Frances Gulland directed her gray Toyota Tundra north and hit the gas. She had more than four hours of driving ahead of her and the rosey flesh carefully stashed in her cooler was already more than twenty-four hours old.

It was early in the morning of November 5, 2017. Her truck and its pop-up camper were already dusty from driving around the desert beach town of San Felipe, on Baja’s Gulf of California. She was headed first to Tijuana, then to San Diego, where a fellow scientist named Phillip Morin would meet her.

Around 3:00 am the previous day, Gulland, a veterinarian and commissioner at the Marine Mammal Commission, gathered as part of a team of nineteen scientists from nine countries to launch a last-ditch effort to protect the world’s smallest porpoise from extinction. They knew the project was risky but were running out of options––the vaquita porpoise is the most endangered cetacean on planet Earth. Only around ten animals are known to be alive. Their demise is mostly due to a fishing technique that uses vertically hanging nets called gillnets, which trap the mammals beneath the ocean’s surface, where they drown.

Gulland’s colleague, Lorenzo Rojas-Bracho, head of marine mammals research at the Comisión Nacional de Áreas Naturales Protegidas in Ensenada, has been studying the genetic diversity of vaquita porpoises in the upper Gulf of California since the early 1990s as part of his master’s thesis, when he first documented extremely low genetic diversity among the population.

Nearly thirty years later, Rojas-Bracho was aboard an inflatable rubber boat in the far northern stretch of the Sea of Cortez, slightly south of the brackish Colorado River Delta. Gulland was in another capture boat, both researchers were waiting for intel from the expedition’s main vessel.

Beneath the white canopy of mission control, Barbara Taylor, a senior scientist in the Marine Mammal and Turtle Division at National Oceanic and Atmospheric Administration, stood behind a pair of oversized binoculars––big enough to have one person at each eyepiece––held upright by a steel support. From the boat, she aimed them at the turquoise waters, scanning for a distinct blot of charcoal gray. It was the team’s second attempt at capturing a vaquita porpoise and relocating it to captivity, where it would be safe from gillnets and, with any luck, extinction.

Rojas-Bracho recalled what Morin, a population genetics and genomics researcher in NOAA’s Marine Mammal Genetics Group, had said to him when he first ran the idea past him: “Lorenzo, if you don’t try it, you will regret it for the rest of your life because that’s in your toolbox for conservation. If it dies, at least you will have tried, and you will have fresh tissues that we can use for genetics. If the vaquita goes extinct at least there is some legacy.”

The second attempt was off to a good start. Taylor had spotted a female porpoise and the team of capture boats relocated her into an awaiting sea pen––two black inner tubes that floated on the sea, holding netting invisible beneath the surface. In the center was a floating animal hospital. A porpoise expert from the Netherlands, who was an advisor on the expedition, said that the relocated female porpoise had seemed calm. But suddenly, she started swimming in erratic patterns around the pen, darting from one rounded edge to another. She was panicking. Her heart raced and veterinarians spent six hours trying to save her after it was clear she couldn't return to the wild. But in the end, the team was forced to resort to their second best option for conservation: extracting the female porpoise’s untainted genetic material.

Time is of the essence once death approaches. The animal’s gut microbiome begins to deteriorate flesh from the inside out. Insects and fungi move in and perform their ecological duty as decomposers. The scientists had an opportunity to collect fresh samples from the deceased porpoise––one complete ovary and the entire thickness of her skin––immediately freeze them at -80 degrees Celsius and transport them to two of the leading animal genetic research laboratories in the world. Both stand just over the US-Mexico border.

“We were working in the dark with flashlights, making sure the application was ready,” says Rojas-Bracho.

They rushed the paperwork that would allow the samples to cross into the US to the right officials within hours of the porpoise’s passing. The passage would require CITES import and export authorization and marine mammal protection permits from the US Fish and Wildlife Service. To preserve time, every part of the paperwork needed to be errorless.

Gulland made it to Tijuana with the samples the following morning. Half of her precious cargo went to the NOAA Southwest Fisheries Science Center in La Jolla and the other half went with Morin to the San Diego Zoo. This way, there were two copies of the DNA in case something happened to one of the labs. They didn’t expect to get another chance to collect genetic material of this quality from a vaquita porpoise.

Morin, Rojas-Bracho, and Taylor are part of a community of scientists racing to archive the genomes of threatened and endangered species. Currently, less than one percent of the more than 13,500 species listed as threatened by the International Union for Conservation of Nature (IUCN) have a published genome. The small bank of information––which includes New Zealand's kakapos, the California condor, and Mexico’s vaquita porpoise––reveals important clues that can help deter their extinction.

