Vaquita Genome Offers Hope for Species’ Survival

Late on a fall evening in 2017, Phillip Morin, a marine mammal geneticist at the National Oceanic and Atmospheric Administration (NOAA) Southwest Fisheries Science Center, pulled off the San Diego freeway into a dimly lit parking lot. As he turned off the ignition, a figure stepped out of the shadows. He handed her an unassuming cooler box, completing a crucial handover—the final step in a sequence of events that was triggered by a tragic death in Mexico only 24 hours prior.

In Mexico’s Gulf of California, a vaquita, one of an estimated 30 remaining at the time, had died during a last-ditch effort to save the species—the most critically endangered marine mammal in the world. With persistent illegal fishing taking its toll on the surviving population, conservationists had no option but to try to bring as many of the remaining animals as possible into captivity close to their sole habitat in the upper reaches of the gulf. A floating sea pen, purpose-built to provide a safe haven for vaquita, was stationed in the shallow waters off the coast. The first animal, a juvenile female, showed signs of stress upon capture and was released back into the wild. The second, an adult female, calmly investigated her new surroundings, but later became stressed and, despite valiant efforts by veterinarians and cetacean care experts, suffered cardiac failure.

“It ripped your heart out,” says Barbara Taylor, marine mammal conservation geneticist at the Southwest Fisheries Science Center. The loss of the adult female signaled the end of the captivity program—the risk of losing another vaquita was too great. But she did not die in vain.

The grief-stricken team performed a necropsy through the night and collected tissue samples, packing them securely in a cooler box. As the morning light spread over the Mexican coastal town of San Felipe, a van carrying the live vaquita cells sped through the desert toward the U.S. border.

Now, an international team of researchers, in collaboration with the Vertebrate Genomes Project, has used her living cells to generate the most complete high-quality genome sequence of any dolphin, porpoise or whale. The genomic analysis, published in Molecular Ecology Resources in October, reignites hope for the fast-disappearing species. It confirms that the small remaining population is genetically healthy and can still recover if authorities enforce existing conservation measures.

At four feet long, vaquitas are the smallest cetaceans in the world. The dark bold markings around their eyes and mouth lend them a joviality that belies the severity of their plight. A resurgence in gillnet fishing—walls of netting suspended in the water column that indiscriminately kill the marine mammals as bycatch—has taken out half of the population annually in recent years. The latest estimate, based on acoustic and photographic monitoring, suggested that fewer than 19 animals remained in the fall of 2018, down from around 600 in the 1980s.

Despite the Mexican government’s temporary ban on gillnets in 2015, which was made permanent in 2017, use has rocketed due to illegal fishing for totoaba, a fish about the same size as the vaquita. The totoaba’s spawning ground overlaps with the vaquita’s only habitat. Poachers prey on the fish for their swim bladders, which are smuggled by organized criminal syndicates to China. Investigations by Earth League International found totoaba swim bladder retailing at $46 per gram on the Chinese market in 2018—higher than the price of gold.

The captivity plan aimed to hone captive breeding efforts by using tiny biopsies of skin from live animals to sequence the species’ genome. Following the 2017 fatality, the fresh tissue samples from multiple organs would generate a ‘reference quality’ genome—a platinum-standard record of the vaquita’s full set of chromosomes. “We had a one-time opportunity to generate the reference genome of the vaquita to understand its evolutionary and population history and to use that information to plan optimal conservation action,” says Morin, lead author of the study.

Getting the tissues to a laboratory quickly was critical, as reference genome assembly requires living cells. The team had planned ahead: protocols and permits were in place to expedite the samples through the desert, across the border and into the hands of Morin at the Southwest Fisheries Science Center. He then arranged an after-hours transfer to the San Diego Frozen Zoo—a storage facility affiliated with the world-famous San Diego Zoo for the genetic material of rare, threatened and endangered species—where the cells were cultured to maintain viability.

Scientists have known for years that the vaquita has very low genetic diversity, provoking erroneous claims that the species is doomed to extinction through such processes as inbreeding depression—expression of harmful versions of genes in small populations through inbreeding. Such claims have enabled indifferent policy makers to absolve themselves of the responsibility to take conservation action.

The new study confirms that vaquita have thrived in low numbers for hundreds of thousands of years and the species’ low genetic diversity does not condemn it to extinction.

