Category Archives: endangered species

The Most Highly Polluted Mammals: Killer Whales

Killer whales (Orcinus orca) are among the most highly polychlorinated biphenyl (PCB)–contaminated mammals in the world, raising concern about the health consequences of current PCB exposures.  Until they were recognized as highly toxic and carcinogenic, polychlorinated biphenyls (PCBs) were once used widely. Their production was banned in the United States in 1978, though they are still produced globally and persist in the environment. Persistent organic compounds, like PCBs, magnify across trophic levels, and thus apex predators are particularly susceptible to their ill effects. Desforges et al. looked at the continuing impact of PCBs on one of the largest marine predators, the killer whale. Using globally available data, the authors found high concentrations of PCBs within killer whale tissues. These are likely to precipitate declines across killer whale populations, particularly those that feed at high trophic levels and are the closest to industrialized areas.

Jean-Pierre Desforge, Predicting global killer whale population collapse from PCB pollution, Science, Sept. 28, 2018

Amazon Turtles are Back! Thanks to Local Vigilantes

The historically over-exploited Giant South American Turtle is making a significant comeback on river beaches in the Brazilian Amazon thanks to local protection efforts, say researchers at the University of East Anglia.  Their results, published in Nature Sustainability, show that Giant Turtle populations are well on their way to full recovery on beaches guarded by local vigilantes. There are now over nine times more turtles hatching on these beaches than there were in 1977, equivalent to an annual increase of over 70,000 hatchlings.  The beach survey showed that, of over 2000 turtle nests monitored on protected beaches, only two per cent were attacked by poachers. In contrast, on unprotected beaches, poachers had harvested eggs from 99 per cent of the 202 nests surveyed.The beach protection programme along the Juruá river is part of the largest community-based conservation programme in the Brazilian Amazon. Beaches are guarded on a shoestring budget by local communities carrying out round-the-clock beach surveillance throughout the five-month turtle breeding season.

Prof Carlos Peres, from UEA’s School of Environmental Sciences and a senior author on the study, said: “This study clearly demonstrates the effectiveness of empowering local management action by stakeholders who have the largest stake and a 24/7 presence at key conservation sites. The beaches protected by local communities represent noisy islands of high biodiversity, surrounded by lifeless unprotected beaches, which are invariably empty and silent.”

Excerpts from Amazon turtle populations recovering well thanks to local action, Nov. 3, 2018

Sequencing All Species: the Earth BioGenome Project

In the first attempt of its kind, researchers plan to sequence all known species of eukaryotic life—66,000 species of animals, plants, fungi, and protozoa—in a single country, the United Kingdom. The announcement was made here today at the official launch of an even grander $4.7 billion global effort, called the Earth BioGenome Project (EBP), to sequence the genomes of all of Earth’s known 1.5 million species of eukaryotes within a decade.

In terms of genomes sequenced, the eukaryotes—the branch of complex life consisting of organisms with cells that have a nucleus inside a membrane—lag far behind the bacteria and archaea. Researchers have sequenced just about 3500 eukaryotic genomes, and only 100 at high quality.

The U.K. sequencing effort—dubbed The Darwin Tree of Life project—will now become part of the EBP mix…Also announced today was a memorandum of understanding for participating in EBP. It has been signed by 19 institutions, including BGI Shenzhen, China; the Royal Botanic Gardens, Kew; and Sanger. 

Excerpts from Erik Stokstad, Researchers launch plan to sequence 66,000 species in the United Kingdom. But that’s just a start, Science, Nov. 1, 2018

Meddling with Nature: Is it Right? Is it Fair?

Many envisioned environmental applications of newly developed gene-editing techniques such as CRISPR might provide profound benefits for ecosystems and society. But depending on the type and scale of the edit, gene-edited organisms intentionally released into the environment could also deliver off-target mutations, evolutionary resistance, ecological disturbance, and extinctions. Hence, there are ongoing conversations about the responsible application of CRISPR, especially relative to the limitations of current global governance structures to safeguard its use,   Largely missing from these conversations is attention to local communities in decision-making. Most policy discussions are instead occurring at the national or international level even though local communities will be the first to feel the context-dependent impacts of any release. ..