Conservation biologists have been using genetics for decades, to decode the ways different populations of animals have adapted to things like climate change and pollutants, and to better understand how close a population is to extinction. But most of the work has been done using short fragments of DNA, which leaves holes in the information and requires an abundance of precious time to assemble.

“Without a reference genome, it’s like trying to put together a puzzle without knowing what it’s supposed to be,” says Ben Novak, lead scientist of Revive and Restore, a wildlife conservation organization that focuses on harnessing biotechnology. “But having a reference genome is like not only having the picture on the box, but the picture being the exact same size as the puzzle. It’s like a template you can put each piece on top of."

On their own, reference genomes can tell conservation biologists which populations of animals need genetic intervention and how the species reacted to past global climatic changes, like the Ice Ages and the shocking bouts of abrupt warming and cooling throughout the last glacial period.

But one reference genome can’t stand alone in most real world acts of conservation. Scientists need to compare the genes of multiple animals within a species to determine which populations are genetically unique from each other, which populations are mating with one another, and how to stop diseases that are catalysts for extinction.

“A single individual reference genome doesn't necessarily give you a great deal of the insights you need to do interesting work in conservation. The real bread and butter of making conservation better through genomics is having multiple animals and being able to quickly piece together information from that DNA using the reference genomes as a guide,” says Novak.

According to Gernot Segelbacher, co-chair of the IUCN Species Survival Commission’s Conservation Genetics Specialist Group, scientists can still get information about a species the old-school way––from a snippet of its DNA. However, besides making it easier to fit pieces of a genomic puzzle together, having the entire genome gives a clear picture of the demographic history of an animal that reaches back hundreds of generations. Remarkably, scientists can unravel the history of an entire population from the genome of just one individual.

“That opens a Pandora’s box. There’s a whole range of future possibilities,” says Segelbacher.

These possibilities include de-extinction.

In the nineteenth century, there were more passenger pigeons on Earth than any other bird species. Flocks numbered in the billions. They gathered on a new patch of New England forest every few weeks. Of the 350 known pigeon species, the passengers were the only ones to spend a hundred percent of their lives being social. Up to a thousand birds would wrap their red-orange talons around the branches of a single tree when a flock landed to rest or mate. They bred in colonies and roosted wing-to-wing, with multiple couples happily weaving their nests onto the same branch. The destructive nature of this socializing kept the forest healthy. Branches of hemlock, northern white cedar, sugar maple, and balsam poplar trees would bow and then snap under the weight of their visitors, poking a hole in the canopy that allowed sunlight to reach the forest floor. The creatures who preferred the dark moved to new ground, making room for those who preferred light. The light coaxed new generations of flora to germinate. Because of the birds, the forest was a habitat mosaic.

But in 1911, passenger pigeons abruptly went extinct after just a few decades of being used for target practice by European settlers. But Novak believes reference genomes can help patch this ecological tear.

Bioinformaticians have already assembled ninety percent of the passenger pigeon’s genome. They painstakingly compared snapshots of 120-year-old DNA from four passenger pigeons to a reference genome of the living band-tailed pigeon that served as a close, albeit imperfect, map.

To start on the next phase, Novak is working to recruit a team that can determine which fixed genes make up a passenger pigeon. The team will be looking for genes that are the same across all four specimens, potentially resulting in graduated tail feathers, a social disposition, and reaching nearly adult size a mere two weeks after birth––all traits unique to the passenger pigeon. If the genes differ, that will tell the team that those genes are likely responsible for variations, like the exact hue of a bird’s feathers, which are unique to that individual, but not characteristic to the entire species.

Put another way: “Eye color doesn’t make you a human, it makes you, you. But the fact that you have genes that ensure you have two eyes on your face that sit on either side of a front-facing nose, that’s something that makes you part of the human race,” explains Norvak.

Their goal isn’t to resurrect the long-extinct passenger pigeon. Instead, they want to fabricate an entirely new species that is as close as possible to the extinct species, and at the very least can play the same ecological role as the passenger pigeon once did. When the team identifies which genes make a passenger pigeon social, graduated-tailed, and fast-growing, in theory, they can create a hybrid using a close relative. Employing CRISPR technology, Novak’s future team will overwrite the genes of living band-tailed pigeons with genes that will, if all goes according to plan, restore a hyper-social pigeon population to the forests of New England.

“If there was any other hyper-social pigeon available in the world we could just relocate it. But we don’t have that so we have to go back to the original blueprint,” says Novak, adding that an exact replica would be the second-fastest way to their goal, but science hasn’t made that possible yet, at least for passenger pigeons.

