title: Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany. hofreite@eva.mpg.de
authors.forename: Johannes
authors.initials: J
authors.lastname: Krause
authors.forename: Tina
authors.initials: T
authors.lastname: Unger
authors.forename: Aline
authors.initials: A
authors.lastname: Noçon
authors.forename: Anna-Sapfo
authors.initials: AS
authors.lastname: Malaspinas
authors.forename: Sergios-Orestis
authors.initials: SO
authors.lastname: Kolokotronis
authors.forename: Mathias
authors.initials: M
authors.lastname: Stiller
authors.forename: Leopoldo
authors.initials: L
authors.lastname: Soibelzon
authors.forename: Helen
authors.initials: H
authors.lastname: Spriggs
authors.forename: Paul H
authors.initials: PH
authors.lastname: Dear
authors.forename: Adrian W
authors.initials: AW
authors.lastname: Briggs
authors.forename: Sarah C E
authors.initials: SC
authors.lastname: Bray
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.forename: Gernot
authors.initials: G
authors.lastname: Rabeder
authors.forename: Paul
authors.initials: P
authors.lastname: Matheus
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
authors.forename: Montgomery
authors.initials: M
authors.lastname: Slatkin
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
authors.forename: Michael
authors.initials: M
authors.lastname: Hofreiter
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D053476:Extinction, Biological; D005580:Fossils; D049810:Genetic Speciation; D054629:Genome, Mitochondrial; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D001503:Ursidae / Q000145:classification / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial