Research and Rescue: Saving Species from Ourselves

Ashley Braun | Longreads | October 2019 | 23 minutes (4,191 words)

On a crisp December afternoon, I convince my sister’s family to visit an unusual exhibit in the Cincinnati Zoo. Countless holiday lights glow in the surrounding trees as we walk toward a statue roughly the size of a chicken. The sculpture is of a pigeon, and we stand admiring how it gracefully arcs its smooth, bronze neck toward the sky while bending down its saw-toothed tail.

This memory of a bird recalls Martha, the very last passenger pigeon on earth, who died at the Cincinnati Zoo and Botanical Garden in 1914. Most zoo-goers breeze past the sculpture, as if this pigeon were of no more interest than the kind that pecks through garbage. After we approach, my nieces, ages 5 and 11, flank the statue, downhill from a quiet Japanese-style pagoda, the aviary where Martha had spent her final years.

“Do you know what extinction means?” I ask the girls. They nod.

It’s when bad people come after you and kidnap you, ventures the 5-year-old. I smile, and as we walk into Martha’s pagoda, I try to explain what happens when the last of a living thing dies and there are no more like it anywhere, and never will be again.

Aunt of the year, I had just revealed a bitter truth to my 5-year-old niece.

I soon learned, however, that extinction is not actually so straightforward. We humans tend to tinker, to tweak. We try to fix what we have broken. Even as we attempt to preserve other living things — northern white rhinoceros, California condor, black-footed ferret — we change them. And that’s nothing new in human history.

“We have been doing this for as long as we have existed,” paleogeneticist Beth Shapiro tells me. “It’s not as if we have been completely innocent of manipulating species for the last 100,000 years.”

We hunt, breed, cultivate, and domesticate. Directly and indirectly, we leave the annotations of humanity written in the spaces where creatures live, in the quality of their neighborhoods, in their behavior, and even in the makeup of their DNA.

That’s true even for species like the passenger pigeon, which, as I told my surprised nieces, some researchers are trying to bring back from extinction. Or at least, they’re trying to bring back a façade of one.

Biotech to the Rescue?

Advances in biotechnology, from unlocking a creature’s genetic code to reprogramming the trajectory of its cells and editing its genes, are opening up new possibilities for conservation biology. With these tools in hand, humans are now confronted with opportunities previously relegated to imagination or science fiction. They offer astounding potential for making edits carefully, precisely, intentionally. They are giving renewed hope for still-struggling species pulled from the brink of extinction — and for species that human actions have already pushed over that edge.

However, humanity’s attempts to correct or rebalance our previous tinkerings with nature have sometimes led to further disaster. In 1935, cane toads arrived in Australia, brought from South and Central America to gobble up the beetles plaguing Queensland’s sugar cane fields. But these toxic toads poisoned and devastated a number of species, including the curious-looking and carnivorous marsupial known as the northern quoll. By 2003, the Australian government moved an insurance population of quolls to offshore islands free of cane toads. In 2015, after successfully training some of these house cat–sized animals to avoid the taste of cane toads, researchers reintroduced quolls to a national park on the mainland. But the island sanctuaries, also free of quoll predators like the dingo, became another kind of undoing: The trained quolls passed over eating cane toads, yes, but suddenly they became easy dinner for dingoes, who wiped out most of the reintroduced animals. In just over a decade without predators, quolls became naive to creatures they had spent 3,500 years evolving to escape.

Advances in biotechnology, from unlocking a creature’s genetic code to reprogramming the trajectory of its cells and editing its genes, are opening up new possibilities for conservation biology.

On the other side of the Pacific Ocean, hunting and pollution from DDT, among other factors, led California sea lion populations to plummet in the mid-20th century. With the help of strong legal protections passed in 1972, the population of these marine mammals has skyrocketed, heralding a successful recovery. So successful, in fact, that sea lions have become a pest in the efforts to preserve imperiled salmon and steelhead, long-dwindling fish species pinched by dammed rivers and shrinking habitat. Since 2008, sea lions voraciously dining on endangered fish near the Bonneville Dam, at the border of Oregon and Washington, have been targeted for lethal removal by the government. Nature is a tangled web of relationships, and the sea lions serve as a fable for human triumph in preserving one species while failing to save others intricately connected to it.

Ben Novak, the lead scientist working to rekindle the spirit of the passenger pigeon, helped me begin to understand some of the complexities of extinction. Since he was a teenager in North Dakota, Novak has been enamored with these hypersocial birds, legendary for blackening the skies over eastern and midwestern North America with flocks of more than a billion in the 1800s.

“De-extinction was never about creating replicas of extinct species. We can’t,” Novak says. Instead, he explains, it is about creating something that looks and acts like an extinct species, an imitation that can fill an ecological hole caused by extinction.

Novak works for the nonprofit Revive & Restore, which is exploring de-extinction for the passenger pigeon, heath hen, and woolly mammoth. But that “reviving” work is only part of his organization’s mission; the majority of its work focuses on restoring threatened species that haven’t yet gone extinct. Unifying this work, as Tom Maloney, the nonprofit’s former conservation science director, tells me, is the drive to explore and develop potential “genomic and biotech tools to address some conservation challenges today.”

Years of human-caused problems, including overhunting, habitat loss, and introduced diseases, have fractured and shrunk many wildlife populations. Smaller, scattered groups can become genetically isolated and inbred. On top of potential impacts like infertility, low genetic diversity means fewer options for species to adapt to changing environments.

Imagine a species’ entire population as a series of interconnected ponds. Individuals — and their genes — can flow between ponds when they overcome various barriers, such as geography. The more individuals, the larger the ponds. The more genes, the more options for life to find ways to thrive. A fairly successful yet underused approach to fixing the problems in a species with small, disconnected “ponds,” or populations, involves bringing new animals — and by association, their new genes — from one pond to another to boost its growth, a technique known as “genetic rescue.” This becomes more challenging when a species is reduced to a single pond.

As Maloney explains, Revive & Restore wants to evaluate today’s biotechnology tools — such as genome sequencing and genetic engineering — and their potential for taking genetic rescue to the next level. Sequencing a black-footed ferret genome reveals the complete DNA package of that species and can help decipher things like where genes responsible for certain traits are located, what those genes affect, and how much genetic variation exists for a trait. These insights — knowing which genes lead to a drop in ferret fertility, for example — could hypothetically guide wildlife managers to introduce ferrets with certain genetic profiles from one population to another.

The Black-Footed Ferret’s Disappearing Act

The next step could mean moving from genetic insights to an intervention like genetic engineering for black-footed ferrets, an exploratory effort with which Novak is also deeply involved. While that move may sound desperate compared to more traditional conservation measures, the prospects for these raccoon-masked relatives of the common ferret have been desperate for a long time.

With swift, serpentine bodies and keen, bewhiskered noses, black-footed ferrets are built to hunt prairie dogs. They live in the sprawling burrows of, and feast almost exclusively on, these rodents, a quirk of evolution that served this member of the weasel family well until Europeans began ranching and farming the North American Great Plains. European Americans brought habitat destruction, poison, and, via a ship from Asia, the non-native sylvatic plague to the American West, decimating both prairie dogs and their once-top predator.

Twice in the 20th century, black-footed ferrets, whose habit of popping their heads out of burrows lends them an inquisitive air, were presumed extinct. Then, in 1981, after a ranch dog named Shep brought home a dead ferret, biologists sought out and found a pocket of these ferrets alive near a small Wyoming town. With plague and canine distemper virus threatening to wipe out the newly rediscovered species, researchers gathered the remaining ferrets into captivity. Eighteen survived, but some were closely related, which meant that, genetically speaking, the entire species appeared to have been reduced to seven individual animals.

“That’s how we got to be in such poor genetic shape,” says Travis Livieri, a wildlife biologist who has worked with these ferrets since 1995. “Which is kind of where Revive & Restore comes in.”

While a captive breeding and reintroduction program has boosted the population of black-footed ferrets up to about 650 animals today, roughly split between captivity and the wild, they have shown signs of fertility issues, and all ferrets require immunization against plague.

“Giving a vaccination and a booster shot to every single ferret that’s born in the wild is not a sustainable plan,” Maloney says.

Still, two black-footed ferrets who died in the 1980s — but whose genes aren’t represented in today’s population — persist in the San Diego Zoo’s Frozen Zoo. Here, cells from each animal live on in vials, frozen to around -321 degrees Fahrenheit in shining vats of liquid nitrogen. In 2014, Revive & Restore sequenced their genomes as well as those of two modern black-footed ferrets, one of which was sired in 2010 using frozen sperm taken from a wild ferret from the 1980s. The results offered hope that researchers can turn frozen ferret DNA into a genetic booster shot for today’s populations.

