The sequencing of the nuclear genome from an ancient finger bone found in a Siberian cave shows that the cave dwellers were neither Neandertals nor modern humans.

An international team of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany) has sequenced the nuclear genome from a finger bone of an extinct hominin that is at least 30,000 years old and was excavated by archaeologists from the Russian Academy of Sciences in Denisova Cave in southern Siberia, Russia, in 2008. A team at Harvard Medical School led the population-genetics analysis.

These findings are published in the December 23 issue of Nature.

Earlier this year Svante Pääbo and his colleagues showed that the mitochondrial DNA from the finger bone displayed an unusual sequence suggesting that it came from an unknown ancient hominin form. Now, using techniques the researchers developed to sequence the Neandertal genome earlier this year, they have sequenced the nuclear genome from the bone.

The researchers found that the individual was female and came from a group of hominins that shared an ancient origin with Neandertals, but subsequently diverged. They call this group of hominins Denisovans. Unlike Neandertals, Denisovans did not contribute genes to all present-day Eurasians. However, Denisovans share an elevated number of genetic variants with modern-day Papua New Guinean populations, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians.

In addition, a Denisovan tooth found in the same cave shows a morphology that is distinct from Neandertals and modern humans and resembles much older hominin forms. Bence Viola, a scientist at the Max Planck Institute of Evolutionary Anthropology comments, “The tooth is just amazing. It allows us to connect the morphological and genetic information.”

David Reich, an associate professor at Harvard Medical School who led the population genetic analysis, says, “The fact that Denisovans were discovered in Southern Siberia but contributed genetic material to modern human populations from New Guinea suggests that Denisovans may have been widespread in Asia during the Late Pleistocene.”

According to Svante Pääbo of the Max Planck Institute of Evolutionary Anthropology, “In combination with the Neandertal genome sequence, the Denisovan genome suggests a complex picture of genetic interactions between our ancestors and different ancient hominin groups.”

This research was funded by the Max Planck Society and the Krekeler Foundation (Germany), the National Institutes of Health (USA) and the National Science Foundation (USA).

CITATION:

Nature, Volume 468 Number 7327, December 23, 2010

“Genetic history of an archaic hominin group from Denisova Cave in Siberia”

David Reich (1,2*), Richard E. Green (3,4*), Martin Kircher (3*), Johannes Krause (3,5*), Nick Patterson (2*), Eric Y. Durand (6*), Bence Viola (3,7*), Adrian W. Briggs (1,3), Udo Stenzel (3), Philip L. F. Johnson (8), Tomislav Maricic (3), Jeffrey M. Good (9), Tomas Marques-Bonet (10,11), Can Alkan (10), Qiaomei Fu (3,12), Swapan Mallick (1,2), Heng Li (2), Matthias Meyer (3), Evan E. Eichler (10), Mark Stoneking (3), Michael Richards (7,13), Sahra Talamo (7), Michael V. Shunkov (14), Anatoli P. Derevianko (14), Jean-Jacques Hublin (7), Janet Kelso (3), Montgomery Slatkin (6) and Svante Paabo (3)

(1) Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
(2) Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
(3) Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
(4) Department of Biomolecular Engineering, University of California, Santa Cruz 95064, USA.
(5) Institut fur Naturwissenschaftliche Archaologie, University of Tu bingen, Tu bingen 72070, Germany.
(6) Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
(7) Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
(8) Department of Biology, Emory University, Atlanta, Georgia 30322, USA.
(9) Division of Biological Science, University of Montana, Missoula, Montana 59812, USA.
(10) Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
(11) Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.
(12) CAS-MPS Joint Laboratory for Human Evolution and Archaeometry, Institute of Vertebrate Paleontology and Paleoanthropology of Chinese Academy of Sciences, Beijing 100044, China.
(13) Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
(14) Paleolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia.

*These authors contributed equally to this work.