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.
via Wired https://www.wired.com
June 24, 2022 at 04:11AM