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Cave Bear Mitochondrial Genome Sequenced, Provides Clues to Bear Evolution

This article has been updated to clarify the fact that the ancestors of cave bears, not the species of cave bear analyzed for the study, diverged from the ancestors of brown bears and polar bears 1.6 million years ago.
 
NEW YORK (GenomeWeb News) – Cave bears belonged to a sister group to modern day polar bears and brown (grizzly) bears, according to phylogenetic analyses of the newly sequenced cave bear mitochondrial genome.
 
A team of researchers from France and the Netherlands sequenced ancient mitochondrial DNA extracted from skeletal fragments of an extinct cave bear, Ursus spelaeus, found in a cave in southern France. The work, appearing online last night in the Proceedings of the National Academy of Sciences, suggests that cave bears' ancestors diverged from those of brown bears and polar bears some 1.6 million years ago. It also highlights the feasibility of analyzing cave bear DNA — a task that has proven challenging in the past.
 
“These molecular data enable establishing the chronology of bear speciation, and provides a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA,” the authors wrote.
 
Cave bears lived in Europe and the Near East between 300,000 and 15,000 years ago. As their name suggests, the animals seem to have lived almost exclusively underground in caves.
 
Short cave bear mitochondrial sequences have been amplified in the past. For this paper, though, the researcher set out to sequence the cave bear’s entire mitochondrial genome from 32,000-year-old bone fragments found in the Chauvet-Pont d’Arc cave in southern France.
 
The cave is already famous for housing well-preserved natural and man-made samples: in 1994, researchers discovered charcoal drawings done tens of thousands of years ago — the oldest rock art pictures discovered so far. The cave also contained thousands of skeletal pieces and more than 90 percent of these belong to cave bears.
 
But despite the constant temperature and absence of damaging UV light, the researchers noted, analyzing the cave bear DNA was demanding since the samples were not as well maintained as those from ancient animals — notably the woolly mammoth — that have been exceptionally well-preserved in permafrost.
 
The researchers used PCR amplification and sequencing of overlapping fragments to reconstruct the 16,810 base pair cave bear mitochondrial genome. After using nearly 250 primer pairs to amplify 150 to 180 base-pair bits of mitochondrial DNA at a time, they confirmed their initial sequence results by having collaborators at another institute repeat the analysis.
 
“Our analytical procedure rested on the design of a series of bear-specific oligonucleotide primers that were used to generate hundreds of overlapping DNA fragments enabling the characterization of a complete cave bear mitochondrial genome,” the authors explained.
 
Just like bears living today, the cave bear mitochondrial genome appears to contain 13 protein coding genes, 22 transfer RNA genes, and two genes coding for ribosomal RNA.
 
But there were species-specific differences too. By comparing the cave bear mitochondrial genome with those of the eastern and western brown bear lineages, as well as ten published mitochondrial genome sequences from modern bear species, the team was able to look at how cave bears fit into the bear tree.
 
Their phylogenetic and gene-by-gene analyses suggested that cave bears belong to a sister group to polar bears and brown bears, with the ancestors of each diverging some 1.6 million years ago during the Early Quaternary period — long before the polar-brown bear lineage diversified. Eastern and western brown bears seem to have diverged just 550,000 years ago with the polar-western brown bear split occurring about 350,000 years ago.
 
To put this in perspective, the giant panda lineage appears to have diverged from Ursidae species about 12 million years ago, whereas the precursor to South American spectacled bears diverged from other bear species around 6.3 million years ago. Meanwhile, the group to which most modern bears belong appears to have undergone extensive radiation within the past two to three million years.
 
With the cave bear mitochondrial genome sequence in hand, researchers say, it should be possible to tease apart even more precise information about the timing and nature of bear evolution. And, researchers say, it illustrates the potential of studying ancient DNA from the Chauvet-Pont d’Arc cave and similar environments.
 
“The mitogenomic analysis definitely assesses the cave bear as a sister taxon to the brown bear and polar bear clade, and displays the tempo of bear history during the Pliocene and Pleistocene,” the authors concluded. “Our study also demonstrates the feasibility of retrieving complete mitochondrial genomes from the subterranean milieu, an environment that contains remains for a variety of extinct species, and points to the painted cave of Chauvet-Pont d’Arc as a reservoir for paleogenetic investigations.”
 

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