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International Team Sequences Ancient Polar Bear Mitochondrial Genome

By Andrea Anderson

NEW YORK (GenomeWeb News) – An international research team led by investigators at the University of Oslo's Natural History Museum has sequenced the mitochondrial genome of an ancient polar bear, finding new clues about polar bears' evolutionary history and relationship to brown bears.

In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, researchers from Norway, Iceland, and the US used Roche 454 sequencing to sequence the complete mitochondrial genome from 110,000- and 130,000-years old polar bear remains found in Norway several years ago.

The findings suggest the ancient polar bear lived right around the time that the lineage leading to modern polar bears divergence from the lineage of a closely related group of brown bears — called the ABC brown bears — found on Alaska's Admiralty, Baranof and Chichagof Islands.

"It's basically a transitional link between brown bears and polar bears," co-lead author Charlotte Lindqvist, an evolutionary biology researcher at the University of Buffalo who performed some of the work as a post-doctoral researcher at the University of Oslo Natural History Museum, told GenomeWeb Daily News. "It truly is between at least brown bears from the ABC islands and polar bears."

Lindqvist and her co-workers isolated DNA from ancient polar bear remains found at the Poolepynten site in western Norway's Svalbard Archipelago in 2004. The jawbone and canine tooth found at that site represent a rare find, partly because of polar bears' sea ice environment.

"Because polar bears live on the ice, their dead remains fall to the bottom of the ocean or get scavenged," senior author Øystein Wiig, a polar bear expert at the University of Oslo Natural History Museum, said in a statement. "They don't get deposited in the sediments like other mammals."

The researchers first isolated DNA from the jawbone sample and verified that the remains came from a polar bear using PCR analysis. Collaborators at Pennsylvania State University's Center for Comparative Genomics and Bioinformatics then sequenced the mt genome using the Roche 454 Life Sciences GS FLX platform.

Overall, the team noted, the polar bear DNA was well preserved. And some 40 percent of the 77 million base pairs of sequence generated corresponded to polar bear DNA. Meanwhile, almost 55 percent of the sequences appear to be bacterial and about 4.5 percent represent human sequences. The remaining DNA sequences came from archaea or other organisms.

"It is believed that due to their constant low temperatures, glacial ice, and permafrost environments provide ideal conditions for long-term survival of DNA molecules," the team wrote, "and indeed, some of the oldest authenticated DNA results have been reported from ice and permafrost cores."

The researchers aligned the ancient sequences to the polar bear mt reference genome, generating an average of 14 times coverage for the ancient polar bear mt genome.

They also sequenced six mitochondrial genomes from contemporary polar and brown bears — two Alaskan polar bears, three brown bears from the related ABC brown bear population, and one brown bear from Alaska's Kodiak Island.

When they compared all seven mt genomes to published mt genomes, including those of cave bear, sloth bear, and Asian and American black bears, the team found that the ancient cave bear lies at or near the point at which the ancestors of polar bears and ABC brown bears diverged roughly 152,000 to 190,000 years ago.

"[B]oth cladistically and anagenetically, this ancient specimen existed very close to the most recent common ancestor of polar bears and brown bears," the researchers explained.

The results also hint at the mean age of polar bears overall, which the team pegs at around 134,000 years old. That suggests polar bears survived past environmental changes — namely an interglacial warming period. The most recent divergences in the so-called "crown group" of modern polar bears, meanwhile, seem to have occurred within the past 45,00 years or so.

"Certainly [polar bears] have experienced climate changes and they have survived through a warming period in the past," Lindqvist said. Still, she cautioned, it's unclear what this means for current polar bears' chances of adapting to climate change or other alterations to their environment.

"Polar bears have evolved into a very specialized species," Lindqvist explained, noting that this specialization is reflected in everything from polar bears' diet and environment to their appearance and morphology. "It seems likely that changes in the current environment would certainly have implications for polar bears."

When the team used carbon and nitrogen stable isotope experiments to look at the ancient polar bear's diet, they found evidence suggesting it resembled that of modern polar bears — at the top of the Arctic marine food chain.

The researchers plan to sequence the ancient polar bear's nuclear genome once a modern polar bear genome is available to use as a reference, Lindqvist said. "Since the DNA is so remarkably well preserved, it should be possible to sequence at least a large potion of the nuclear genome."

So far they haven't settled on a sequencing technology for that project, she added, since new advances are coming out so frequently.

Last spring, researchers from BGI-Shenzhen announced that they plan to sequence the modern day polar bear nuclear genome.