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

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.

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid ofYersinia pestisfrom victims of the Black Death

“…Sequence clustering revealed between 228 and 84,244 unique fragments for the individual human teeth mapping to the reference mtDNA (Table 1), thus revealing high quantities of mtDNA fragments in all 10 human extracts with low quantities in two of the SNS human control extracts. The cave bear control sample yielded 15 mtDNA fragments, 6 of which aligned to the human mtDNA and 9 were identical or highly similar to the cave bear mtDNA genome (21). No human mtDNA fragments were found in the extraction blank.…”

Revising the recent evolutionary history of equids using ancient DNA

“…Indeed, the relatively short sequences we have generated cannot clearly resolve the exact branching order of major taxonomic groups and the bootstrap values, posterior probabilities, and approximate likelihood ratio tests (aLRT, SH-like) for these nodes were generally not strong. Recently, the use of whole mitochondrial genome sequences from Pleistocene fossils has helped resolve the rapid radiation events within elephantids (31) and ursids (47). Such a mitogenomic approach is likely to uncover the phylogenetic relationships within caballines and New World horses (Fig.…”

Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet

“…This work was under review and in the publication process when a cave bear mitochondrial genome sequence was obtained from a bone sample found in Gamssulzen Cave, Austria (36). The Chauvet and Gamssulzen cave bear mitochondrial genome sequences are highly homologous and locate at similar positions in a phylogenetic tree.…”