish whether the DNA they recognize comes from the ancient human sample or was introduced much later, for instance, by the archaeologists who handled the bones. Therefore, conclusions about the genetic make-up of ancient humans were filled with uncertainty.

Using the remains of humans that lived in Russia approximately 30,000 years ago, research by Dr. Svante Pääbo and his colleagues from the Max-Planck Institute for Evolutionary Anthropology (Leipzig, Germany) and published online on December 31, 2009, in the journal Current Biology, now make use of the latest DNA sequencing techniques to overcome this problem. These techniques, known as "second-generation sequencing,” enable the researchers to "read” directly from ancient DNA molecules, without having to use probes to multiply the DNA. Moreover, they can read from very short sequence fragments that are typical of DNA ancient remains because over time the DNA strands tend to degrade.

By contrast, DNA that is younger and only recently encountered the sample would consist of much longer fragments. This and other characteristics, such as the chemical damage incurred by ancient as opposed to modern DNA, effectively enabled the researchers to differentiate between genuine ancient DNA molecules and modern contamination. "We can now do what I thought was impossible just a year ago-- determine reliable DNA sequences from modern humans--but this is still possible only from very well preserved specimens,” stated Dr. Pääbo.

The application of this technology to the remains of members of the human species that lived tens of thousands of years ago now opens a possibility to address questions about the evolution and prehistory of ancient humans that were not possible with previous methods; for instance, whether the humans living in Europe 30,000 years ago are the direct ancestors of present-day Europeans or whether they were later replaced by immigrants that brought new technology such as agriculture with them.

Related Links:
Max-Planck Institute for Evolutionary Anthropology