DNA analysed from early European
By Paul Rincon
Science reporter, BBC News
Distinguishing ancient DNA from modern has been difficult until now
Scientists have analysed DNA extracted from the remains of a 30,000-year-old European hunter-gatherer.
Studying the DNA of long-dead humans can open up a window into the evolution of our species (Homo sapiens).
But previous studies of this kind have been hampered by scientists' inability to distinguish between the ancient human DNA and modern contamination.
In Current Biology journal, a German-Russian team details how it was possible to overcome this hurdle.
Svante Paabo, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and colleagues used the latest DNA sequencing techniques to study genetic information from human remains unearthed in 1954 at Kostenki, Russia.
Excavations at Kostenki, on the banks of the river Don in southern Russia, have yielded large concentrations of archaeological finds from the Palaeolithic (roughly 40,000 years ago to 10,000 years ago). Some of the finds date back as far as 45,000 years.
The ironic thing is that our group has been one of those that raised this issue
Professor Svante Paabo, Max Planck Institue
The DNA analysed in this study comes from a male aged 20-25 who was deliberately buried in an oval pit some 30,000 years ago.
Known as the Markina Gora skeleton, it was found lying in a crouched position with fists reaching upwards and a face orientated down towards the dirt. The bones were covered in a pigment called red ochre, thought to have been used in prehistoric funeral rites.
The type of DNA extracted and analysed is that stored in mitochondria - the "powerhouses" of cells. This mitochondrial DNA (mtDNA) is passed down from a mother to her offspring, providing a unique record of maternal inheritance.
Using technology pioneered in the study of DNA from Neanderthal bones, they were able to distinguish between ancient genetic material from the Kostenki male and contamination from modern people who handled the bones, or whose DNA reached the remains by some other means.
The ancient skeleton was unearthed in 1954 at Kostenki in Russia (Courtesy of Vladimir Gorodnyanskiy)
The new approach, developed by Professor Paabo and his colleagues, exploits three features which tend to distinguish ancient DNA from modern contamination. One of these is size; fragments of ancient DNA are often shorter than those from modern sources.
Previous ancient DNA studies used the widespread polymerase chain reaction (PCR) technology. PCR amplifies a few pieces of genetic material, generating thousands to millions of copies of a sequence. But the researchers found many fragments of ancient DNA were too small to be amplified by PCR.
A second characteristic of ancient DNA was its tendency to show particular changes, or mutations, in the genetic sequence at the ends of DNA molecules.
A third feature was a characteristic breakage of molecules at particular positions in the DNA strand.
The apparent ease with which modern DNA can infiltrate ancient remains has led many researchers to doubt even those studies employing the most rigorous methods to weed out contamination by modern genetic material.
"The ironic thing is that our group has been one of those that raised this issue," Professor Paabo told BBC News.
"To take animal studies on cave bears, for example, if we use PCR primers specific for human DNA on cave bear bones, we can retrieve modern human DNA on almost every one. That has made me think: 'how can I trust anything on this'."
Large concentrations of Palaeolithic finds have come from Kostenki
Using the new techniques, the researchers were able to sequence the entire mitochondrial genome of the Markina Gora individual.
Future studies like the one in Current Biology could help shed light on whether the humans living in Europe 30,000 years ago are the direct ancestors of modern populations or whether they were replaced by immigrants who introduced farming to the continent several thousand years ago.
The modern gene pool contains a wide variety of mtDNA lineages. Studying these maternal lineages provides scientists with clues to the origins and histories of human populations.
Scientists look for known genetic signatures in order to classify an individual's mtDNA into different types, or "haplogroups". These haplogroups represent major branches on the family tree of Homo sapiens.
The researchers were able to assign the Kostenki individual to haplogroup "U2", which is relatively uncommon among modern populations.
U2 appears to be scattered at low frequencies in populations from South and Western Asia, Europe and North Africa.
Despite its rarity, the very presence of this haplogroup in today's Europeans suggests some continuity between Palaeolithic hunters and the continent's present-day inhabitants, argue the authors of the latest study.
U2, along with closely related haplogroups such as U5, are among those which could plausibly have arrived in Europe during the Palaeolithic.
Geneticists use well-established techniques to "date" particular genetic events, such as when a haplogroup first diversified. The "U" branch (comprising haplogroups U1, U2, U3 and so on) appears to be more ancient than many other genetic lineages found in Europe.
A recent study found a very high percentage of U types in the skeletal remains of ancient hunter-gatherers from Central Europe compared with later farming immigrants and modern people from the region.
Meanwhile, an analysis last year of mtDNA from 28,000-year-old remains unearthed at Paglicci Cave in Italy showed this individual belonged to haplogroup "H" - the most common type found in modern Europeans.