CRISPR gene editing and other related genetic technologies are groundbreaking in their ability to precisely and inexpensively alter the genome of any species. CRISPR-based gene drives hold particular import because they are designed to rapidly spread genetic changes—including detrimental traits such as infertility—through populations of sexually reproducing organisms, to potentially reach every member of a species. Villages in Burkina Faso are weighing the release of gene drive–bearing mosquitoes that could suppress malaria. Nantucket Island residents in the United States are considering the release of genetically engineered white-footed mice to deplete Lyme disease reservoirs. New Zealand communities are discussing the possibility of using genetic methods to eliminate exotic predators.

But what if a gene drive designed to suppress an invasive species escaped its release site and spread to a native population? Or if a coral species gene edited to better adapt to environmental stressors dominated reef ecosystems at the expense of a diversity of naturally evolving coral species and the fish that depend on them ? The gravity of these potential outcomes begs the question: Should humans even be meddling with the DNA of wild organisms? The absence of generally agreed on answers can be used to support calls for moratoria on developing and releasing genetically altered organisms, especially those with gene drives (6).

However, the promising benefits of environmental gene editing cannot be dismissed. Gene drives may provide a long-sought-after tool to control vectors of infectious disease and save millions of human lives. Projects to conserve ecosystems or promote species resilience are often intended to repair human-inflicted environmental damage. Put simply, either using this technology irresponsibly or not using it at all could prove damaging to humans, our welfare, and our planet.

At the international level, the Convention on Biological Diversity (CBD) has enlisted an expert technical panel to, in part, update its Cartagena Protocol (of which the United States is not a party) that oversees transboundary transport of living modified organisms to accommodate gene drive–bearing organisms. The International Union for the Conservation of Nature (IUCN) is also developing policy to address the release of gene-edited organisms. Although the CBD and the IUCN offer fora to engage diverse public feedback, a role largely fulfilled by civil society groups, none of these agencies currently use the broad and open deliberative process we advocate….

Different societal views about the human relationship to nature will therefore shape decision-making. Local community knowledge and perspectives must therefore be engaged to address these context-dependent, value-based considerations.  A special emphasis on local communities is also a matter of justice because the first and most closely affected individuals deserve a strong voice in the decision-making process…Compounding this challenge is that these decisions cannot be made in isolation. Organisms released into local environments may cross regional and even international borders. Hence, respect for and consideration of local knowledge and value systems are necessary, but insufficient, to anticipate the potentially ramifying global implications of environmental release of gene-edited organisms. What is needed is an approach that places great weight on local perspectives within a larger global vision…

The needs of ecosystems could also be given voice to inform deliberative outcomes through custodial human proxies. Inspired by legislative precedent set by New Zealand, in which the Whanganui River was granted legal “personhood,” human representatives, nominated by both an international body like the IUCN and the local community, would be responsible for upholding the health and interests of the ecosystems in question. Proposed gene-editing strategies would be placed in the larger context of alternative approaches to address the public health or environmental issue in question…d

An online registry for all projects intending to release genetically engineered organisms into the environment must be created. Currently, no central database exists for environmental gene-editing applications or for decision-making outcomes associated with their deployment, and this potentially puts the global community at risk…A global coordination task force would be charged with coordinating multiple communities, nations, and regions to ensure successful deliberative outcomes. As a hypothetical example, genetic strategies to eliminate invasive possums from New Zealand must include representatives from Australia, the country likely to be affected should animals be transported outside the intended range. Similarly, the African Union is currently deliberating appropriate governance of gene drive–bearing mosquitoes to combat malaria on a regional scale. 

Excerpts from Natalie Kofl et al.,  Editing nature: Local roots of global governance, Science Magazine, Nov. 2, 2018

De-Extinction: Bring Back the Passenger Pigeon

The Crispr-Cas9 system consists of two main parts: an RNA guide, which scientists program to target specific locations on a genome, and the Cas9 protein, which acts as molecular scissors. The cuts trigger repairs, allowing scientists to edit DNA in the process. Think of Crispr as a cut-and-paste tool that can add or delete genetic information. Crispr can also edit the DNA of sperm, eggs and embryos—implementing changes that will be passed down to future generations. Proponents say it offers unprecedented power to direct the evolution of species.

The technology is widely used in animals. Crispr has produced disease-resistant chickens and hornless dairy cattle. Scientists around the world routinely edit the genes in mice for research, adding mutations for human diseases such as autism and Alzheimer’s in a search of possible cures. Crispr-edited pigs contain kidneys that scientists hope to test as transplants in humans.  Crispr has been discussed as a de-extinction tool since its earliest days. In March 2013 the conservation group Revive & Restore co-organized the first TedXDeExtinction conference in Washington, D.C. Revive & Restore was co-founded by Stewart Brand, the creator of the counterculture Whole Earth Catalog and a vocal advocate for a passenger pigeon revival.

