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Intronic Sequence Analysis Indicates Longer than Anticipated Evolutionary History for Polar Bear

By Andrea Anderson

NEW YORK (GenomeWeb News) – An international group led by German investigators has found genetic evidence contradicting the notion that the polar bear is a relatively young and quickly evolving species.

As they reported online today in Science, the team sequenced and compared around 9,000 bases of nuclear genome sequence each from nearly four-dozen polar, brown, or black bears, focusing on intronic sequences. Analyses of this data indicated that polar and brown bears diverged from one another some 600,000 years ago — far earlier than a 120,000- to 150,000-year split estimated from some mitochondrial DNA analyses.

"We know much better now when polar and brown bears diverged," German Biodiversity and Climate Research Centre researcher Axel Janke, the study's senior author, told GenomeWeb Daily News. "Now we see that [the polar bear] is a really distinct species with its own long evolutionary history."

Independent teams at the University of California, Santa Cruz in the US and BGI in China are working to sequence and analyze the polar bear nuclear genome. But to date, most of the genetic data used to discern the animal's evolutionary history and relationships with other species have come from mitochondrial DNA, Janke explained, which is relatively easy to get a hold of and found in high copy numbers in cells.

For instance, a University of Oslo-led team nabbed enough mtDNA from ancient polar bear remains found in Norway to sequence the animal's complete mitochondrial genome, which they then compared with mitochondrial sequences from modern day polar and brown bears.

Results of that analysis, published in the Proceedings of the National Academy of Sciences in 2010, suggested that polar bears were most closely related to an Alaskan brown bear population known as the ABC brown bears, prompting authors of the study to peg polar bear divergence at around 134,000 years ago.

That sort of mtDNA-based work led many to believe that polar bears had developed the specialized physical features and lifestyle habits needed to adapt to their arctic environment relatively quickly.

Even so, mitochondrial sequences are maternally inherited and do not offer information on genetic patterns on the paternal size, Janke explained, noting that "mitochondrial DNA tells one side of the story — the so-called matriline or maternal story."

And the picture of polar bear evolution became further complicated by research pointing to the possibility that polar and brown bear species have been hybridizing with one another for 100,000 years or more, including a mtDNA-based phylogenetic study published in Current Biology last summer that proposed a shared maternal ancestry between polar bears and brown bears from Ireland and Britain.

If historical hybridizations between polar and brown bears did occur, the brown bear-related mtDNA in modern-day polar bears would not reflect the divergence time between the species, but rather the time since such hybridizations.

"This is very interesting in itself," Janke said. "But this does not tell us very much about the polar bear-brown bear split and the evolution of the two species."

"The [nuclear] genome tells the more complete story," he added, "because it's inherited from both parents."

In an effort to look at divergence using some of this nuclear information, he and his colleagues sequenced DNA from the introns of genes, which generally evolve more quickly than protein-coding sequences.

The group used Sanger sequencing to look at 9,116 bases of sequence from 14 loci per individual in 19 polar bears, 18 brown bears, and seven black bears.

With a so-called Bayesian multilocus coalescent approach, the team then incorporated sequence information at the intronic loci into a phylogenetic tree representing polar, brown, and black bear relationships. To help pin down divergence times, they also included sequences from the much more distantly related giant panda in the analysis.

Rather than supporting a relatively recent evolutionary split between polar and brown bears, the team's results indicated that the species diverged from one another an estimated 603,000 years, with more recent hybridization events introducing evolutionarily younger brown bear mitochondrial sequences into polar bear populations.

That means that the polar bear has had much more time to adapt to it's environment than thought from studies suggesting more recent divergence times, Janke said, noting that the adaptation rate now predicted for polar bears is on par with findings for other artic vertebrates such as the polar fox.

Despite their unexpectedly long evolutionary history, though, polar bears appear to have fairly low genetic diversity — a feature that researchers attributed to past bottlenecks in polar bear populations, which they believe were likely climate related.

"There's no other extraordinary event in the earth's history that could explain the population bottlenecks of the polar bears," Janke said, "so we suspect it to have been climate change."

While the polar bears' environment is thought to have been particularly cold and ice-rich around the time that the species began emerging in the mid-Pleistocene era, he explained, the rest of the Pleistocene was marked by several climate shifts and intermittent ice ages that could have affected the populations.

For present-day polar bear populations, Janke added, the low genetic diversity of polar bears compared to brown bears is a concern, since it is expected to make the animals more vulnerable to disease, environmental perturbations, or other challenges.

"It does not have much genetic leeway to adapt to all the threats that polar bears are under right now," he said. "It is not just climate change being discussed right now, it is also environmental toxins, habitat destruction, and so on."

For their part, Janke and his colleagues are currently looking at nuclear loci in additional bear species, including the spectacled bear and sun bear, to get a more complete picture of bear divergence times.

The group has also sequenced and assembled the brown bear genome and is interested in comparing it with the genome of the polar bear to not only explore the consequences of past hybridization events but also to look at adaptation-related genetic differences between the species.

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