Don’t blame genetics if we lose the world’s rarest marine mammal

Scientists were ready to try almost anything in 2017 to save the vaquita, one of the world’s rarest animals. The species’ numbers had plummeted from 600 individuals down to just 30 over the last two decades, mostly because so many vaquitas had suffocated in gillnets — large wall-like fishing nets designed to snag in the gills of fish — in the northern Gulf of California in Mexico.

“It was completely out of control. And it was clear that there was no [fishing] enforcement going on. So the situation became really desperate really fast,” says Barbara Taylor, a senior biologist at the National Oceanic and Atmospheric Administration who has been working with vaquitas for over 30 years.

Despite their worries about how individual vaquitas might respond to captivity, Taylor and her collaborators decided to initiate a captive breeding program, hoping to grow the population under protected conditions. It didn’t work. The first vaquita they captured panicked and had to be released very quickly. The second was an older female that seemed fine at first, but suddenly died of a shock-induced heart attack before the scientists could release her. Devastated by the loss of a breeding female, the team immediately ended the program. Taylor says they don’t intend to try again, even though the vaquita population has since dwindled to fewer than 10.

But there is a silver lining. Despite her passing three years ago, this female is still contributing to the preservation of her species. Researchers recently used a complete genome sequenced from live cultures of her cells to demonstrate that the vaquita is not genetically destined for extinction.

The finding gives researchers a stronger platform to call for increased regulations. In the past, critics of tougher fishing regulations have asserted that conservation efforts are pointless because the vaquita is a hopeless case. But the new genetic data has shown researchers that this simply is not true.

“It gives us a lot more hope that the species could recover on its own,” says Phillip Morin, a population genetics and genomics researcher at NOAA and lead author of the study that analyzed the vaquita’s genome.

Usually, when populations dwindle to nearly zero, a rare species enters an “extinction spiral,” in which inbreeding leads to a lethal proliferation of genetic mutations that lower reproductive success and hasten early death — and ultimately extinction, explains Morin.

Debilitating mutations have historically plagued isolated animal populations such as the wolves of Isle Royale, Michigan, and panthers in the swamps of South Florida. But that’s not happening with the vaquita. “The vaquita is not doomed because of genetic factors,” Morin says. “The data indicates that the vaquita has survived this long, for 250,000 years at this low level of genetic diversity. It will survive just fine if we stop killing them.”

Vaquitas are under extreme pressure due to a booming and illegal net-fishing industry in the Gulf of California. Fishermen in the area leave large gillnets to catch the also-endangered totoaba, a large fish prized in China for the purported medicinal properties of its swim bladders, which can fetch a hefty price on the black market. At about five feet long and around 100 pounds, vaquitas are similar in size to the totoaba, and they often get caught in nets and drown if they cannot free themselves and swim to the surface to breathe.

Despite strong evidence that it is devastating the vaquita population, the totoaba fishing industry keeps growing. According to Lorenzo Rojas-Bracho, the head of marine mammal conservation and research for Mexico’s National Institute of Ecology and Climate Change, fishermen have been dropping increasing numbers of gillnets into the Gulf in hopes of catching enough totoaba during its five-month spawning season to support themselves and their families for the year.

Poverty in the region is the root of the problem. “The social system [involves] illegal harvest of multiple endangered species, an international trade, high-dollar product and, for local fishermen, lack of alternative livelihoods,” says Matthew Leslie, a conservation biologist at Swarthmore College. “[The fishermen] have this opportunity to exploit this resource to gain some sort of toehold in an area that otherwise doesn’t offer much of a toehold.”

Amid such a grim situation for the vaquita, the conclusions of Morin’s genetics study offer a glimmer of encouragement.

Morin and his colleagues are certain that inbreeding is occurring among the few surviving vaquitas. But inbreeding itself isn’t actually the problem in small populations. The problem is what scientists call “inbreeding depression” — the increased chance that individuals will inherit harmful mutations in very small populations, triggering an extinction spiral. Many of these harmful, or deleterious, genetic variations are only passed on when an individual inherits one copy, or allele, of the mutated gene from its mother and one from its father — something that is much more likely to happen if there is substantial inbreeding, but not guaranteed.

And it’s not happening with the vaquita. The secret of the vaquita’s immunity to inbreeding depression, oddly enough, may come from its historically small population. By analyzing the genetic variation found in the modern vaquita genome, researchers were able to estimate that even as long as 250,000 years ago, there were only a few thousand vaquitas in the wild.

“In a population like the vaquita that’s been small for a long time, it had hundreds of thousands of years for the gene pool to purge those deleterious alleles. There’s less of that mutational load,” said Morin.

He explains that the reduction of this mutational load — the number of detrimental genes in a population — was a long-term effect of natural selection. Negative genes showed up quickly and made the animals carrying them less likely to reproduce. When they died, the deleterious alleles died with them, and there simply weren’t many detrimental genes left in the species by the time humans entered the picture.

Now that humans have become part of the vaquita’s story, conservationists are focusing on how to revive the critically endangered species.

Armed with new proof of the vaquita’s continued genetic viability, researchers and conservationists continue to lobby the Mexican government to step up enforcement of bans on the gillnets that endanger them.

“It’s a really important story to say that you don’t need to worry about genetics,” says NOAA’s Taylor. “We did make this argument back in 1997, but it carries a lot more weight when you bring modern methods to bear, and you can say it with more authority, because it’s more data-based and less inference-based.”

International conservation groups and the Mexican government have lately been stepping up their efforts to remove illegal fishing equipment that harms vaquitas. The efforts are being spearheaded by Rojas-Bracho.

The regulation efforts have spurred some pushback, including an attack on a warehouse in Mexico in 2018 described by Rojas-Bracho, during which he said fishermen stole illegal fishing supplies and burned trucks and boats used to monitor the vaquita habitat. In another incident in December 2020, multiple fishing boats attacked two research vessels in Mexico’s vaquita refuge as they attempted to remove gillnets.

The government is specifically getting more serious about enforcing its gillnet ban, according to Rojas-Bracho. Mexican police have also arrested some of the principal leaders behind the illegal fishing, including some with links to organized crime. “I’m always thinking something is going to work. And I’ve been waiting for many decades,” Rojas-Bracho says. But the new data has started to renew his hope. “We know they could recover. And that’s the best news so far.”

No matter what obstacles stand in the way, scientists aren’t giving up on the vaquita. They take heart in small, positive signs like seeing mothers with calves during the last population survey in 2019, even though Rojas-Bracho says they still identified less than 10 individuals. They may be up against slow-moving governments, illegal industries and organized crime, but they at least have genetics on their side.

For those who really care about the vaquita, it’s a place to start.