The last known passenger pigeon—a bird named Martha—died in captivity at a Cincinnati zoo in 1914….The first step was to sequence the passenger pigeon genome…Sequencing an extinct species’ genome is no easy task. When an organism dies, the DNA in its cells begins to degrade, leaving scientists with what Shapiro describes as “a soup of trillions of tiny fragments” that require reassembly. For the passenger pigeon project, Shapiro and her team took tissue samples from the toe pads of stuffed birds in museum collections. DNA in the dead tissue left them with tantalizing clues but an incomplete picture. To fill in the gaps, they sequenced the genome of the band-tailed pigeon, the passenger pigeon’s closest living relative.

By comparing the genomes of the two birds, researchers began to understand which traits distinguished the passenger pigeon. In a paper published last year in “Science,” they reported finding 32 genes that made the species unique. Some of these allowed the birds to withstand stress and disease, essential traits for a species that lived in large flocks. They found no genes that might have led to extinction. “Passenger pigeons went extinct because people hunted them to death,” Shapiro says

.Revived passenger pigeons could also face re-extinction. The species thrived in the years before European settlement of North America, when vast forests supported billions of birds. Those forests have since been replaced by cities and farmland. “The habitat the passenger pigeons need to survive is also extinct,” Shapiro says.  But what does it mean to bring an extinct species back? Andre E.R. Soares, a scientist who helped sequence the passenger pigeon genome, says most people will accept a lookalike as proof of de-extinction. “If it looks like a passenger pigeon and flies like a passenger pigeon, if it has the same shape and color, they will consider it a passenger pigeon,” Soares says.

Shapiro says that’s not enough. Eventually, she says, gene-editing tools may be able to create a genetic copy of an extinct species, “but that doesn’t mean you are going to end up with an animal that behaves like a passenger pigeon or a woolly mammoth.” We can understand the nature of an extinct species through its genome, but nurture is another matter. 

After he determines how passenger pigeon DNA manifests in the rock pigeons, Novak hopes to edit the band-tailed pigeon, the passenger pigeon’s closest living relative, with as many of the extinct bird’s defining traits as possible. Eventually, he says, he’ll have a hybrid creature that looks and acts like a passenger pigeon (albeit with no parental training) but still contains band-tailed pigeon DNA. These new-old birds will need a name, which their human creator has already chosen: Patagioenas neoectopistes, or “new wandering pigeon of America.”

Excerpts from Amy Dockser Marcus, Meet the Scientists Bringing Extinct Species Back From the Dead, WSJ, the Future of Everything, Oct. 11, 2018

Sucking the Life out of Deep Sea

Those involved in deep-sea mining hope it will turn into a multi-billion dollar industry. Seabed nodules are dominated by compounds of iron (which is commonplace) and manganese (which is rarer, but not in short supply from mines on dry land). However, the nodules also contain copper, nickel and cobalt, and sometimes other metals such as molybdenum and vanadium. These are in sufficient demand that visiting the bottom of the ocean to acquire them looks a worthwhile enterprise. Moreover, these metals seldom co-occur in terrestrial mines. So, as Kris Van Nijen, who runs deep-sea mining operations at Global Sea Mineral Resources (gsr), a company interested in exploiting the nodules, observes: “For the same amount of effort, you get the same metals as two or three mines on land.”

Though their location several kilometres beneath the ocean surface makes the nodules hard to get at in one sense, in another they are easily accessible, because they sit invitingly on the seabed, almost begging to be collected. Most are found on parts of the ocean floor like the Clarion Clipperton Zone (ccz), outside the 200-nautical-mile exclusive economic zones of littoral countries. They thus fall under the purview of the International Seabed Authority (isa), which has issued 17 exploration licences for such resources. All but one of these licences pertain to the ccz, an area of about 6m square kilometres east-south-east of Hawaii.

