The Genetics of Conservation

Spirit, or Kermode, bears are color polymorphisms of black bears. Throwbacks to the last ice age, spirit bears live only on two remote British Columbia islands: Princess Royal and Gribbell. Painting: Beth Holland.. The sea was the color of old silver, its surface as smooth as a wave-worn shell. Just after dawn on a cool August day, a group of biologists and naturalists milled around on a dock in remote Klemtu, British Columbia (BC), 530 kilometers due north of Vancouver. The group, including this writer, awaited the motor vessel KX Spirit. Spirit would soon ferry us to a remote island in search of a rare “spirit bear.” Scientists know the bear as Ursus americanus kermodei, or the Kermode bear, named after biologist Frank Kermode. Kermode, a former director of the Royal British Columbia Museum in Victoria, was among the first to research the subspecies. How many spirit bears are alive today? No one knows for sure, but conservation geneticists believe the bears number no more than the hundreds. Photograph: Maximilian Helm, Dresden, Germany. The bear is a color polymorphism of the black bear Ursus americanus. “Spirit bears have one of the most distinctive and conspicuous such polymorphisms of any mammal,” says ecologist Tom Reimchen, of the University of Victoria. Reimchen has spent much of his career studying the bears. “The white morph,” he says, “comes from a mutation at the melanocortin 1 receptor gene, the same locus associated with coat-color variation in other mammals.” The trait is recessive, reported geneticist Kermit Ritland, of the University of British Columbia, in a 2001 paper in Current Biology. Both parents must carry a copy of the mutated gene for their offspring to be white. Spirit bears are throwbacks to the last ice age, a time when being white may have conferred an advantage to animals living near ice-white glaciers. Some scientists think that black bears on what is now the BC coast might have been separated from mainland Canada by ice; then, inbreeding in this “refuge” increased the mutation's frequency. As the glaciers melted, the bears could have been stranded on newly formed islands. Researchers are now making use of the young discipline of conservation genetics to better understand spirit bears and other rare taxa. Conservation genetics focuses on small and fragmented populations, as well as on practical approaches to minimizing harmful effects on them, according to David A. Briscoe, Jonathan D. Ballou, and Richard Frankham, authors of the 2010 book Introduction to Conservation Genetics. “Conservation genetics encompasses the genetic management of small populations to maximize retention of genetic diversity and minimize inbreeding; the resolution of taxonomic uncertainties and delineation of management units; and the use of molecular genetic analyses in forensics and to understand species’ biology,” they write. Conservation genetics is being used around the world to study everything from whale sharks off the Arabian Peninsula to delicate Arabidopsis wildflowers in the United Kingdom (UK) to giraffes in Tanzania. In the case of the spirit bear, “a conservation genetics approach offers us insights into how rare this special white bear is on the landscape,” says conservation biologist Chris Darimont, of the University of Victoria. “It allows us to observe what our eyes cannot see.” By analyzing spirit bears’ hair and scat, “we can estimate how many of the black individuals carry the white form of the coat-color gene,” he says, “giving us insights into the natural processes and human pressures that maintain the white version or lead to its demise.” However spirit bears came to be, today, they live only in two of the most remote places on Earth: British Columbia's Princess Royal Island and Gribbell Island, some 50 miles north of Klemtu. About 1 of every 10 black bears on the two islands is a spirit bear. “The bears are likely a historically stable polymorphism rather than a recent transient polymorphism,” Reimchen says, “as the prevalence of the white bear on these two islands is deeply rooted in the oral history of the First Nations in the region.” It is believed that no more than a few hundred spirit bears now exist, but no one knows exactly how many bears, spirit or otherwise, are in the area, according to Darimont. By “area,” Darimont is referring to the Great Bear Rainforest (GBR), also known as the Central and North Coast forest, a temperate rainforest on BC's Pacific Coast. The GBR is a 6.4-million-hectare expanse that is part of the larger Pacific temperate rainforest ecoregion, the largest coastal temperate rainforest in the world. “It's an incredibly special place for the bears and the many other species that directly or indirectly depend on the Pacific Coast's salmon runs to survive,” says Darimont. Spirit bears are critical to efforts to protect the GBR, a name coined by environmental organizations in the 1990s. The GBR was officially recognized by the BC provincial government in February 2016 in an announcement that 85 percent of the region's old-growth forests would be off-limits to industrial logging. Safeguarding genetically rare spirit bears was central to that decision. Pink salmon are manna for spirit bears. Each fall, this species is among the first of the Pacific Northwest's salmon runs. Pink salmon make their way up streams as early as August. Photograph: Bering Land Bridge National Preserve. From late summer through autumn, spirit bears live along fast-running, boulder-lined streams brimming with salmon, a staple food for the bears. In spring and early summer, they amble through lowland estuaries. There, they feed on protein-packed sedges and on barnacles, mussels, and other invertebrates they wrest from rocks in the intertidal zone. “But they’re always waiting for the return of the salmon in fall,” says Reimchen. How likely is it to glimpse a spirit bear at any time of year? “The chance of seeing a white bear on a given day is almost nonexistent,” says Reimchen. “If it happens, it's usually a once-in-a-lifetime.” Nonetheless, our motley crew, now aboard the KX