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Extinct Cave Bear DNA Sequences Found in Modern-Day Brown Bear Populations

Brown bear.

NEW YORK (GenomeWeb) – A team led by researchers from the University of Potsdam and the University of California at Santa Cruz sequenced four cave bears from the Late Pleistocene period and found that cave bears from the Ursus spelaeus species complex admixed with U. arctos brown bears in the Ice Age, leaving stretches of their DNA in the genomes of brown bears that exist today.

"Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species," co-first authors Axel Barlow, researcher at the University of Potsdam's Institute for Biochemistry and Biology, and James Cahill, an ecology and evolutionary biology researcher at UCSC, and their colleagues wrote in a study appearing online today in Nature Ecology and Evolution.

The researchers sequenced DNA in petrous bone samples from the four cave bears, which were tens of thousands of years old and found at sites in Austria, Spain, and Armenia. They also sequenced one brown bear found in an Austrian cave, which was dated at around 41,200 years old. Along with gene flow between the cave bears and brown bears, the researchers found that 0.9 percent to 2.4 percent of the current brown bear genome, on average, is comprised of cave bear sequence, despite cave bears having gone extinct around 25,000 years ago.

"[W]e have shown that a fraction of the cave bear gene pool survives in the genomes of living brown bears, mirroring the Neanderthal ancestry found in non-African humans, but at a much deeper phylogenetic divergence," the authors reported.

Along with the four ancient cave bears and one ancient brown bear, the researchers used Illumina technology to sequence modern-day brown bears from populations in Georgia, Slovenia, Russia, and Spain. They also tapped into published sequence data for brown, black, polar, Asiatic black, spectacled, and panda bears.

The team's phylogenetic analysis placed the extinct cave bears in a clade beside that leading to polar bears and brown bears, with additional splits among and between cave bears from the Caucasus and Europe.

The researchers went on to investigate differentiation between the cave bear groups, as well as the patterns of admixture between cave bears and brown bears, informed by phylogenetic clues. For example, they saw signs of gene flow in both directions: from brown bears into cave bears, and vice versa.

But the most recent admixture event appeared to involve gene flow from cave bears into brown bears, they reported, leaving the greatest proportion of cave bear DNA in the Georgian brown bear population.

The authors noted that brown bears "represent an excellent opportunity to study the biological implications of admixture in a dynamic multi-species system," since they have received potentially beneficial alleles through past admixtures with cave bears and polar bears.