While the black-footed ferret’s population “pond” has grown in size, much of its genetic diversity was lost when the waters shriveled in the 1900s. Like a pond with low levels of oxygen in its waters, life isn’t impossible for the ferrets, but it is more challenging. Ferret managers want to stir up those proverbial waters and add more oxygen.

Along these lines, in 2018, Revive & Restore acquired an endangered species recovery permit for its pilot experiments to evaluate genomic options that might boost the ferret’s genetic diversity and solve its ongoing plague problem. Currently in the petri dish phase, the team is attempting to clone the cells of a modern domestic ferret and a black-footed ferret that isn’t genetically unique, key steps before making attempts with the precious three-decades-old frozen cells.

Another challenge is getting the ferrets’ immune response from the plague vaccine — their antibodies — to become a trait that wild parents can pass to their young. The research team is starting in lab mice to test delivering the plague antibody’s DNA instructions, which usually appear in immune cells, into fertilized eggs using a virus. The aim is for the offspring of those mice to inherit that immunity. Pending these results, Revive & Restore would seek another federal permit, and welcome public input, before cloning or genetically engineering a living, breathing black-footed ferret.

“It sounds really like high-tech science fiction,” says Revive & Restore’s Bridget Baumgartner, who is working in the lab on the black-footed ferret effort. But the transgenic animals would produce the same antibodies as vaccinated animals. “We’re just skipping the vaccination step.”

Conservation biology experts are fascinated at the possibility of genetically altering ferrets to innately resist plague. Sarah Fitzpatrick, an assistant professor at Michigan State University who researches conservation genetics at its Kellogg Biological Station, thinks Revive & Restore’s immunity effort “could be a great example of when genetic engineering has realistic potential to help conserve a species.” She was less optimistic, however, about the nonprofit’s long-term prospects for rejuvenating ferret diversity, expressing several reservations. For starters, ferrets have a quick generation time and could undergo a lot of adaptation to their particular environments in just a few decades. Introducing genes from animals that lived in the 1980s — who are missing those adaptations — might actually set back a population living in a 21st-century environment. In addition, something called “genomic swamping” can occur when a small, inbred population quickly becomes overwhelmed by a very successful but limited boost in genetic variation. Soon, almost everyone in that population may become related to the newcomers, actually speeding up inbreeding.

Livieri, who has consulted with the team at Revive & Restore, welcomes its pioneering approach. “Plague and genetic diversity are huge challenges. That’s not something that is just going to magically go away over time,” Livieri says.

Still, black-footed ferrets have come far. Livieri recalls his last encounter, in October 2000, with one of the first wild-born ferrets, post-reintroduction. Her young had dispersed, and he knew this old female’s time was limited. “I just sat down on the burrow next to her,” he says, “and I’m sure she didn’t want to hear it, but I thanked her. She was one of the things that gave us hope.”

The Tightrope Walk of the Northern White Rhino

While the black-footed ferret peered into the abyss of extinction and tiptoed back, the more-than-two-ton northern white rhino is currently executing more of a tightrope walk. Just two females of this rhino subspecies remain, and due to frailty in one and a reproductive disorder in the other, neither are able to reproduce, even if they had a mate. Poaching for rhino horn and civil wars in the Democratic Republic of the Congo and nearby Sudan have driven the northern white extinct in the wild. Many refer to this walking-dead state as “functional extinction,” but Novak disagrees.

The living females “cannot by themselves create a new generation, but there are 12 cell lines frozen at the San Diego Frozen Zoo, which could become new individuals” even after the last two animals die, he says. He considers the species evolutionarily frozen in time. This rhino’s “pond” may have shrunk to a puddle, but its edges are frozen, not dry. The species’ future, not yet evaporated, is locked in ice.

A global collaboration borne in San Diego is trying to thaw this powerful and prehistoric-looking animal’s future back into a form most would recognize as rhinoceros. This rhino’s second chance arose from a casual conversation between two scientists who are friends: Oliver Ryder, head of the San Diego Zoo’s Frozen Zoo, and Jeanne Loring, a professor emeritus at Scripps Research and founder of Aspen Neuroscience, who is an avowed lover of zoos (“The one thing I wanted to do when I was a kid was to get locked into the zoo overnight,” she says). Around 2008 and freshly arrived at Scripps, Loring wanted her human stem cell lab to celebrate receiving a major grant and turned to Ryder to inquire about a tour of the San Diego Zoo Safari Park. Her friend said he could arrange it — in exchange for teaching his zoo team about her lab’s stem cell work.

