The Devils Hole pupfish is so inbred that it shouldn’t be alive

A Devils Hole pupfish looks directly into the camera, against a black background.
Speak of the devil. (Image credit: Olin Feuerbacher/USFWS)

The Devils Hole pupfish is small, blue and incredibly endangered. It also may be the most inbred creature on Earth. 

All 263 wild Devils Hole pupfish (Cyprinodon diabolis) live in one location: a 10-foot by 20-foot (3 by 6 meters) cavern in the middle of Devils Hole in Nevada, a detached part of Death Valley National Park, one of the hottest places in the world. Their cavern oasis, located just 50 or so feet (15 meters) below the desert floor, is at least 500 feet (152 m) deep (scientists have yet to find the bottom) and stays at a balmy 92 degrees Fahrenheit (33 degrees Celsius) year-round. The species has lived there, isolated from all other pupfish, for at least 1,000 years, and possibly as long as 20,000 years, according to the National Park Foundation

That isolation has led to some very dramatic genetic consequences, scientists reported Nov. 2 in the journal Proceedings of the Royal Society B. They found that Devils Hole pupfish genomes are 58% identical, on average — "the equivalent of five to six generations of full sibling matings," said Christopher Martin, an evolutionary biologist at the University of California, Berkeley and senior author of the new study. That's enough to make the infamously inbred Habsburg dynasty look wildly diverse.

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For the new study, the researchers sequenced the genomes of eight Devils Hole pupfish, as well as one preserved specimen from the 1980s. They found that the fish were missing some seemingly important genes. For example, they lacked a gene normally involved in producing sperm — one that causes infertility if knocked out in other species. "It's kind of surprising that they're even able to reproduce at all," Martin told Live Science.

The fish had also lost a gene that helps other types of pupfish survive in low-oxygen environments — a surprise, given that the warm, stagnant pool they call home is very deoxygenated. At the moment, it's unclear to what degree the absence of these genes is harming the pupfish's overall health. 

"The genome is a complex place," Martin said. He and his team plan to study the fishes' genetics in greater detail to determine what, exactly, each of their genes is doing and how they're compensating for genomic losses.

The intense inbreeding observed in the fish is likely due to their geographic isolation, coupled with multiple population bottlenecks in recent years. In the past two decades alone, the population nearly crashed twice — dipping to 38 individuals in 2006 and as low as 35 in 2013, according to the U.S. Fish and Wildlife Service.

This unique fish was one of the first species to be officially added to the Endangered Species Preservation Act in 1967, which was later folded into the Endangered Species Act of 1973. Since then, thanks to considerable conservation efforts — including the construction of a 100,000-gallon (379,000 liters) replica of Devils Hole that houses a separate captive-bred pupfish population — the species has survived, though it has not always thrived.

"They're still in a precarious situation," Martin said. "But the good news is that human interventions and accidents haven't really made the population worse than it was … I don't think they're doomed."

Joanna Thompson
Live Science Contributor

Joanna Thompson is a science journalist and runner based in New York. She holds a B.S. in Zoology and a B.A. in Creative Writing from North Carolina State University, as well as a Master's in Science Journalism from NYU's Science, Health and Environmental Reporting Program. Find more of her work in Scientific American, The Daily Beast, Atlas Obscura or Audubon Magazine.