SCUBA divers collect length-frequency and count data on Devils Hole pupfish within the Devils Hole aquifer in southern Nevada.

SCUBA divers collect length-frequency and count data on Devils Hole pupfish within the Devils Hole aquifer in southern Nevada.

Brett Seymour, USDI National Park Service

Bizarre desert-dwelling fish may have evolved just a couple hundred years ago

The middle of the Nevada desert seems an unlikely spot to find a fish. But an underground fissure in scorching-hot Death Valley is the only natural habitat for the endangered Devils Hole pupfish, a silvery blue creature about the size of a pet goldfish.

The water inside Devils Hole is consistently a toasty 32°C, hot enough to kill most other fish. For 2 months of the year, the cavern—which opens into a deep subterranean lake—receives no direct sunlight. And yet scientists believe a small population of pupfish has lived there for 10,000 to 20,000 years, hardy survivors from the days when Death Valley was a fertile oasis.

Now, evidence is growing that these fish might be far younger than previously assumed: A new study suggests that the Devils Hole pupfish actually colonized its watery cavern somewhere between 105 and 830 years ago, making scientists rethink how it got there in the first place.

“Our new estimate of the younger age in a way makes this species even more fascinating because it has so many of these unique traits relative to other pupfish,” says Christopher Martin, a biologist at the University of North Carolina, Chapel Hill, who led the study.

Pupfish first arrived in Death Valley during a wet period, probably when water joined the area to lakes or rivers elsewhere. But as the water dried up and the area turned to desert, the pupfish became isolated in a smattering of springs. Like Darwin’s finches, pupfish in different pools have evolved different traits and become distinct species over the years. They’ve mixed with each other only occasionally, when floods temporarily join isolated pools.

Devils Hole is especially isolated, and the pupfish population there is particularly small, ranging from 35 to 548 fish in the remote cavern since official recordkeeping began in the 1970s. Their survival has been heralded as an evolutionary anomaly, as such populations usually become severely inbred and die out. “All we know about conservation genetics suggests that these populations of very small size should not be able to survive in the long term,” Martin says.

But the long estimate for the Devils Hole pupfish’s survival (and by extension, that of their relatives throughout Death Valley) was based on when events like floods could have brought them there, not their evolutionary history. Martin and his colleagues turned to genetics instead.

To figure out just when the Devils Hole pupfish diverged from its kin, the researchers sequenced 13,000 different stretches of DNA from 56 pupfish from around Death Valley and the world. Those data allowed them to reconstruct the area's pupfish family tree and calculate when the different species emerged.

Although scientists previously believed the first pupfish species came to Death Valley several million years ago, these analyses suggest they arrived around the time of the valley’s most recent flood, just 10,000 years ago. The analysis also suggests the Devils Hole pupfish became isolated from other pupfish in Death Valley fewer than a thousand years ago, much more recently than expected—long after floods could have carried them into their remote cavern, the team reports online today in the Proceedings of the Royal Society B.

Devils Hole pupfish within Devils Hole in southern Nevada.

Devils Hole pupfish within Devils Hole in southern Nevada.

Olin Feuerbacher/USDI Ash Meadows Fish Conservation Facility

The findings build upon those of several smaller studies also suggesting a more recent emergence of the Devils Hole pupfish. "The agreement is striking. I would say there’s mounting evidence that they are younger than we originally envisioned,” says Craig Stockwell, a biologist at North Dakota State University in Fargo who published a similar but smaller genetic analysis in 2014.

“One of the major questions we’ve had about this species for years is how this species originally made it into Devils Hole,” says Sean Lema, a biologist at California Polytechnic State University in San Luis Obispo, who was not involved in the project. “To date, this is really the best attempt to figure out from the genetic evidence, the divergence of this [species].”

Despite its suspected youth, the Devils Hole pupfish has developed some unique features. It’s smaller and less aggressive than its kin. It has larger eyes and darker scales, and it lacks the pelvic fins found on every other desert-dwelling pupfish. If Martin’s analysis is correct, the fish has evolved these traits all within the last thousand years or less—remarkably quickly on an evolutionary timescale.

“I think what’s driving the uniqueness of the Devils Hole pupfish is the uniqueness of the Devils Hole habitat,” Martin says. “It’s one of the most extreme fish habitats I’ve ever seen in nature.” The fish spawn only on a submerged shelf that’s just a few meters on each side, the smallest natural habitat of any vertebrate. Food is scarce in the dark cavern. Such a challenging environment could put extra pressure on the pupfish to change more quickly, although it’s unclear how all of the adaptations are beneficial.

Martin emphasizes that the findings are preliminary, and that further studies are necessary to untangle the evolutionary history of the Death Valley pupfish. For instance, it’s still unclear how pupfish colonized Devils Hole in the first place if floods didn’t wash them in. Martin suggests human intervention could have played a role—Native Americans in the area ate pupfish and might have moved some of them between springs. Birds, too, could have inadvertently transferred fish eggs from one pool to another.

It’s unclear what the future holds for the Devils Hole pupfish—its already small numbers have dipped in recent years, and scientists aren’t sure why. But for now, it’s still holding on. “When I look at this habitat,” says Martin, “I’m amazed.”