Tag Archives: biodiversity

What You Can Do with $1 Million: Saving the New Zealand Parrot

Scientists in New Zealand have genetically sequenced every adult kakapo.  The kakapo, a cuddly bird that lives in New Zealand, is not designed for survival. Weighing up to 4kg, it is the world’s fattest and least flighty parrot. It mates only when the rimu tree is in fruit, which happens every few years.  It evolved in the absence of land-based predators, so instead of soaring above the trees it waddles haplessly across the dry forest floor below. When it stumbles across something that might kill it, it has the lamentable habit of standing still….Such oddities turned the kakapo into fast food for human settlers—and for the cats, rats and possums they brought with them. It seemed extinct by the 1970s, until scientists stumbled on two undiscovered populations in the country’s south. These survivors were eventually moved to small predator-free islands, where the Department of Conservation has spent decades trying to get them to breed…Its patience may finally be rewarded. The rimu was in fruit this year, and more than 80 chicks hatched after a bumper crop, making this the best breeding season on record. Many have survived into adolescence, increasing the number of adult kakapos by a third, to 200 birds.

But another threat to the kakapo is a lack of genetic diversity, because of low numbers and inbreeding. This is one reason why fewer than half of kakapo eggs hatch. By sequencing the genome of every living bird, scientists can identify closely related individuals and prevent more inbreeding by putting them on different islands. Well-matched birds cannot be forced to mate, but artificial insemination is also proving effective. Every bird is fitted with a transmitter to track its slightest movement. If a female mates with an “unsuitable” male, the process can be “overridden” with another bird’s semen. Time is of the essence, so drones are being used to whizz kakapo sperm to the right place.

All these efforts cost almost nz$2m ($1.3m) this breeding season. Yet the kakapo’s future still looks precarious. Earlier this year a fungal disease tore through the population. And tiny as the number of kakapos is, space is running out on the two islands where most of them live. New predator-free havens must soon be found. 

Excerpts from How eugenics is saving a pudgy parrot, Economist, Aug. 31, 2019

The Biopiracy Backlash

Indonesia‘s rich biodiversity and complex geology have lured scientists from abroad for centuries. But a law adopted on 16 July 2019 by Indonesia’s parliament may convince some to go elsewhere. The legislation includes strict requirements on foreign scientists doing research in Indonesia, including the need to recruit local collaborators and a near-ban on exporting specimens, along with stiff sanctions, including jail time, for violators.

Muhammad Dimyati, director-general of research development at Indonesia’s Ministry of Research, Technology, and Higher Education (commonly known as RISTEK) in Jakarta, says the law is needed to protect Indonesia’s natural resources and develop the country’s research enterprise. But some Indonesian scientists fear the consequences. “Our international collaborations will be stifled,” says Berry Juliandi, a biologist at Bogor Agricultural University and secretary of the Indonesian Young Academy of Science. Indeed, marine biologist Philippe Borsa of the French Research Institute for Development in Montpellier says the law—and an increasingly unfriendly climate for foreign researchers—is a reason for him not to return to Indonesia, where he has studied the phylogeography of stingrays.

The new law also establishes the National Research Agency, a giant new institution that may subsume most government research centers, including the Indonesian Institute of Sciences (LIPI) in Jakarta. Details still need to be fleshed out, but some scientists worry the new agency will concentrate too much power in a few hands. The law’s most contentious provisions, however, are those that apply to foreign researchers.

From now on, their research has to be “beneficial for Indonesia.” They need to get ethical clearance from an Indonesian review board for every study, submit primary data and published papers to the government, involve Indonesian scientists as equal partners, and share any benefits, such as the proceeds from new drugs, resulting from the study. Researchers can’t take samples or even digital information out of the country, except for tests that cannot be done in Indonesian labs, and to do so, they need a so-called material transfer agreement (MTA) using a template provided by the government.

In most cases, violators will lose their research permit, but some offenses carry steeper penalties. Scientists who fail to obtain a proper permit will be blacklisted for 5 years; repeat offenders risk a $290,000 fine. Failure to comply with the MTA requirements is punishable by 2 years in prison or a $145,000 fine. ..Indonesia has become increasingly concerned about biopiracy.  In 2018,, for instance, a dispute erupted over a genetic study of Sulawesi’s “sea nomads”—an indigenous fishing group that appears to have evolved bigger spleens to store oxygenated blood during long dives. Indonesian researchers called it an example of Western “helicopter science.”. 

