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Open Access Highly Accessed Research article

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

Johannes Krause1, Tina Unger1, Aline Noçon1, Anna-Sapfo Malaspinas2, Sergios-Orestis Kolokotronis34, Mathias Stiller1, Leopoldo Soibelzon5, Helen Spriggs6, Paul H Dear6, Adrian W Briggs1, Sarah CE Bray7, Stephen J O'Brien8, Gernot Rabeder9, Paul Matheus10, Alan Cooper7, Montgomery Slatkin2, Svante Pääbo1 and Michael Hofreiter1*

Author Affiliations

1 Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

2 Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA

3 Department of Ecology, Evolution and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, MC5557, New York, NY 10027, USA

4 Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA

5 Departamento Científico Paleontologia de Vertebrados, Museo de La Plata. Paseo del Bosque, (1900) La Plata, Buenos Aires, Argentina

6 MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK

7 Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia

8 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA

9 Department of Paleontology, University of Vienna, 1090 Vienna, Austria

10 Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK 99775, USA

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BMC Evolutionary Biology 2008, 8:220  doi:10.1186/1471-2148-8-220

Published: 28 July 2008

Abstract

Background

Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods.

Results

We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes.

Conclusion

Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations.