Polar Bear Genome Reflects Climate Change

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800px-Polar_bear_with_young_-_ANWRSad polar bears clinging to tiny ice floes have come to symbolize the threat of climate change to wildlife. A glimpse into their genomes and those of brown bears reveals that shrinking ice may already be bringing the two species into close enough contact that hybrid polar/brown bears may become more common.

Past polar bear population sizes have tracked with climate, swelling in cold times and shrinking with the heat. Their numbers have plunged over the past 500,000 years, while their populations have become even less genetically diverse than our own, leaving the bears vulnerable to sudden environmental changes.

BROWN BEAR MEETS POLAR BEAR

Dr. Charlotte Lindqvist (The University at Buffalo)

Dr. Charlotte Lindqvist (The University at Buffalo)

Charlotte Lindqvist, PhD, an assistant professor of biological sciences at the University at Buffalo, traces her fascination with Ursus maritimus to the natural history museum in Norway, where she worked with the oldest known polar bear remains, dating from 130,000 to 110,000 years ago. In a paper published in PNAS a year ago, Dr. Lindqvist and colleagues at 13 institutions in the US, Canada, Europe, Asia, and Mexico analyzed 28 sequenced bear genomes, including deep coverage for one polar bear, 3 brown bears, and one black bear plus lower coverage for the 23 others, including the approximately 120,000-year-old polar bear jawbone from the museum in Svalbard, Norway.

Their findings, using “molecular clocks” based on known mutation rates for certain DNA sequences, push back the date of divergence between brown and polar bears from less than a million years ago to four or five million years ago. Yet the telltale sequences of A, T, C and G also reveal that the two types of bears meet up once in awhile, to dine on beached blubber, and, rarely, to mate.

Brown bears sharing whale blubber and sperm with female polar bears gave rise to the so-called “ABC” bears, for the Admiralty, Baranof, and Chichagof islands of the Alexander Archipelago off the coast of southeastern Alaska, their home today. ABC bears look like any other brown bears, but harbor some polar bear DNA. However, the mitochondrial and nuclear genomes of the bears tell different stories. (The tiny mitochondrial genome traces the maternal line; DNA in the nucleus is from both parents.)

Extraction of Neanderthal DNA at the Max Planck Institute for Evolutionary Anthropology (NHGRI)

Extraction of Neanderthal DNA at the Max Planck Institute for Evolutionary Anthropology (NHGRI)

“For many years all we had was mitochondrial evidence, and that showed the ABC bears were more closely related to polar bears than other brown bears. But nuclear DNA showed the ABC bears grouping with other brown bears,” Dr. Lindqvist explains. Polar bear DNA sequences in brown bears mean they’ve mated. Perhaps this happened in the same way that Neanderthal and Denisovan DNA sequences entered our own genomes as our ancestors from Africa encountered these others in geographical areas called ,”refugia” where they’d sheltered and maintained their own gene pools during tough times and climes.

Overlapping habitats explain the sighting of wild brown/polar hybrids in the Northern Beaufort Sea, as well as second generation offspring. “In arctic Canada historically polar bears well-adapted to living on sea ice didn’t come into contact with brown bears. But now they are more in contact and we are starting to see hybrids. It’s rare, but may become more common. In Alaska, brown bears and polar bears stay on land during the summer and feed on the same bone piles. Maybe they’ve found a way to co-exist without interacting much,” suggests Dr. Lindqvist.

But are the meetings and matings of brown and polar bears new? Yes and no.

POSSIBLE EFFECTS OF CLIMATE CHANGE
“Clearly the polar bear lineage has experienced many warming and cooling periods. But these natural oscillations are different today because they still occur, but over a higher and continually increasing baseline due to the accumulation of greenhouse gases. So even if polar bears have experienced climate change in the past, it’s getting warmer and they are going to lose more habitat, and if it continues we can only imagine we’re going to lose polar bear populations. But what, exactly, will happen is hard to predict,” Dr. Lindqvist says.

Another danger of climate change altering habitats is that polar bears may encounter animals that carry pathogens to which the displaced arctic residents aren’t immune. The situation is a little like Europeans unleashing smallpox on immunologically naive Native American populations.

cheetahThe diminishing genetic diversity seen among polar bears could be a danger sign. In contrast, cheetahs are famously genetically uniform. Their numbers plummeted through a population bottleneck about 10,000 years ago, as the most recent ice age ended, and since then natural selection has maintained a set of genes well-adapted to their environment, which hasn’t changed that much since our ancestors stopped killing them en masse. In the 1980s several studies reported the dire effects of the cheetahs’ genetic uniformity, but it turned out that captive populations didn’t exactly echo the state of their wild cousins. The wild cheetah population remains quite small, but is much healthier than their genetic uniformity would imply. Here’s a good explanation.

