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Edited by Francisco J Ayala, University of California, Irvine, CA, and approved August 22, 2008 (received for review July 1, 2008)
Abstract
Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.
Footnotes
- 1To whom correspondence should be addressed. E-mail: jean-marc.elalouf{at}cea.fr
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Author contributions: C.B., B.R., and J.-M.E. designed research; C.B., N.C., M.d.D., P.F., M.P., F.M., E.B.-C., E.B., R.K., C.L., J.v.d.P., and J.-M.E. performed research; C.B., N.C., M.d.D., E.B.-C., E.B., R.K., B.R., D.C., J.v.d.P., and J.-M.E. analyzed data; and C.B., D.C., J.v.d.P., and J.-M.E. wrote the paper.
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The authors declare no conflict of interest.
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This article is a PNAS Direct Submission.
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Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. DQ227308, EU327344, and EU497665).
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This article contains supporting information online at www.pnas.org/cgi/content/full/0806143105/DCSupplemental.
- © 2008 by The National Academy of Sciences of the USA
- Céline Bona,
- Nicolas Caudya,
- Maud de Dieuleveulta,
- Philippe Fosseb,
- Michel Philippec,
- Frédéric Maksudd,
- Éliane Beraud-Colombe,
- Eric Bouzaide,
- Rym Kefie,
- Christelle Laugierf,
- Bernard Rousseauf,
- Didier Casaneg,
- Johannes van der Plichth, and
- Jean-Marc Elaloufa,i,1
- aService de Biologie Intégrative et Génétique Moléculaire,
- fService de Chimie Bioorganique et de Marquage, Institut de Biologie et Technologies de Saclay, Commissariat à l'Énergie Atomique Saclay, 91191 Gif-sur-Yvette Cedex, France;
- bCentre National de la Recherche Scientifique Unité Mixte de Recherche 5608, Université Toulouse le Mirail, 31058 Toulouse Cedex 1, France;
- cMuséum d'Histoire Naturelle, 28 Boulevard des Belges, 69000 Lyon, France;
- dService Régional de l'Archéologie, 32 Rue de la Dalbade, BP811 31080 Toulouse cedex 6, France;
- eInstitut National de la Santé et de la Recherche Médicale U600, Hôpital Sainte Marguerite, 270 Boulevard Sainte Marguerite, 13009 Marseille, France;
- gLaboratoire Evolution, Génomes et Spéciation, Unité Propre de Recherche 9034 Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France;
- hRadiocarbon Laboratory, Groningen University, Nijenborgh 4, 9747 AG Groningen, The Netherlands; and
- iFaculty of Archaeology, Leiden University, P.O. Box 9515, 2300 RA Leiden, The Netherlands
-
Edited by Francisco J Ayala, University of California, Irvine, CA, and approved August 22, 2008 (received for review July 1, 2008)
Abstract
Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.
- ancient DNA
- pleistocene
- Ursus spelaeus
Footnotes
- 1To whom correspondence should be addressed. E-mail: jean-marc.elalouf{at}cea.fr
-
Author contributions: C.B., B.R., and J.-M.E. designed research; C.B., N.C., M.d.D., P.F., M.P., F.M., E.B.-C., E.B., R.K., C.L., J.v.d.P., and J.-M.E. performed research; C.B., N.C., M.d.D., E.B.-C., E.B., R.K., B.R., D.C., J.v.d.P., and J.-M.E. analyzed data; and C.B., D.C., J.v.d.P., and J.-M.E. wrote the paper.
-
The authors declare no conflict of interest.
-
This article is a PNAS Direct Submission.
-
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. DQ227308, EU327344, and EU497665).
-
This article contains supporting information online at www.pnas.org/cgi/content/full/0806143105/DCSupplemental.
- © 2008 by The National Academy of Sciences of the USA
Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet
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