That conversation led to a side project between the San Diego Zoo Institute for Conservation Research and Loring’s lab, which by 2011 was reprogramming frozen cells from northern white rhino skin into flexible stem cells capable of becoming any other cell type. The egg and sperm cells cultivate the most interest, and the goal is to create and unite them. To date, however, scientists have achieved this feat only in mice, so numerous challenges separate stem cells from baby rhinos.

Today, the San Diego Zoo has built a specialty laboratory for this work, after Loring’s team trained the zoo’s scientists. According to geneticist Marisa Korody, who works in the lab, they have reprogrammed nine of the 12 northern white rhino cell lines into stem cells from the Frozen Zoo. Much of the recent work has been “identifying and optimizing and applying the human technology to the rhinos,” says Korody.

But even creating a northern white rhino embryo in a petri dish wouldn’t be enough. That baby needs a womb in which to spend the next 16 months before birth. I meet the southern white rhinos with those wombs at the San Diego Zoo Safari Park on a sunny afternoon. These six large ladies, potential surrogate mothers, seem feisty, snorting and throwing around heft and horn over the hay in their muddy enclosure, though Loring describes them as “adorable” and “easily trained.” Two of them, Amani and Victoria, are pregnant, artificially inseminated via another southern white from an adjacent pen. I later learned that Victoria gave birth to a healthy southern white calf this past July.

The zoo is developing these and other advanced reproductive science techniques, including training the massive mothers-to-be to amble up for rectal ultrasounds, in anticipation of one day implanting a northern white rhino embryo into their southern white rhino wombs. Figuring out how to implant rhino embryos is also on the team’s to-do list, a task that has taken on new urgency. This September another international team announced it has harvested fertilized eggs from the last two northern whites using frozen sperm from deceased rhino fathers. That team, under the banner of the BioRescue project, successfully created two embryos, currently frozen, and plans to transfer them to surrogate southern white mothers in Kenya and the Czech Republic. Avantea, the Italian biotech firm that produced the precious embryos, said they “are confident” their team can produce another 12 to 15 in the next three years, and the San Diego Zoo confirmed ongoing discussions about their six southern white rhinos potentially becoming mothers for future embryos. But after their births, would these implanted northern white rhino babies someday face a similar fate as the genetically bottlenecked black-footed ferrets, whose metaphorical pond is larger but low on oxygen?

“We have as much genetic diversity in those cell lines as there is in the southern white population now,” Barbara Durrant, a reproductive physiologist with the zoo, says of the northern whites. Southern whites also nearly disappeared, but thanks to measures protecting and managing the population in private game reserves and conservation areas, they rebounded from fewer than 100 animals around the year 1900 to around 20,000 today. Developing these advanced reproductive technologies, the team says, can help other endangered rhinos.

Should the last northern whites die before a test-tube baby is born raises the question of whether a resurgence would count as de-extinction. Novak says no, because he doesn’t think they qualify as truly extinct in the first place. With living cells, and now even living embryos, in the freezer, the genetic line would remain unbroken for this species, just temporarily on ice. But resurrection? Maybe.

Ethicist Greg Kaebnick agrees it would be a continuation of the same species, requiring plenty of human intervention, but not a wholly human-fabricated imitation.

The latter is the realm of the passenger pigeon.

The Passenger Pigeon, Biological Storms, and Gene-Editing

My sister’s family and I shuffle through Martha’s memorial at the Cincinnati Zoo. The pagoda is lovely, its wide, wooden doors carved with birds and its rafters ornamented with origami pigeons. Model passenger pigeons tend a stillborn nest, their red, glassy eyes oblivious to the newspaper reproductions that hang behind them, lamenting their extinction. Placards detail their journey from massive migratory flocks, total population of perhaps 5 billion to zero in a few decades. Humans hunted the birds out of existence for food and sport. The telegraph, 19th-century social media, revealed their colonies’ real-time locations to industrious hunters who felled their oak and beech homes and stole or crushed their nests. Railroads, newly connecting the nation, hauled away the hoards of slate-blue bodies with russet breasts to far-off cities.

Elegized by American conservationist Aldo Leopold in 1947 as “a biological storm,” the pigeons reshaped the continent’s forests, as their colonies broke open canopies like lightning and fertilized soils with excrement and corpses. This is the ecological hole Novak is seeking to fill. With no passenger pigeon cells alive anywhere, he is turning to their closest living relative, the band-tailed pigeon, aiming to edit its genome to display critical passenger pigeon traits, such as tail shape and social behavior. (Those traits eventually will be gleaned from at least four genomes sequenced from museum specimens of passenger pigeons.) Similar efforts are underway to edit the genome of cattle breeds, transferring the natural trait of one to another.

