100,000-year-old polar bear genome reveals ancient hybridization with brown bears

An analysis of ancient DNA from a 100,000-year-old polar bear has revealed that extensive hybridization between polar bears and brown bears occurred during the last warm interglacial period in the Pleistocene, leaving a surprising amount of polar bear ancestry in the genomes of all living brown bears.

The study, led by scientists at the University of California, Santa Cruz, was published June 16 in Nature Ecology & Evolution. The researchers obtained ancient DNA from the skull of a juvenile polar bear that was found in 2009 on the coast of the Beaufort Sea in Arctic Alaska. Scientists nicknamed the bear 'Bruno,' although DNA analysis later showed it to be a female.

"The availability of Bruno's paleogenome has made it possible to detect an ancient admixture event that impacted all living brown bears," said first author Ming-Shan Wang, a postdoctoral scientist in the UCSC Paleogenomics Lab.

Corresponding author Beth Shapiro, professor of ecology and evolutionary biology at UC Santa Cruz and an investigator at the Howard Hughes Medical Institute, said the team's genomic analyses show that Bruno belonged to a polar bear population that was ancestral to living polar bears. At some point, probably after around 125,000 years ago, she said, the polar bear lineage leading to Bruno and the brown bear lineage leading to all living brown bears crossed paths and hybridized.

As a result of this ancient admixture, polar bear ancestry accounts for as much as 10% of the genomes of brown bears living today. "We never would have seen this without Bruno's genome, because all living brown bears have that admixture as part of their genomes," Shapiro said.

Although polar bears and brown bears are distinct species with striking differences in appearance, behavior, and habitats, they are closely related and can readily hybridize when their ranges overlap. Reports of hybrids have increased in recent years as the climate warms and disappearing sea ice forces polar bears onto Arctic coastal areas, while brown bears expand their range northward.

Previous studies of ancient DNA have shown that admixture has occurred in certain populations of brown bears at least four different times between around 15,000 and 25,000 years ago. In all cases, the direction of gene flow was from polar bears into brown bears.

"The admixed individuals, if they survive, do so as brown bears, perhaps because they have difficulty hunting successfully on the sea ice if they are not completely white," Shapiro explained. "Polar bears have always been a small population with not much genetic diversity."

The new study did find some evidence of possible gene flow from brown bears into Bruno's lineage, but the absence of admixture in polar bears today supports the idea that brown bear ancestry reduces a bear's fitness for life as a polar bear. After diverging from brown bears about 500,000 years ago, polar bears evolved into highly specialized hunters of marine mammals on the Arctic sea ice. Brown bears, in contrast, are generalists ranging widely across North America, Europe, and Asia.

Bruno lived during a time of changing climate after the peak of a warm interglacial period when temperatures and sea levels were considerably higher than they are now. Similar conditions can be expected in the future as a result of rapid climate change driven by the burning of fossil fuels and other human activities. As Arctic sea ice declines, many polar bear populations are already struggling to survive.

"If the rapid, unnatural, and severe human-caused warming of the Arctic we are documenting today continues unabated, it is uncertain whether polar bears will have a sea ice habitat to return to and survive genetically," said coauthor Ian Stirling, a polar bear biologist and research scientist with Environment and Climate Change Canada.

According to Shapiro, "We shouldn't be surprised to see admixture happening again today as the climate changes and these species are overlapping and encountering each other again in the wild. Climate change allows gene flow to occur between what we think of as different species."

Climatic shifts that have brought polar bears and brown bears together in the past include glacial periods when sea ice was more extensive, allowing polar bears to mix with brown bears in southeast Alaska, the Kuril Islands, and even Ireland. The brown bears in these locations (now extinct in Ireland) acquired additional polar bear genes on top of the ancient admixture revealed by Bruno's genome.

As for what brown bears might have gained from their polar bear ancestry, scientists can only speculate. "It's possible that brown bears got something cool from polar bears, but we can't say for sure at this point," Shapiro said.

Finding Bruno's skull was serendipitous. Coauthors Pamela Groves, Daniel Mann and Michael Kunz from the University of Alaska Fairbanks were walking the Beaufort Sea coastline in 2009 surveying for recent coastal erosion when they stumbled upon the skull resting just above the high tide line.

"We weren't even looking for bones, as typically we find ancient bones a hundred miles inland where they have been stored in permafrost along sleepy rivers," said Groves. Since polar bears spend most of their lives at sea, finding any polar bear remains is extremely unusual. Bruno is the only ancient polar bear skull ever recorded and the only ancient polar bear bone known from North America.

"Understanding how past changes in climate drove interactions between organisms is critical to predicting how current changes will create new admixtures, increase disease transmission, or impact natural resources or society," said Leslie Rissler, program director at the U.S. National Science Foundation, which funded the research.

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How species form: What the tangled history of polar bear and brown bear relations tells us

A new study is providing an enhanced look at the intertwined evolutionary histories of polar bears and brown bears.