It’s another story entirely for the recently-extinct. Scientists are very close to being able to use reference genomes for more pure de-extinction projects that chase a one-to-one replica of a species that no longer exists, but whose genetic code was carefully harvested and stored away.

On a Monday in 2018, Sudan, the world’s last male northern white rhino, laid in clay-colored dirt next to the caretakers and armed guards tasked with protecting him at the Kenyan sanctuary, where a stream of tourists visited him during the last years of his life. When Sudan’s lungs would no longer inflate and his heart went still, scientists immediately harvested DNA samples before the tissue began to decompose. They even collected the forty-five-year-old male’s sperm. The last two remaining female northern white rhinos won’t be enough to save the population, but they have supplied the female half of the DNA that every mammal requires. Due to the quick action following Sudan’s death, researchers have synthetically created twelve northern white rhino embryos. They predict a Southern white rhino mother, their closest living relative, will soon gestate and deliver a northern white rhino baby with the help of genetic conservation.

“They will definitely be successful,” says Novak.

Scientists are also using reference genomes to save species before they are fated to extinction.

In Australia, researchers are using the Tasmanian devil reference genome, which was published in 2012, to cure cancer. Since the mid-'90s, a communicable cancer has decimated eighty percent of wild Tasmanian devils. But some Tasmanian devils are resistant to the contagious cancer. Understanding which genetic variations enable this cancer resistance has directed breeding programs that are attempting to spread this resistance into the populations. The information the reference genome can provide about resistance to contagious cancer may also be the precipice for developing a vaccine against the disease. It’s “extremely complicated to do this with a partial genome,” says Segelbacher.

Still, he says, the most useful application of reference genomes is its ability to help scientists better understand the genetic history of a population. Looking back at genetic changes can give scientists clues about how a species has survived past threats, and how it might adapt to a post-climate-change planet.

“Having more information also helps you determine how long a current bottleneck has existed, which is something you can’t necessarily see with just pieces of the genome,” says Segelbacher.

A bottleneck occurs when a gene pool becomes so shallow that the species reaches the point of no return. It’s a critical point on the path to extinction, and by better understanding where a species is in this process, humans can calculate when to intervene in an attempt to undo the damage their roads, dams, fences, boats, and pesticides have caused. If a species is nearing a bottleneck, biologists can stage a genetic rescue, introducing new breeders into the population to flush the gene pool with new material.

However, this isn’t always necessary, and that’s just as important to understand.

When Morin got half of the vaquita samples back to a lab at the San Diego Zoo, they went to work.

There are a few types of whole genome sequencing machines, but at baseline, they all use the same general process. First, enzymes break down the sample’s cellular walls, freeing long strands of DNA trapped inside the nucleus and mitochondria. Then, the genetic material undergoes a sonic bath that breaks it up into pieces, revealing a stew of base pairs. These base pairs are reassembled into a kind of two-dimensional code that computers turn into a three-dimensional genomic map.

The vaquita porpoise genome is now one of the most complete logged so far. It has taken twenty years of piecing together partially degraded samples, mostly taken from corpses entangled in gillnets. But thanks to the genetic information extracted from the fresh samples collected in 2017, the genome is now 99.92 percent assembled, including twenty-one complete pairs of autosomes and the entire X chromosome. That leaves one unsequenced set of Y chromosomes, unavailable in a female genetic sample.

The result is more proof that what Rojas-Bracho suspected to be true in the ’90s was, indeed, happening: The vaquita porpoise reference genome showed that, against genetic logic, this community of tiny cetaceans has thrived with bottleneck-levels of genetic diversity for thousands of years. The populations of vaquitas that swam in the Gulf of California before gillnets were introduced are genetically the same as the few that remain today.

This means that the population of roughly ten individuals can create a viable, thriving population using just their slim gene pool. That’s partly because inbreeding actually phased out harmful mutations, leaving a genetically shallow but quite healthy population of porpoises.

“The research we have done with vaquita genetics is going to change how we look at conservation and view genetic variability. It shows us that many of the populations we were dooming to extinction aren’t as hard off as we thought,” says Rojas-Bracho.

Although genetic data has the power to turn sci-fi fantasies into conservation reality, Taylor, of NOAA, thinks it’s equally important to use the tool to improve conservation in a much simpler way: “The root of all conservation is changing human behavior,” she says.

A popular excuse made by those who are against gillnet restrictions off the coast of Baja is that due to the lack of genetic diversity in the remaining population of vaquita porpoises, the species isn’t viable anyway. But the reference genome has confirmed the opposite to be true.

“If you have this solid science that shows they would have a good chance of recovering from ten individuals if humans just stopped killing them, you take away the basis of that excuse,” says Taylor. ♦