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

Johannes Krause,Helen Spriggs,Gernot Rabeder,Aline Noçon,Anna-Sapfo Malaspinas,Sarah Ce Bray,Paul H Dear,Sergios-Orestis Kolokotronis,Tina Unger,Michael Hofreiter,Paul Matheus,Stephen J O'Brien,Montgomery Slatkin,Alan Cooper,Svante Pääbo,Adrian W Briggs,Mathias Stiller,Leopoldo Soibelzon

doi:10.1186/1471-2148-8-220

Abstract

BackgroundDespite 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.ResultsWe 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.ConclusionSequences 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.

Highlights

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
For the remaining five living bear species, we sequenced the entire mtDNA in overlapping fragments using a 2-step multiplex PCR approach [7] and a mixture of direct sequencing and sequencing multiple clones (EMBL:FM177759, EMBL:FM177761, EMBL:FM177763, EMBL:FM177764, EMBL:FM177765)
We examined whether more sequence data would improve our estimates on divergence times by plotting the posterior means of divergence times against the width of their corresponding 95% credibility interval, following Yang and Rannala [22]

Summary

Introduction

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. Despite numerous morphological and molecular studies on the phylogenetic relationship among Ursidae members, no consensus exists with regard to either their phylogeny or their taxonomic nomenclature (Table 1). Molecular studies for a long time failed to conclusively resolve the phylogenetic relationships among the members of the bear subfamily Ursinae [5], which includes all living bear species except the giant panda and the spectacled bear, from here on referred to as ursine bears. The phylogenetic uncertainty has resulted in major taxonomic confusion Based on both morphological and molecular data up to six different genera (Ursus, Helarctos, Euarctos, Selenartos, Thalarctos and Melursus; i.e. one for each species) have been suggested for the extant ursine bears (Table 1)

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Discussion

Conclusion