Reconstruction of the vaquita population history revealed that the species’ isolated habitat in the upper Gulf of California has sustained a population of roughly 5,000 for more than 250,000 years. Surviving in such low numbers for a long period has given the vaquita time to weed out harmful mutations and reach genetic stability, whereby individuals are robust and well adapted to their environment, according to the study.

“The genome allowed us to understand why [vaquita] have low diversity, and how that may actually be a good thing for surviving the current crisis if we can protect the remaining individuals and give the species a chance to recover naturally,” says Morin.

Consistent sightings of healthy, vigorous vaquitas in the field confirm that the population does not suffer health issues that might indicate inbreeding depression. In recent years, scientists have observed vaquita mothers with calves, including one female with different calves in 2017 and 2018—the first evidence of annual breeding. “I have witnessed with my own eyes that vaquitas are breeding as fast as they can; the calves are fat and healthy,” says Taylor, co-author of the genome study. “The only dead animals that you see are in nets.”

Taylor says that the new evidence is proof that genetic factors cannot be used as an excuse to stop taking conservation action. “People need to know when their inaction to reduce human-caused mortality is the solid reason for driving a species extinct.”

Chris Kyriazis, a doctoral candidate at UCLA who was not involved in the study, is using the vaquita’s genomic information in computer simulation models to reveal whether the population can recover from its current plunge. “By controlling variables in the models according to what is known about vaquita biology and genetics, we can study how effective different policy decisions will be,” he says. His models show that elimination of gillnet fishing would lead to a healthy recovery.

But the odds are stacked against recovery. Eradication of illegal gillnets, even within the small area designated as a vaquita refuge, is difficult to achieve. During the 2018 season alone, efforts by the Mexican government, WWF-Mexico and marine conservation organizations removed 400 gillnets from vaquita habitat. Marine conservation group Sea Shepherd recently resumed its campaign alongside Mexican authorities and the local community, suspended due to Covid-19 earlier this year, to remove the illegal gillnets. “The fight to save a species must continue, even during these challenging times,” said Jacqueline Le Duc, captain of Sea Shepherd’s vessel Sharpie, in a statement.

The next few months are critical. The totoaba spawning season, which triggers the onslaught of illegal gillnet fishing, begins in November and runs through to May. Evidence from around the world suggests that Covid-19 has spurred illegal poaching as poverty-stricken communities struggle to get by.

Protecting the few surviving vaquita through the retrieval of illegal gillnets, collective global action to halt illegal fishing and trade and encouraging fishing communities in the upper Gulf of California to move away from gillnets towards sustainable fishing practices are now critical priorities, according to the World Wildlife Fund. However, in a region plagued by organized crime and the undercurrent of corruption that accompanies it, initiatives aimed at improving governance and transitioning communities to alternative fishing gear often have little impact.

Fishing is the most important economic activity in the upper gulf. Regulation of fishing activity so that it is legal and not harmful to vaquita is of utmost importance to both vaquita and the communities that depend on the ocean for their livelihoods. Yet the relevant authorities have been “largely absent” in implementing regulations and rolling out alternative gear to enable legal fishing, according to a 2017 UNESCO-IUCN monitoring mission. Neither have they taken convincing action to prosecute illegal fishermen, nor criminal syndicates linked to the totoaba trade. In a further blow to fishermen, the compensation program for not fishing has now been cancelled, according to the IUCN Species Survival Commission, Cetacean Specialist Group. Such inaction by Mexican authorities has led to the resumption of unauthorized fishing with gillnets in recent years and has stoked an atmosphere of desperate uncertainty in the region.

Earlier this year, in an effort to precipitate committed action from Mexican authorities the U.S. National Marine Fisheries Service announced an embargo on seafood caught in the northern Gulf of California. With fishermen hard hit by a lack of access to important U.S. markets, Mexican authorities are under pressure to comply with international standards by stepping up enforcement of gillnet bans and accelerating the development of alternative, vaquita-friendly fishing gear.

Lorenzo Rojas-Bracho of Mexico’s National Commission of Natural Protected Areas and chair of the International Committee for the Recovery of the Vaquita knows the struggle well. He has worked on saving the vaquita for more than 20 years. “Everybody has to be on the same page; it involves major social and cultural changes and it involves political will,” he says.

Nonetheless, he remains optimistic. “Recently, some fishermen have been able to catch more using the alternative gear than they did with traditional gillnets,” he says. “So that means it can work.”

For geneticist Taylor, the objective is clear. “The recovery of the vaquita depends on fishermen being able to make a living without killing vaquitas,” she says. “Now is a pivotal time to push for changes.”