Ancient DNA and the Population Genetics of Cave Bears (Ursus spelaeus) Through Space and Time

Abstract

The cave bear spread from Western Europe to the Near East during the Riss glaciation (250 KYA) before becoming extinct approximately 12 KYA. During that period, the climatic conditions were highly dynamic, oscillating between glacial and temperate episodes. Such events have constrained the geographic repartition of species, the movements of populations and shaped their genetic diversity. We retrieved and analyzed ancient DNA from 21 samples from five European caves ranging from 40 to 130 KYA. Combined with available data, our data set accounts for a total of 41 sequences of cave bear, coming from 18 European caves. We distinguish four haplogroups at the level of the mitochondrial DNA control region. The large population size of cave bear could account for the maintenance of such polymorphism. Extensive gene flow seems to have connected European populations because two haplogroups cover wide geographic areas. Furthermore, the extensive sampling of the deposits of the Scladina cave located in Belgium allowed us to correlate changes in climatic conditions with the intrapopulational genetic diversity over 90 KY.

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

“…These primers proved to be highly efficient for PCR amplification (Fig. 2), and generated a DNA fragment that displayed seven substitutions with the closest brown bear sequence, but was identical to sequences for the cave bear B haplogroup obtained in Scladina (40,000 to 45,000 years-old samples) (13). These data therefore strongly support the notion that we have retrieved authentic cave bear DNA.…”

“…Consequently, cave bear mitochondrial genome fragments have only been retrieved as short sequences that up to now could be assembled into a partial control region and a single protein coding gene (11,12), which together span Ͻ10% of the expected 17 kb mitochondrial genome. Phylogenetic analysis carried out using the available sequence information (12)(13)(14) supported one hypothesis drawn from morphometric studies of fossil records (10) arguing for an early split of the cave bear from the brown bear lineage. However, considering the accumulating evidence demonstrating that long sequences are often necessary to obtain correct phylogenies (5), it is highly desirable to better characterize the cave bear mitochondrial genome.…”

“…For the two others, we recorded C instead of T residues, suggesting that the Chauvet-Pont d'Arc sample had been better preserved from cytosine deamination, the most frequent damage observed in ancient DNA (18,19). The cave bear sample from La Balme à Collomb was also analyzed for a highly variable fragment of the control region (13), in which it displays two differences with Chauvet Us18. This supports the notion that the two cave bear specimens correspond to different haplotypes.…”

Surprising migration and population size dynamics in ancient Iberian brown bears ( Ursus arctos )

“…1 A) was estimated with the long dataset by using a closely related outgroup [the cave bear, U. spelaeus (24); see SI Dataset 4 for accession numbers]. Although partially unresolved, it has a similar topology to those published previously using mtDNA datasets from both extant and extinct European brown bears (4,20).…”

Looking backwards to look forwards: conservation genetics in a changing world

“…Acknowledging the importance of applying an accurate rate, Korstein et al (2009) incorporated sequence data from the cave bear (Ursus spelaeus) based on ancient DNA sequences (after Orlando et al 2002). On this basis they derive a mutation rate within the brown bear lineages that is six times higher than the rate along the basal branch comparing the two species.…”