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

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

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

“…3A and Figs. S3 and S4) comparable to recently reported phylogenies based on complete mt genomes and nuclear sequences (2,3,25). The phylogenetic results clearly demonstrate, with high support, the close relationship of the subfossil specimen to modern polar bear (Fig.…”

“…S2). These seven complete mt genomes from ancient and modern bears were aligned to previously published mt genomes, including two mt genomes each from polar bear and brown bear (3,22,23). The four modern polar bears included represent well the distinct genetic clusters of polar bear populations identified from microsatellite analyses (24).…”

“…Dating of divergence events within the brown bear/polar bear lineage were estimated using a Bayesian "relaxed molecular clock" approach (44) in the software BEAST (45) v. 1.4.8 using variable parameter sets and datasets (Table S2). Following suggestions to use calibration points as close as possible to dates being estimated when timing recent divergences (46), a mean age of 120 ky for the Poolepynten subfossil polar bear was used in addition to data from carbon-dated specimens (2,3,26). Results were assessed with Tracer (47) v. 1.4.1, and maximum clade credibility trees were produced with TreeAnnotator v. 1.4.8.…”

“…For example, it is widely accepted that anatomically modern humans evolved in Africa around 200-160 thousand years ago (kya), expanded into most habitable parts of the Old World between 90 and 40 kya (1), and swiftly radiated in phenotypic traits readily recognized in modern populations. Ursine bears have themselves diverged recently into a number of different species (2,3). The polar bear (Ursus maritimus Phipps 1774), which is the largest of the six extant ursine bear species, currently has a circumpolar distribution, their range determined by the extent of Arctic sea ice.…”

Further constraints on the Chauvet cave artwork elaboration

“…14 C dating of large mammal bones, all species being included (Ursus spelaeus and Capra ibex), range from 42 cal 14 C ka BP to 23 cal 14 C ka BP (27,28,29)-the youngest age being associated with an ibex bone (19 105 AE 150 14 C yr BP). This date fits tightly with the last two rockfall events.…”