Spirit, pressed onward. Spirit backed out of its berth at the Spirit Bear Lodge dock and threaded north through foggy, narrow straits. A point of land emerged from the mist, the tip of Princess Royal Island. Spirit's captain, who is known simply as “Moose” and is a member of Canada's Kitasoo/Xai’xais First Nation, dropped anchor off Princess Royal Island and lowered a Zodiac boat over the side. The rest of us, including crewmembers Mercy Georgia Starr Mason, also a Kitasoo/Xai’xais member, and Elissa Crouse, climbed aboard. Mason and Crouse guided us to a shoreline where the boulders were taller than us. An hour of rainforest bushwhacking later, Mason and I perched on a wet, mossy log halfway down a narrow path to a steep creek. The creek would soon be filled with pink salmon making their journey upstream to spawn. Princess Royal Island has some 30 major salmon streams. Reimchen and others have found that white bears have an advantage over black bears in catching salmon: The salmon cannot see white fur as clearly as they can black fur, report Reimchen and Dan Klinka, also of the University of Victoria, in a 2017 paper published in the Biological Journal of the Linnean Society. Because salmon are the major source of protein for both spirit and black bears, “the greater capture success by white bears could facilitate the persistence of this color polymorphism,” says Reimchen. Whither go the salmon, he believes, so go the spirit bears. Biologists are obtaining detailed information about whale-shark populations from environmental DNA (eDNA). Organisms continuously shed DNA into the environment, including in the sea. Photograph: Derek Keats, Johannesburg, South Africa. DNA barcoding of fins sold for shark-fin soup shows that many of the fins are in fact from threatened shark species. Photograph: Cedric Seow From our spot on the trail, we heard waves breaking on a beach. We were a short distance from where the creek meets the sea. Suddenly, Mason motioned to me to be very quiet. We watched as a bear that was almost as white as a polar bear made its sure-footed way down a rocky ledge to the creek below. There it “snorkeled” for salmon, dunking its head in the water and peering from left to right and back again in search of an unwary fish. Over the course of an hour, the spirit bear padded from one spot to another down the creek. But no salmon that day. How much longer will spirit bears survive? “Despite their small population size and the destabilizing effects of immigration [the influx of black bears that do not carry the recessive mutation], the historical persistence of these bears indicates high resiliency of this polymorphism,” write Reimchen and Klinka. Numbers of salmon returning to the rivers of western North America over the last century, however, have declined by 90 percent, a result of logging effects on spawning grounds and other factors. “That may limit spirit bears’ long-term prospects,” Reimchen says. On a hopeful note, Ritland and Philip Hedrick, of Arizona State University, state in the journal Evolution that “the spirit bear may be an example of incipient speciation and a model for evolutionary biology.” To peer into what the future may hold for terrestrial and marine species, ­scientists are looking at environmental DNA, also called eDNA. Organisms continuously shed DNA into the environment in tissues, cells, and wastes. eDNA molecules are found in water, air, soil, and sediments and can persist for thousands of years. Technologies for detecting trace amounts of eDNA have greatly improved over the past decade, and new sequencing techniques allow for DNA from several genomes and taxonomic groups, such as animals, plants, fungi, and bacteria, to be analyzed at the same time. Genetic variations in DNA isolated from water samples, for example, can be used to estimate population sizes of aquatic species and to investigate relatedness among different populations of the same species. Other applications include determination of predators and prey in a location; detection of species shifts as a result of climate change; and identification of invasive species, such as those moving from port to port via international shipping. Last summer, researchers collected eDNA samples in Khutze Inlet in the GBR as part of a project called Canada C3: Coast to Coast to Coast. Initial results show signs of salmon and their bear predators. Further insights into the bears’ dependence on salmon, say the biologists, are on the horizon. Half a world away, off the Arabian Peninsula, scientists have obtained detailed genetic information about the region's whale shark (Rhincodon typus) population using eDNA. The results were published in the 16 November 2016 issue of the journal Nature Ecology and Evolution. Every year from May through September, hundreds of whale sharks come together along the coast of Qatar to feed on the eggs of tuna that have spawned there. Whale sharks are globally endangered, but monitoring methods for the sharks have been lacking, says geneticist Philip Francis Thomsen, of the Center for GeoGenetics at the University of Copenhagen. He and colleagues used fragments of DNA in Qatar waters to study the sharks. The biologists matched eDNA results with those from whale-shark tissue samples. “This project was a unique opportunity to test the potential of the DNA method because we had a large number of tissue samples to compare the eDNA results with,” says Thomsen. The more tuna DNA there was in a water sample, the larger the amount of whale-shark DNA, suggesting that eDNA can be used to study entire marine food webs. Among the threats to whale sharks is the popularity of shark-fin soup. Researchers have found that the majority of shark fins sold around the globe for soup are from endangered species. Biologists collected 129 samples from fish markets in Canada, China, and Sri Lanka. Using DNA barcoding technology, they found that 71 percent of dried fins and gills from the markets came from species listed as at risk and therefore banned from international trade. The results were published in Scientific Reports on 25 August 2017. Twelve of the 