The licensees include Belgium, Britain, China, France, Germany, India, Japan, Russia, Singapore and South Korea, as well as several small Pacific island states. America, which is not party to the United Nations Convention on the Law of the Sea that established the isa, is not involved directly, but at least one American firm, Lockheed Martin, has an interest in the matter through a British subsidiary, uk Seabed Resources. And people are getting busy. Surveying expeditions have already visited the concessions. On land, the required mining machines are being built and tested. What worries biologists is that if all this busyness does lead to mining, it will wreck habitats before they can be properly catalogued, let alone understood.

 Some of the ccz’s creatures stretch the imagination. There is the bizarre, gelatinous, yellow “gummy squirrel”, a 50cm-long sea cucumber with a tall, wide tail that may operate like a sail. There are galloping sea urchins that can scurry across the sea floor on long spines, at speeds of several centimetres a second. There are giant red shrimps, measuring up to 40cm long. And there are “Dumbo” octopuses, which have earlike fins above their eyes, giving them an eerie resemblance to a well-known cartoon elephant…Of 154 species of bristle worms the surveyors found, 70% were previously unknown. 

the Whale fossils, sea cucumbers and shrimps are just the stuff that is visible to the naked eye. Adrian Glover, one of Dr Amon’s colleagues at the Natural History Museum, and his collaborators spent weeks peering down microscopes, inspecting every nook and cranny of the surfaces of some of the nodules themselves. They discovered a miniature ecosystem composed of things that look, at first sight, like flecks of colour—but are, in fact, tiny corals, sponges, fan-like worms and bryozoans, all just millimetres tall. In total, the team logged 77 species of such creatures, probably an underestimate.

Inevitably, much of this life will be damaged by nodule mining. The impacts are likely be long-lasting. Deep-sea mining technology is still in development, but the general idea is that submersible craft equipped with giant vacuum cleaners will suck nodules from the seafloor. Those nodules will be carried up several kilometres of pipes back to the operations’ mother ships, to be washed and sent on their way.

The largest disturbance experiment so far was carried out in 1989 in the Peru Basin, a nodule field to the south of the Galapagos Islands. An eight-metre-wide metal frame fitted with ploughs and harrows was dragged back and forth repeatedly across the seabed, scouring it and wafting a plume of sediment into the water…. The big question was, 26 years after the event, would the sea floor have recovered? The answer was a resounding “no”. The robots brought back images of plough tracks that looked fresh, and of wildlife that had not recovered from the decades-old intrusion.

Conservation and seabed minerals: Mining the deep ocean will soon begin, Economist, Nov. 10, 2018

Preserving Snow Leopard for Eternity

The breeding of the highly-endangered snow leopard in the Himalayan nature park Himachal Pradesh resort (India) is set to begin with zoo authorities in Darjeeling agreeing to lend it a pair.  “The Padmaja Naidu Himalayan Zoological Park in Darjeeling is providing us a pair of snow leopards for conserving bloodlines of the highly endangered species in the participatory zoos,” state Chief Wildlife Warden S.S. Negi told IANS….

In 2004, snow leopard Subhash and his sibling Sapna were brought to Kufri, 15 km from the state capital Shimla, from Darjeeling under an exchange programme.Officials said the breeding programme couldn’t be initiated as they belonged to the same bloodline. Sapna died of disease in 2007…

The Darjeeling zoo is internationally recognised for its 33-year-old conservation breeding programme for the snow leopard, with 56 births.

Forest Minister Thakur Singh Bharmouri said the central government-funded Snow Leopard Conservation Project of Rs.5.15 crore ($758,000) is under way in the Spiti Valley, which lies in the state’s northernmost part and runs parallel to Tibet.The programme would take care of restoring the snow leopard’s habitat, he said. Studies by the state wildlife department show the presence of seven to eight snow leopards per 100 sq km in the Spiti Valley.The department is already monitoring the habitat, range and behaviour of snow leopards in the Valley through camera traps (automatic cameras).As per the information gleaned from these devices, the snow leopard population is estimated to be 28 in Spiti and its nearby areas, and 29 in the rest of the state.

“We will soon start radio-collaring five to six snow leopards in Spiti and other areas to monitor their behaviour and, of course, habitat and range,” an official of the state’s wildlife wing told IANS.  Each radio collar costs around Rs.300,000 and can send signals for at least 18 months. “But the cost of procuring data sent through radio collars is quite expensive,” he said.

The problem of starting the radio collar installations is the non-availability of tranquillising drugs in India as prescribed by our international partner, Snow Leopard Trust,

Excerpt from Himachal to begin breeding the highly-endangered snow leopards,  India Live Today, June 28, 2016