Becoming separate species did not completely stop these animals from mating with each other. Scientists have known this for some time, but the new research draws on an expanded dataset -- including DNA from an ancient polar bear tooth -- to tease out more detail.

The story that emerges reveals complexities similar to those that complicate human evolutionary history.

"The formation and maintenance of species can be a messy process," says Charlotte Lindqvist, PhD, associate professor of biological sciences in the University at Buffalo College of Arts and Sciences, and an expert on bear genetics. "What's happened with polar bears and brown bears is a neat analog to what we're learning about human evolution: that the splitting of species can be incomplete. As more and more ancient genomes have been recovered from ancient human populations, including Neanderthals and Denisovans, we're seeing that there was multidirectional genetic mixing going on as different groups of archaic humans mated with ancestors of modern humans. Polar bears and brown bears are another system where you see this happening."

"We find evidence for interbreeding between polar bears and brown bears that predates an ancient polar bear we studied," she says. "And, moreover, our results demonstrate a complicated, intertwined evolutionary history among brown and polar bears, with the main direction of gene flow going into polar bears from brown bears. This inverts a hypothesis suggested by other researchers that gene flow has been unidirectional and going into brown bears around the peak of the last ice age."

The study will be published the week of June 6 in the Proceedings of the National Academy of Sciences. It was led by Lindqvist at UB in the U.S.; Luis Herrera-Estrella at the National Laboratory of Genomics for Biodiversity (LANGEBIO) in Mexico and Texas Tech University in the U.S.; and Kalle Leppälä at the University of Oulu in Finland. Tianying Lan, PhD, a former UB postdoctoral researcher now at Daicel Arbor Biosciences, was co-first author with Leppälä.

The concept of Arctic-adapted polar bears capturing genetic material from brown bears, which are adapted to life in lower latitudes, is one of several findings of possible interest for scientists concerned with climate change impacts on threatened species.

As the world warms and Arctic sea ice declines, polar bears and brown bears may run into each other more frequently in places where their ranges overlap. This makes their shared evolutionary history a particularly intriguing subject of study, Lindqvist says.

Splitting of species can be a messy process

As Lindqvist explains, scientists once thought modern humans and Neanderthals simply split into separate species after evolving from a common ancestor. Then, researchers found Neanderthal DNA in modern Eurasian people, implying that modern human populations received an influx of genes from Neanderthals at some point in their shared evolutionary history, she says.

Only later did scientists realize that this genetic intermingling also supplemented Neanderthal populations with modern human genes, Lindqvist adds. In other words, interbreeding can be complex, not necessarily a one-way street, she says.

The new study on bears reveals a remarkably similar story: The analysis finds evidence of hybridization in both polar bear and brown bear genomes, with polar bears in particular carrying a strong signature of an influx of DNA from brown bears, researchers say. Earlier research proposed the inverse pattern only, Lindqvist says.

"It's exciting how DNA can help reveal ancient life history. Gene flow direction is harder to determine than merely its presence, but these patterns are vital to understanding how past adaptations have transferred among species to give modern animals their current features," says Leppälä, PhD, postdoctoral researcher in the research unit of mathematical sciences at the University of Oulu.

"Population genomics is an increasingly powerful toolbox to study plant and animal evolution and the effects of human activity and climate change on endangered species," says Herrera-Estrella, PhD, President's Distinguished Professor of Plant Genomics and director of the Institute of Genomics for Crop Abiotic Stress Tolerance in the Texas Tech Department of Plant and Soil Science. He is also a professor emeritus at LANGEBIO. "Bears don't provide simple speciation stories any more than human evolution has. This new genomic research suggests that mammalian species groups can hide complicated evolutionary histories."

Evidence from modern bear genomes -- and DNA from an ancient tooth

The study analyzed the genomes of 64 modern polar and brown bears, including several new genomes from Alaska, a state where both species are found.

The team also produced a new, more complete genome for a polar bear that lived 115,000 to 130,000 years ago in Norway's Svalbard archipelago. DNA for the ancient polar bear was extracted from a tooth attached to a subfossil jawbone, which is now housed at the Natural History Museum at the University of Oslo.

Using this dataset, researchers estimate that polar bears and brown bears started to become distinct species about 1.3 to 1.6 million years ago, updating prior assessments made by some of the same scientists. The age of the split has been and remains a topic of scientific debate, with past interbreeding and limited fossil evidence for ancient polar bears among factors that make the timing hard to pinpoint, Lindqvist says.

In any case: After becoming their own species, polar bears endured dramatic population decline and a prolonged genetic bottleneck, leaving these bears with much less genetic diversity than brown bears, the new study concludes. The findings confirm past research pointing to the same trends, and add evidence in support of this hypothesis.

Together with the analysis of gene flow, these findings are providing new insights into the messy, intertwined evolutionary history of polar bears and brown bears.

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