Megalara garuda

A 2017 document introducing the new law, signed by RISTEK Minister Mohamad Nasir, singled out another alleged example: the discovery of Megalara garuda, a giant venomous wasp, on Sulawesi, published in 2012 by entomologist Lynn Kimsey of the University of California (UC), Davis, along with a German researcher who found the same insect in a Berlin collection. LIPI entomologist Rosichon Ubaidillah tells Science that he and a junior colleague collected the wasps and that he suggested the name garuda—a mythical bird and national symbol of Indonesia—during a visit to UC Davis. But neither of them was a co-author on the paper; Ubaidillah was mentioned in an acknowledgement, his colleague not at all. Kimsey violated a memorandum of understanding between LIPI and UC Davis, he adds. LIPI, enraged, asked Kimsey to return the wasps she took home.

Excerpts from Dyna Rochmyaningsih, Indonesia gets tough on foreign scientists, Science, July 26, 2019

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

Eradicate Mosquitoes Forever: Gene Drives

The mosquitoes are being fitted with a piece of dna called a gene drive. Unlike the genes introduced into run-of-the-mill genetically modified organisms, gene drives do not just sit still once inserted into a chromosome. They actively spread themselves, thereby reaching more and more of the population with each generation. If their effect is damaging, they could in principle wipe out whole species.. If gene drives were to condemn to a similar fate the mosquitoes that spread malaria, a second of humankind’s great scourges might be consigned to history.

Gene drives can in principle be used against any creatures which reproduce sexually with short generations and aren’t too rooted to a single spot. The insects that spread leishmaniasis, Chagas disease, dengue fever, chikungunya, trypanosomiasis and Zika could all be potential targets. So could creatures which harm only humankind’s dominion, not people themselves. Biologists at the University of California, San Diego, have developed a gene-drive system for Drosophila suzukii, an Asian fruitfly which, as an invasive species, damages berry and fruit crops in America and Europe. Island Conservation, an international environmental ngo, thinks gene drives could offer a humane and effective way of reversing the damage done by invasive species such as rats and stoats to native ecosystems in New Zealand and Hawaii.

Such critics fear that the laudable aim of vastly reducing deaths from malaria—which the World Health Organisation puts at 445,000 a year, most of them children—will open the door to the use of gene drives for far less clear-cut benefits in ways that will entrench some interests, such as those of industrial farmers, at the expense of others. They also point to possible military applications: gene drives could in principle make creatures that used not to spread disease more dangerous… The ability to remove species by fiat—in effect, to get them to remove themselves—is, like the prospect of making new species from scratch, a power that goes beyond the past ambit of humankind.

Gene drives based on crispr-Cas9 could easily be engineered to target specific bits of the chromosome and insert themselves seamlessly into the gap, thus ensuring that every gamete gets a copy . By 2016, gene drives had been created in yeast, fruitflies and two species of mosquito. In work published in the journal Nature Biotechnology in September, Andrea Crisanti, Mr Burt and colleagues at Imperial showed that one of their gene drives could drive a small, caged population of the mosquito Anopheles gambiae to extinction—the first time a gene drive had shown itself capable of doing this. The next step is to try this in a larger caged population.

There are also worries about how gene drives might be used to create a weapon. …The need to find ways to guard against such attacks is one of the reasons that the Pentagon’s Defence Advanced Research Projects Agency (darpa) gives for its work on gene drives. Renee Wegrzyn, programme manager for darpa’s “Safe Genes” project, says the work is to prevent “technological surprise”, whether in the form of an unintended consequence or nefarious use. One of the academic teams she funds has made progress in developing anti-crispr enzyme systems that one day might be able to inhibit a drive’s operation.

Oversight needs not just to bring together a range of government agencies; it requires co-operation between governments, too. The Cartagena Protocol on Biosafety, which entered into force under the un Convention on Biological Diversity (cbd) in 2003, provides controls on the transfer of genetically modified organisms. But how it applies to gene drives is unclear—and besides, America has never ratified the convention. An attempt to ban gene-drive research through the cbd, which was backed by the etc Group and other ngos, failed at the convention’s biennial meeting in Cancún in 2016…Like the reintroduction of vanished species advocated by the rewilding movement, gene-drive technology will provide new arenas for the fight between those who wish to defend nature and those who wish to tame it.

Excertps from Gene Drives: Extinction on Demand, Economist, Nov. 10, 2018, at 24

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

Unjustifiable Extinctions

The world’s botanic gardens contain at least 30% of all known plant species, including 41% of all those classed as ‘threatened’, according to the most comprehensive analysis to date of diversity in ‘ex situ’ collections: those plants conserved outside natural habitats.

