Extinct Human Fossil’s Complete Genome Decoded

German scientists have completed the entire genome sequence of a Denisovan, a relative of an Asian group of extinct humans related to Neandertals.

In 2010, Dr. Svante Pääbo, from the Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany), and his colleagues presented a draft version of the genome from a small fragment of a human finger bone discovered in Denisova Cave in southern Siberia. The DNA sequences showed that this individual came from an earlier unknown group of extinct humans that have become known as Denisovans. Together with their sister group the Neandertals, Denisovans are the closest extinct relatives of currently living humans.

The Leipzig team has now developed sensitive novel techniques, which have allowed them to sequence every position in the Denisovan genome about 30 times over, using DNA extracted from less than 10 milligrams of the finger bone. In an earlier draft version published in 2010, each position in the genome was determined, on average, only twice. This degree of resolution was enough to establish the relationship of Denisovans to Neandertals and modern-day humans, but frequently made it impossible for researchers to study the evolution of specific parts of the genome. The now-completed version of the genome allows even the small differences between the copies of genes that this individual inherited from its mother and father to be differentiated.

On February 8, 2012, the Leipzig group made the entire Denisovan genome sequence available to researchers over the internet. “The genome is of very high quality,” said Matthias Meyer, who developed the techniques that made this technical feat possible. “We cover all nonrepetitive DNA sequences in the Denisovan genome so many times that it has fewer errors than most genomes from present-day humans that have been determined to date.”

The genome represents the first high-coverage, complete genome sequence of an archaic human group--a huge advance in the study of extinct forms of humans. “We hope that biologists will be able to use this genome to discover genetic changes that were important for the development of modern human culture and technology, and enabled modern humans to leave Africa and rapidly spread around the world, starting around 100,000 years ago,” said Dr. Pääbo.

The genome is also expected to reveal new aspects of the history of Denisovans and Neandertals. The scientists plan to present an article describing the genome later in 2012. “But we want to make it freely available to everybody already now,” said Dr. Pääbo. “We believe that many scientists will find it useful in their research.”

The project is made possible by funding from the Max Planck Society and is part of efforts since almost 30 years by Dr. Pääbo’s group to study ancient DNA. The finger bone was found by Prof. Anatoly Derevianko and Prof. Mikhail Shunkov, from the Russian Academy of Sciences (Moscow) in 2008 during their excavations at Denisova Cave, a unique archeological site that contains cultural layers indicating that human occupation at the site began up to 280,000 years ago. The finger bone was found in a layer that has been dated to between 50,000 and 30,000 years ago.

The genome is available as a Public Data Set via Amazon Web Services (AWS) as well as at the Max Planck Website (please see Related Links below).

Related Links:
Max Planck Institute for Evolutionary Anthropology
Denisovan Genome at Max Planck
Public AWS Dataset