A replica of the tiny Denisovan finger bone where the DNA sequence was recovered, resting on a hand. Image: Max Planck Institute for Evolutionary AnthropologyDenisovian Gene sequence offers insight into our own past
In 2010, Svante Pääbo and his colleagues from the Max Planck Institute for Evolutionary Anthropology, in Leipzig 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 the individual came from a previously unknown group of extinct humans that have become known as Denisovans. Together with their sister group the Neanderthals, Denisovans are the closest extinct relatives of currently living humans.
A breakthrough discovery
Originally Professor Anatoly Derevianko and Professor Michail Shunkov from the Russian Academy of Sciences sent a fragment of the bone from Siberia to a team led by Svante Pääbo which he thought might belong to an early modern human, but the results came back as a complete surprise.
The fragment was discovered in 2008 during their excavations at Denisova Cave, a unique archaeological site which contains cultural layers indicating that human occupation at the site started up to 280,000 years ago. The finger bone was found in a layer which has been dated to between 50,000 and 30,000 years ago.
DNA analysis revealed a human who was neither a Neanderthal nor a modern human but the first of a new group of ancient humans.
Excavation in the east gallery of the Denisova Cave, where scientists discovered a tooth and finger bone from a new branch of the human family tree. Image: Max Planck Institute for Evolutionary Anthropology
New techniques
Now thanks to new technology that can unravel and amplify fragmented ancient DNA, the researchers report in the journal Science that they have recovered a complete view of the genome from the finger bone, thanks in part to using two molars.
“We’ve determined the genome sequence from this little finger bone to a quality like what we’d determine for a person today. Every position in the genome has been sequenced on average 30 times over,” said Dr. Pääbo at a news teleconference.
The picture of this girls genome is now as complete as that of modern day human genomes, and shows she had brown eyes, hair and skin and the research now sheds new light on the genetic differences between modern humans and their closest extinct relatives.
Denisovan molar, one of the three sources of DNA for the high-coverage genome sequencing. Image: Max Planck Institute for Evolutionary Anthropology
“The genome is of very high quality”, says Matthias Meyer, who developed the techniques that made this technical feat possible. “We cover all non-repetitive 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”.
“For most of the genome we can even determine the differences between the two sets of chromosomes that the Denisovan girl inherited from her mother and father.” Pääbo said.
The scientists compared the girl’s genome with that of Neanderthals and 11 modern humans from around the world which allowed them to catalogue the changes within a gene that make modern humans different from the two groups of extinct humans that were our closest relatives.
They include changes to only a single DNA letter in several genes involved in the wiring of the brain and nervous system, as well as those that affect the eye and the skin allowing us an unprecedented understanding of this individual.
Remarkable detail of genetic material
The most detailed genetic analysis to date of the Denisovans confirms that interbreeding also occurred with ancestors of some people alive today – including people in Papua New Guinea retaining about 3% of the genomes and faint traces of Denisovan DNA lingering in the Han and Dai people from mainland China.
The thoughts now are the further refinement of the Neanderthal genome and the potential we will soon discover further close cousins in our evolutionary past.
Source: Max Planck Institute for Evolutionary Anthropology/Science
More Information
- Meyer, et al. (2012), A High-Coverage Genome Sequence from an Archaic Denisovan Individual Science 1224344DOI:10.1126/science.1224344
- Excellent analysis here : John Hawks weblog – Denisova at high coverage
- Scientific American guest blog by Ricki Lewis | The Denisova Genome and Guys Banging Rocks
- Live Science report: Genome of Mysterious Extinct Human Reveals Brown-Eyed Girl
The Denisova Genome Consortium have chosen to release the raw sequence data and alignments.
Provided here are the alignments using BWA to the human (hg19/GRCh37) and chimpanzee (panTro2) genomes.
Download data
The sequence and alignment data is made available through:
- local site: http://cdna.eva.mpg.de/denisova/
- Amazon Web Services: The alignments and raw sequence data are available as a public data set via Amazon Web Services (AWS) at http://aws.amazon.com/datasets/2357.
In keeping with the Ft. Lauderdale principles, the data are available for use, but users are expected to allow the data producers to make the first presentations and to publish the first paper containing genome-wide analyses of the data. Researchers who use small amounts of the data (eg: for single locus analyses) are not required to request permission. Researchers who have queries about whether they may present or submit Denisova genome data for publication may contact Svante Pääbo.
When using the Denisova genome data is it best to cite our most recent publication:
Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Paabo S: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010, 468:1053-1060. FULL TEXT