The study, in September 2017 in the journal Nature Plants, found that the global network of botanic gardens conserves living plants representing almost two-thirds of plant genera and over 90% of plant families.  However, researchers from the University of Cambridge discovered a significant imbalance between temperate and tropical regions. The vast majority of all plants species grown ex situ are held in the northern hemisphere. Consequently, some 60% of temperate plant species were represented in botanic gardens but only 25% of tropical species, despite the fact that the majority of plant species are tropical.

For the study, researchers analysed datasets compiled by the Botanic Gardens Conservation International (BGCI)….

“The global network of botanic gardens is our best hope for saving some of the world’s most endangered plants,” said senior author Dr Samuel Brockington, a researcher at Cambridge’s Department of Plant Sciences as well as a curator at the University’s own Botanic Garden….“Currently, an estimated one fifth of plant diversity is under threat, yet there is no technical reason why any plant species should become extinct.   “If we do not conserve our plant diversity, humanity will struggle to solve the global challenges of food and fuel security, environmental degradation, and climate change.”

The plants not currently grown in botanic gardens are often more interesting than those that are, say the researchers. Hydrostachys polymorpha, for example, an African aquatic plant that only grows in fast flowing streams and waterfalls, or the tiny parasitic plant Pilostyles thurberi – only a few millimetres long, it lives completely within the stem tissue of desert shrubs.  Species from the most ancient plant lineages, termed ‘non-vascular’ plants, are currently almost undocumented in botanic gardens – with as few as 5% of all species stored in the global network. These include plants such as the liverworts and mosses.

“Non-vascular species are the living representatives of the first plants to colonise the land,” said Brockington. “Within these plants are captured key moments in the early evolutionary history of life on Earth, and they are essential for understanding the evolution of plants”

Excerpts from World’s botanic gardens contain a third of all known plant species, and help protect the most threatened, Press Release of Botanic Gardens Conservation International, Sept. 25, 2016

Waterbird Habitats Lacking

The spring of 2017 50 million waterbirds will move from their winter homes in South-East Asia, Australia and New Zealand to their breeding grounds in Russia, Mongolia, northern China, the Korean peninsula, Japan and even Alaska. They rely on intertidal flats teeming with nourishing molluscs, worms and crustaceans, as well as plants, to supply the food that fuels their journeys.  Of the eight big flyways, the East Asian-Australasian is also the one displaying the sharpest decline in the number of birds. Of its 155-odd waterbird species, at least 24 are now globally threatened. They include the diminutive spoon-billed sandpiper, a wader whose numbers are down to fewer than 200 pairs.

Transiting one of the world’s most dynamic industrial regions is clearly taking a toll. Asia’s migratory waterbirds face immense pressures, from hunting, pollution, ingested plastic and competition from aquaculture. But the biggest disaster is the destruction of coastal way-stations. Since 1950 China has lost over half its coastal wetlands to “reclamation”. According to the International Union for Conservation of Nature (IUCN), the Yellow Sea, into which the Yellow River flows, has lost over 35% of intertidal habitat since the early 1980s. An especially destructive moment was the run-up to the Beijing Olympics of 2008, for which a lot of heavy industry was moved from the capital to the coast.

Xianji Wen, who works for the WWF, describes the Yellow Sea as a “bottleneck” for the whole flyway: so many waders pass through it that the loss of habitat there is particularly consequential. Four-fifths of Asia’s red knots, having wintered in Australasia, stop on their way north at one spot, Luannan, east of Beijing. The bar-tailed godwit flies non-stop from New Zealand to the Yellow Sea—over 6,000km. After recovering there, the species flies non-stop again to its breeding grounds in the extreme north of Russia.  Populations of both species have crashed by over a third, probably because of coastal development…..

There is a silver lining, however. The vast middle class created by the region’s breakneck growth is becoming interested in conservation…In China several hundred birdwatchers gather for the spring migration by the Yellow Sea near the North Korean border. And Mr Wen says that local governments in China increasingly take pride in the acclaim they win for conservation schemes—several work with the WWF. In 2016 China and New Zealand even signed an agreement—an “air bridge” between the two countries—to protect the habitat of the bar-tailed godwits, whose annual departure, Maori mythology holds, is for the homeland of the ancestors who first colonised New Zealand.

South Korea’s conservation movement is feeble. But the government of North Korea, by failing to develop the country, has inadvertently preserved a greater share of valuable waterbird habitats. It recently agreed to designate one as a protected site under the “Ramsar” international convention on wetlands….

Excerpt from Canaries in the Coal Fumes, Economist, Apr. 22, 2017