What Polar Bear Genomes May Reveal About Life in a Low-Ice Arctic

Around 100,000 years ago, a polar bear found herself a few miles from present-day Lonely, Alaska. There, near the sea, the bear died.

But her contribution to science had just begun. In 2009, a team of researchers from the University of Alaska stumbled upon the bear’s skull on the beach—looking “really fresh,” says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz. The scientists nicknamed the bear “Bruno.”

Bruno is now one of the oldest kinds of polar bears to have DNA fully analyzed using whole genome sequencing—a powerful method that reads out an animal’s entire genetic code, offering scientists a high-resolution look at differences that may have shaped a species’ evolution over time. Reading Bruno’s DNA helped Shapiro and her team determine that around 120,000 to 125,000 years ago, when ice levels were similarly low as they are today, polar bears and brown bears may have shared territory and mated. Shapiro, along with Kristin Laidre (a researcher at the Polar Science Center at the University of Washington), also used whole genome sequencing to identify a new, present-day subpopulation of polar bears in Southeast Greenland that has survived in lower sea-ice conditions. Their teams published these findings in the journals Science and Nature Ecology and Evolution last week.

Parsing the genes of individual polar bears, especially on the whole genome scale, is a relatively recent accomplishment. Previously, scientists used microsatellite data: a comparatively cheap and easy method that is akin to spot-checking the genome. Imagine the genome as a biological map, in which everything is made up of a combination of four letters, or nucleic acid base pairs. Scientists find areas of interest on the genome—sort of like searching for biological “landmarks.” Then they compare the number of little DNA phrases that repeat at those landmarks (which are called microsatellites) to determine how closely related two organisms are.

This method has provided an accessible search strategy, but a patchy view of the genome. “Microsatellites are so boring,” says Shapiro.

“You don’t really get as good resolution as when you look at whole genomes,” agrees Charlotte Lindqvist, an evolutionary biologist at the University at Buffalo. (She is unaffiliated with the new studies but was the first to publish whole genome sequencing of polar bears in 2012.)

But whole genome sequencing does much more than spot-check. Instead, it looks at everything. Because it provides such a high-resolution view of which base pairs go where, researchers can see exactly where tiny genetic differences between species lie. “The whole genome data we’ve provided is way more powerful,” says Shapiro.

Collecting that data from Bruno was relatively straightforward. Shapiro’s team extracted one of the bear’s teeth from her skull, ground the tooth’s root into powder, and extracted its DNA in order to sequence it. “Despite its really old age, and probably because of its good survival, we were able to get a whole genome,” Shapiro says. “It’s one of the oldest high-coverage genomes published.”

By contrast, teasing out DNA from living polar bears proved quite a challenge. To collect samples of the Southeast Greenland bears, Laidre and her team used several methods. One was to physically capture the bear, put a tracking collar on it, and in the process collect some blood or fat. Another was to use a remote biopsy dart, shot from the window of a helicopter, that could take a small plug of skin off the bear. Finally, the scientists were able to collect samples donated by Indigenous hunting communities.

The polar bears weren’t super enthusiastic about letting go of their DNA. After the researchers had collected and preserved the DNA in tubes, “the bears came and got their samples back,” Shapiro says. Laidre had to go outside, banging pots and pans together, to retrieve the bag of samples. “That’s the only time they tried to steal my samples,” Laidre says.

The study of the Southeast Greenland bears revealed two curious things. First, DNA analysis showed that they belong to a unique gene pool, separate from those of neighboring bear populations in Northeast Greenland, as well as in other areas of Alaska, Russia, and Canada.

“They’re the most genetically distinct subpopulation of polar bears that are out there,” Shapiro says. “They are more genetically different from their nearest neighbor—subpopulations—of polar bears than any other two pairs of populations of polar bears are to each other.”

The second thing, which the researchers had determined through over a decade of monitoring, is that these bears seem to have adapted to conditions with lower levels of sea ice, or frozen ocean. Polar bears normally rely on it to find their prey: They stand very still near a seal’s breathing hole in the ice to grab it when it comes up for air, or they swim around and ambush the seals from the water. Southeast Greenland is below the Arctic Circle, so the climate is warmer earlier in the year. As a result, the sea ice is not as stable or long-lasting as it is further north. “They live in a place that has a short sea ice season, shorter than what we think polar bears can survive in—about 100 days a year,” Laidre says.