Polar bears face a different set of circumstances than cheetahs. With a shrinking and changing habitat, the bear population needs genetic diversity, so that individuals with some gene variants can survive whatever happens – and leave healthy offspring.

“The genomic data indicate that genetic diversity really went down at some point. There may have been warming periods when the animals retreated to refugia, and then as the earth cooled, they expanded throughout the northern hemisphere along the circumpolar region, and were well adapted. But what happens if their habitat changes, as it seems to be doing now? They may not have a good genetic buffer for experiencing changes in the environment, including transfer of pathogens,” Dr. Lindqvist says.

Polar bears are also at a disadvantage because they are specialists. Their thick layers of body fat and black skins hold in heat, while their white fur provides camouflage for hunting on the ice. But like a New York City resident who won’t venture much farther north than the Catskills, the polar bear’s habitat is very restricted. Unlike a NYC resident, however, polar bears’ food choices are few, but they eat all the time – only the pregnant hibernate.
Brown-bear-in-springBrown and black bears occupy much more diverse territory than polar bears, and would live in the US outside Yellowstone national park if we humans hadn’t transformed the landscape. They eat fish and other meat, vegetables, berries, and whatever they can pilfer from campsites. The more discerning polar bears prefer seal blubber but will eat bird eggs or whale leftovers if seals are scarce.

 

POSITIVE SELECTION – THE BRUSHSTROKES OF EVOLUTION
Natural selection as Charles Darwin described it was mostly negative – individuals ill-equipped to deal with life were less likely to have healthy offspring than others, and over time, this weeding out sculpted populations. In contrast, positive selection reflects gene variants that give an individual a reproductive advantage. (Darwinian “fitness” refers to reproduction or a trait that fosters successful reproduction – not being physically fit.)

Genomes bear signs of positive selection for traits that give a species an advantage: a variant of a gene that is present among many if not all members of one species, but is not in closely related species. The telltale gene variant must change the amino acid in the encoded protein, and produce an effect that makes sense, such as altering metabolism to conserve heat.

(ASIDE: By “actually changing the amino acid” I mean a DNA change that alters the amino acid that the DNA triplet encodes. A change of CCG to CCC, for example, would still place proline in the protein. An unchanged protein offers nothing for natural selection to act upon. But a change of CCG to ACG specifies threonine, not proline, and if the change is in an important part of the protein, could affect the body in a way that responds to an environmental change. This is why I hate the rampant misuse of “genetic code” in place of “genome sequence.” There isn’t a “human genetic code,” it’s universal. All of us on earth use the same DNA triplets to specify the same amino acids. I know, “genetic code” is like “computer code.” But we textbook authors have to be precise and historically accurate. Michael Jackson having a different genetic code from, say, a hippopotamus or cactus, alters the meaning.)

I digress. Anyway, the genomes of the brown and polar bears have 1,374 areas that differ more in sequence than chance might explain. It is in those areas where the researchers trolled for genes that might make sense in explaining the adaptations (inherited traits) that enable the polar bears to live at the edges of the ice.

Here are a few candidate genes whose variants unique to polar bears might have molded their adaptations to the present environment, and could fall victim to negative selection should global warming continue.

ALDH7A1 encodes an aldehyde dehydrogenase that powers polar bear metabolism in the cold. Will it be adaptive in melting ice?

DAG1 encodes part of the group of glycoproteins that, when mutant, cause muscular dystrophies. Perhaps the variant unique to polar bears keeps their muscles strong, as the black bear version maintains muscles during hibernation.

BTN1A1 encodes butyrophilin, which ups the fat content of milk, providing insulation.

FTO, with the insensitive name “fat mass and obesity associated,” has variants that make us, mice, rats, and other apes retain weight. Polar bears too.

PLTP encodes phospholipid transfer protein, which controls metabolism of HDL, helping to pile on the pounds after eating blubber.

800px-Appaloosa_stallionEDNRB (endothelin receptor type B) and TRPM1 (a transient receptor potential cation channel) are pigmentation genes that keep melanocytes out of the polar bear’s hairs, making the coat white. TRPM1 is very variable among the ursids. It also bestows different coat colors to Appaloosa horses and might explain the horses of a different color in Oz.

Postscript: The genome sequence of the 120,000-year-old polar bear that left its jawbone in the Norwegian museum revealed that it’s just a regular polar bear – but with enough genetic diversity, compared to the genomes of its modern descendants, to suggest that the sad polar bears pivoting on shrinking ice floes may indeed be the last of their kind.

Thanks to my daughter Carly Lewis for inspiring this blog post.

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