“What we’re doing with a passenger pigeon is essentially the same thing,” Novak says. “We’re moving in several genes and creating a genome that ultimately has the majority parentage of one species and a small contribution of another.”

A precise hybrid, he calls it, made possible by the blockbuster gene-editing technique known as CRISPR (clustered regularly interspaced short palindromic repeats), has enabled scientists to precisely shape an organism’s genetic makeup with unprecedented ease. At the moment, however, Novak’s ambitions remain only a remote possibility. For starters, no one knows which genes made a passenger pigeon unique, and most bird research involves chickens, a poor model for pigeons and wild birds.

Novak’s Ph.D. research with Monash University in Australia focuses on developing animal husbandry and genetic engineering protocols to make the common pigeon a better proverbial lab rat for genomics research. While the passenger pigeon’s “pond” dried up when Martha died more than a century ago, Novak essentially wants to create a new, very similar pond, drawing water from the healthy pools of band-tailed pigeons. But developing the tools to pour new life into a desiccated species is one challenge, and deciding how — and whether — to use that power is another.

***

Editing an animal’s genome gives many biologists pause. Fitzpatrick considers Revive & Restore’s gene-editing efforts “extremely intriguing,” but says she does “not think they represent the most effective or realistic ways that genomic tools can be used to conserve species.” One reason, she says, is that some traits, such as behaviors, can have complex genetic foundations, drawing from multiple genes sprinkled across the genome. That presents challenges for both identifying and targeting the right complement of genes to recreate, say, a hypersocial pigeon.

Doing nothing is morally difficult for humans, especially when we are responsible for the troubles in the first place.

Shapiro, who advised Novak’s master’s research in her University of California–Santa Cruz lab, wonders whether, if successful, de-extinction is even the right thing for the ecosystem. Should Revive & Restore eventually genetically edit band-tailed pigeons to look and act more like shadow passenger pigeons, they likely would be more biological drizzle than storm. By most estimations, reintroducing shadow passenger pigeons into the wild would only achieve a fraction of their former ecological power.

Still, Shapiro, who sits on Revive & Restore’s board of directors, wholeheartedly supports its version of genetic rescue for endangered species like the black-footed ferret and thinks the nonprofit is proceeding responsibly. Yet, she worries, with good reason, “that everybody is going to be so scared that we don’t have all the information, that they’re never going to take a risk.” Instead, she thinks we should work to better understand these technologies, adding them to our conservation toolkit alongside more traditional measures like protecting land.

***

Inside the San Diego Zoo, just past the elephants, a sign reads, WE DON’T HAVE TO BE THE CAUSE OF EXTINCTIONS. Yet, unless we act, some of those extinctions are inevitable.

So: to genetically modify or not?

That tension runs through these projects, often prompting comments from critics about how researchers are “playing God” or interfering “too much” with the natural world. Yet doing nothing is morally difficult for humans, especially when we are responsible for the troubles in the first place. How do we balance the urge to intervene, to save, to revive, against a revulsion for over-humanizing nature, in an already humanized world?

Changing genomes doesn’t especially bother Kaebnick. The ethicist recognizes the excitement and spectacle around these technologies, but for him, the story behind human interactions with nature matters more than concerns about “playing God.” “To talk about something as ‘natural’ is to say something about how it got to be the way it is, why it is the way it is, or why it’s there at all,” he says. “There’s a place for humans in the story without it completely undermining naturalness.”

And as Livieri points out, coming up with the tools for recovering wildlife, whether gene editing or habitat protection, isn’t the hardest part. It’s engaging people with the natural world. “If we don’t have the political and social will to do it, all the tools in the world won’t mean a darn thing,” he says.

One wall inside Martha’s pagoda touts the Cincinnati Zoo’s efforts to save threatened species, including the cheetah, an iconic animal that requires large swaths of well-protected land to survive. My five-year-old niece, looking crushed, whimpers to my sister, who hugs and tries to reassure her daughter. Cheetahs are my niece’s favorite animal, and she doesn’t want them to disappear.

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Ashley Braun is a science and environmental journalist based in Seattle, Washington. In addition to her work as a fact-checker and editor, she has written for The Atlantic, Slate, Scientific American, Science, Discover, and Hakai Magazine.

Editor: Katie Kosma
Fact-Checker: Sam Schuyler
Copyeditor: Jacob Z. Gross