To compensate for the shorter season, the bears have adapted by making use of another ice source: glacier ice that breaks off the Greenland ice sheet in slow motion to form a landscape of freshwater ice. Laidre and her colleagues noticed that during the period with no sea ice, the bears could still use this glaciated landscape to hunt for seals—employing the same ambushing techniques.

The bears’ genetic isolation and their adaptation to a low-sea-ice environment make sense if you consider the local geography: Fenced in by ice sheets, water, currents, and uninhabitable environments, the bears didn’t really move around. “You’re kind of at the end of the road when you get to Southeast Greenland,” Laidre says. “There’s nothing left. You don’t walk back because there’s a very strong current and it’s really poor sea ice.”

But do these behavioral changes in the bears’ hunting habits correspond to changes in their comparatively distinct genome? The scientists don’t have an answer yet. “We don’t even know that the behavioral differences and the demographic differences and physiological differences that Kristen [Laidre] has observed, if those are genetic changes or just part of the flexibility of the normal polar bear genotype,” Shapiro says. “That’s a great thing to focus on in the future, because it would be really interesting to understand.”

Shapiro’s Nature Ecology study also focused on what may have happened to other polar bear genomes during periods of low ice—in this case, around 120,000 or 125,000 years ago when, according to Shapiro, Arctic ice levels were similar to the present day’s. But here, she looked at the relationship between polar bears and brown bears. 

Her team constructed a phylogenetic tree—sort of like an evolutionary map showing how the bears diverged from a common ancestor over time—using Bruno’s genome and those of currently living polar bears, brown bears, and a black bear. (Shapiro was able to utilize one of Laidre’s Southeast Greenland polar bear genomes in her analyses, although the time gap between its life and Bruno’s is enormous. The sample pool, she says, is “missing 100,000 years of evolution.”)

From this and other analyses, the scientists gained some evidence that about 20,000 years before Bruno was born, brown bears and polar bears mixed to generate hybrid offspring. The scientists hypothesized that during this warm period, polar bears might have made their way on shore. The carcasses of the marine mammals they hunted could have attracted brown bears—leading to mating opportunities. As a potential result of this ancient interbreeding, Shapiro says, up to 10 percent of the genome of the modern brown bear comes from polar bear ancestry.

Figuring out how and when polar bears and brown bears commingled, further specialized, or diverged is a difficult task, given the limited fossil record and complexities of evolution. “Evolution is a messy process,” says Andrew Derocher, a polar bear researcher at the University of Alberta who was unaffiliated with the studies. He likens the process of evolutionary speciation to a “massive bunch of vines that are creeping up the base of a tree,” crisscrossing and entangling. “Eventually, some of those vines might get their own trajectory, and that’s what our species are,” he says. “But in this process, they can cross over, they can reconnect and fuse, and it’s certainly impossible to pull it apart, because they’re so interconnected.”

Still, these two studies are linked, Laidre says, “in the sense of: Where have polar bears persisted when sea ice was low, and how?” The research may provide some insight into how bears in the past—and today’s Southeast Greenland bears—have survived in warmer climates with less ice.

But how genetic changes manifest in physical form, and how those changes may have helped bears survive past warming events, are still open questions, the scientists say. And these study results shouldn’t make us feel that the problem of Arctic warming is resolved, or that today’s bears can easily adapt to rapidly shrinking levels of sea ice. “It seems like global warming is happening too fast,” Lindqvist says. She wonders if the polar bears “can keep up.”

After all, polar bears depend on seals as their food source—and those seals depend on sea ice. “There’s parts of the Arctic that used to be excellent seal habitats and excellent polar bear habitats,” Derocher says. “But there’s no sea ice there anymore. And as a result, there’s virtually no bears. There’s very few seals, and the ecosystem has basically unraveled.”

What, then, might actually help? “Global action on climate change,” Laidre says. “That’s it.”

What Polar Bear Genomes May Reveal About Life in a Low-Ice Arctic

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