20 shark and ray species the researchers uncovered, including whale sharks, are protected under the Convention on International Trade in Endangered Species (CITES). The scientists were especially surprised to find that whale-shark fins and gills were being sold. Despite the controversy around shark-fin soup and the fact that several of these shark species are threatened, in many places, there is a large market for shark fins, according to Dirk Steinke, an integrative biologist at the Centre for Biodiversity Genomics at the University of Guelph in Canada. Steinke is a coauthor of the Scientific Reports paper. Protection of sharks is hard to enforce, say Steinke and colleagues, because shark fins are dried and processed before they are sold, making it difficult to identify the species. “DNA barcoding is an ideal tool for identifying dried samples or samples that have been processed,” Steinke says. “It provides enforcement agencies with a way of detecting whether fins and gills are from legally imported species.” Biologists can now rapidly read the DNA of almost any organism, anywhere. Here, researchers use real-time nanopore sequencing to analyze an entire hillside of plants in the United Kingdom's Snowdonia National Park. Photograph: Alexander Papadopulos/Royal Botanic Gardens, Kew. Scientists can now rapidly read the DNA of any organism, almost anywhere. In a paper published on 21 August 2017 in Scientific Reports, researchers at the Royal Botanic Gardens, Kew, detailed botanical results obtained with portable, real-time DNA sequencers. Real-time nanopore sequencing, as the relatively new DNA sequencing method is known, is enabling rapid species identification at low cost and with minimal equipment. Kew scientists used the DNA sequencer MinION to analyze an entire hillside of plants in the UK's Snowdonia National Park. It was the first time genomic sequencing of plants had been performed in the field. The botanists rapidly identified two white-flowered plants, Arabidopsis thaliana and Arabidopsis lyrata ssp. petraea. The researchers sequenced random parts of the plants’ genomes, avoiding the time-consuming process of targeting specific pieces of DNA, the more traditional approach for identifying species. “Accurate species identification is essential for evolutionary and ecological research, in the fight against wildlife crime, and for monitoring rare and threatened species,” says Alexander Papadopulos, a Kew scientist and coauthor of the Scientific Reports paper. “Our experiments show that by sequencing random pieces of a genome in the field, it's possible to get very accurate identification of a specimen within a few hours of collecting it.” More than 11,000 kilometers away from the fields of Snowdonia, conservation genetics is also being employed in Africa. There, giraffes peacefully browse flat-topped acacias, their legs and necks nearly hidden in the trees. The quietly ambling animals are often overlooked; attention usually focuses on iconic African species such as elephants, lions, and rhinos. As a result, giraffes are undergoing a silent extinction, scientists say. Giraffes have moved from species of Least Concern to Vulnerable on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. But which giraffes? Biologists had long recognized one giraffe species and nine subspecies. Then, ecologists began a genetic analysis of giraffe relationships. Giraffes, it turns out, are not one species but four. “The genetic differences between giraffes are at least as great as those between polar bears and brown bears,” says scientist Julian Fennessy, director of the Giraffe Conservation Foundation, based in Namibia. He and geneticist Axel Janke, of Goethe University in Germany, led the research team. The unexpected findings, reported in the journal Current Biology in September 2016, highlight the need for in-depth studies of and greater conservation efforts for these four genetically isolated species, the biologists say. The researchers have continued their efforts, with new results expected before long. Southern giraffes, with some 52,000 remaining in the wild, are the most numerous of all giraffe species. Photograph: Giraffe Conservation Foundation. Giraffes, conservation geneticists have discovered, are not one species with several subspecies but rather comprise four species. Image: Giraffe Conservation Foundation. “We were surprised at the findings because coat patterns and other differences among giraffes are limited,” says Janke. “Giraffes are also assumed to have similar ecological requirements across their range, but no one really knows because they’ve been largely overlooked by science.” At the start of the project, Fennessy and Janke, along with other scientists, out to how living in different parts of are to The biologists at DNA from of giraffes across Africa. “The populations of all nine recognized giraffe says The long to be is alive in very small on islands off Photograph: The analysis shows that there are four of giraffes, the researchers do not with other in the As a result, the giraffes be recognized as four giraffe giraffe giraffe and giraffe giraffes into four and other may have populations long for new species to the scientists giraffes number than in the wild, and giraffes, than “That some of the most endangered large in the says Southern giraffes, however, are their in South according to biologist of South African National Over the past the giraffe population in National for example, has increased The is not as for giraffes, a subspecies of which number a is a small what about is the and of all individuals of a species,” write geneticist of the and colleagues in a paper in the journal But the always and found and for which there is no is an that is listed by the as our it had been in the says “It's been a for But there were that the might be alive in the A D. at the one obtained more than a from an “If its identification was state and colleagues in “the would have to be to in the But was it at research that the is most to species in so the botanists to that for of any D. 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