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In an astonishing feat of DNA analysis, a German team has published the full genome of an extinct human group, the Denisovans, known only from a bone fragment and two teeth found in a Siberian cave.
Scientists from the Max Planck Institute for Evolutionary Anthropology in Leipzig had just a 10 milligram (0.00035oz) sample from a girl’s broken finger bone which Russian archaeologists had discovered in Denisova Cave in the Altai Mountains. She lived between 30,000 and 80,000 years ago – the dating remains uncertain.
Using new techniques for amplifying and analysing tiny amounts of DNA, they were able to provide a picture of the Denisovan genome almost as sharp and complete as the best modern human genome. The DNA was so well preserved because of the site’s exceptionally cold conditions.
“No one thought we would have an archaic human genome of such quality,” said Matthias Meyer, co-author of the findings. “Everyone was shocked . . . That includes me.”
However, the genome analysis, published in the journal Science, leaves many questions about the Denisovans unanswered. The researchers know little about the physical appearance of the girl, beyond the fact that her genes would have given her dark skin, eyes and hair.
“The truth is, of course, that one can say little about how people look from just studying their DNA sequences,” said Svante Pääbo, the project leader.
The analysis confirms that Denisovans were a separate species or sub-species, distinct from the Neanderthals and ancestral modern humans with whom they shared the Eurasian continent for tens of thousands of years. They were more closely related to Neanderthals than modern humans.
Both Neanderthals and Denisovans contributed a little to the genome of some modern Europeans and Asians but not to Africans, suggesting that modern humans interbred to a limited extent with the Neanderthals and Denisovans they would have encountered after moving out of Africa into Eurasia about 70,000 years ago.
Comparison of the ancient genome with modern humans around the world shows that the highest proportion of Denisovan DNA, about 3 per cent, occurs among today’s inhabitants of Papua New Guinea.
Although the researchers have only one Denisovan genome, they could distinguish the contributions of the girl’s two parents – and from these they concluded that Denisovans had very low levels of genetic diversity, though there was no evidence of inbreeding.
A big uncertainty is how long ago Denisovans and Neanderthals split from ancestral modern humans. It could have been at any point between 170,000 and 700,000 years, the researchers say.
“Since the split from modern humans the population [of Denisovans] seems to have been pretty small for a long period of time, hundreds of thousands of years,” said David Reich of Harvard Medical School, who worked with the German group on the analysis.