Svante Pääbo, the Swedish director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and his team analysed some four billion base pairs of DNA from Neanderthals – a species which died out more than 30,000 years ago.
An initial analysis of the resulting genome sequence draft reveals that Neanderthals left traces of themselves in the genomes of some modern humans, the study, published in this month's Science journal, revealed.
"The comparison of these two genetic sequences enables us to find out where our genome differs from that of our closest relative," Pääbo said in a statement.
The analysis of over 1 billion DNA fragments comes from bones found in Croatia, Russia, Spain, as well as from the original Neanderthal found in Germany.
The scientists developed a new method of separating DNA microbes that had lived in the bones over the last 40,000 years and the true DNA of the Neanderthals themselves, the statement said. Enough DNA fragments were retrieved to account for over 60 percent of the entire Neanderthal genome.
"Over 95 percent of the DNA in one sample originated from bacteria and micro-organisms which colonised the Neanderthal after his death," Pääbo said.
After comparing the human and Neanderthal genome sequences, they discovered that contrary to the common belief that the two species are not related, it appears the two actually bred enough for traces to appear in between one and four percent of modern human DNA.
Previous tests carried out on the DNA of Neanderthal mitochondria, which represented just a tiny part of the whole genome, had not found any evidence of such interbreeding or "admixture."
"Those of us who live outside Africa carry a little Neanderthal DNA in us," Pääbo said.
Neanderthals are slightly more closely related to humans from outside Africa than to Africans, suggesting a contribution of Neanderthal DNA to the genomes of present-day non-Africans, the research revealed.
Neanderthals show the same relationship with all humans outside Africa, whether from Europe, east Asia or Melanesia. The researchers offered a plausible explanation for the relationship.
"Neanderthals probably mixed with early modern humans before Homo sapiens split into different groups in Europe and Asia," said Pääbo.
This could have occurred in the Middle East between 100,000 and 50,000 years ago before the human population spread across East Asia. Archaeological findings in the Middle East have shown that Neanderthals and modern humans overlapped in time in this region. To date, no Neanderthal remains have been so far found in East Asia. They lived in Europe and Western Asia.
Now the group is working to determine which modern human genes may have come from Neanderthals and whether they provided an evolutionary advantage. So far, they have found genes related to cognitive function, metabolism and cranial features, the collar bone, and rib cage, the statement said.
"We will also decode the remaining parts of the Neanderthal genome and learn much more about ourselves and our closest relative," Pääbo said.