HomeScienceGeneticsOne of the world's most inbred animals lives in Death Valley

One of the world’s most inbred animals lives in Death Valley

Death Valley derives its fame from extremes. The 3.3 million hectare park is one of the hottest and driest places in the world. Still, the park isn’t that one-dimensional – it has a lot more depth than you might think.

A vast network of water systems snakes beneath Death Valley’s surface, taking the form of a maze of subterranean caves and lakes. When rain or melting snow seeps through the ground, the water enters an aquifer and eventually collects in the underground waterway. The process is slow. It takes about 10,000 years for a single molecule of water to reach these caverns from the surface, according to the National Park Service.

The entrance to this abyss is called Devils Hole, and the name fits the place. Head to this part of Death Valley and you’ll find a hole in the earth with water hot enough for the devil himself. The narrow passage descends into cavernous, seemingly unreachable depths. Divers have explored as low as 500 feet below the surface and still haven’t reached the bottom.

A small underwater world

Despite the great depth, many biologists focus their attention on the first 25 meters of Devils Hole, where there is a compact plate with shallower water. Here, the Devils Hole pupfish (Cyprinodon diabolis) makes its home. Its area of ​​10 by 20 feet (3 by 6 meters) gives it the smallest known range of any vertebrate species.

In addition to cramped quarters, this part of Devils Hole presents other challenges for aquatic life. It has a nearly constant temperature of 34 °C (93 °F) and does not receive direct sunlight in winter (limiting the growth of algae, which the pupfish eat). For most fish, life in a pitch-black bubble bath would be unbearable. Add to that the poor concentration of dissolved oxygen, which would be lethal to many underwater organisms, and you can understand why the Devils Hole pupfish doesn’t have to worry about someone else moving in.

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In fact, you won’t find the Devils Hole pupfish anywhere else. The 30 known species of pupfish, so named for their playful, puppy-like movements, share a common ability to withstand harsh living conditions. But even among this rugged group, the Devils Hole pupfish takes the extreme lifestyle to a new level. Their mere existence amounts to a miracle. In 2013, their number dropped to just 35 individuals. Today, the number of Devils Hole pupfish individuals hovers around 263, the highest recorded population in 19 years.

There are many reasons why this pupfish is doomed: Climate change, habitat degradation, lower water levels, and human activities all threaten this isolated population. But we were never really confident that the Devils Hole pupfish would stick around. Scientists and policymakers chose to classify the species as endangered in 1967, almost immediately after the Endangered Species Act – called the Endangered Species Preservation Act at the time – went into effect.

Many sympathize with the pupfish as an underdog who was on the verge of losing but kept fighting. You may have even heard of it on the famous podcast Criminal, which documented the public outcry that arose when a few people unknowingly partied a little too hard near Devils Hole. People really care about these fish.

A shallow genetic pool

Now new research has identified another obstacle to their survival: incest.

The isolation of Devils Hole makes finding a new partner a challenge. It’s kind of like constantly bumping into your ex at the store, if your ex was also your cousin. Earlier this month, scientists reported results in Proceedings of the Royal Society from a genetic analysis done on the Devils Hole pupfish. The researchers found that the species’ sequences are 58 percent identical on average, which is “the equivalent of five to six generations of complete sibling matings,” said Christopher Martin, an evolutionary biologist at the University of California, Berkeley, and co-author of the paper. The researchers estimate that the Devils Hole Pupfish is the most inbred species in the world.

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In this study, the researchers sequenced the entire genome of eight Devils Hole Pupfish and one preserved specimen from the 1980s. They also determined the genomes of related species in the surrounding areas.

Specimens from the 1980s helped the researchers determine that the population was highly inbred, even before population bottlenecks in 2013 and 2017. This finding suggests that the pupfish has a history of repeated population contractions. Unsurprisingly, the Devils Hole pupfish harbors a significantly higher mutation load than any of the other desert pupfish in the study.

Pupfish Mutations

The researchers found some serious harmful genetic mutations. For example, the eight specimens had mutations in a gene related to sperm morphology. This makes it surprising that the fish can reproduce at all. They also found five genetic deletions associated with hypoxia or oxygen deprivation. Changes in these genes are not surprising, given that Devils Hole is a very hypoxic environment.

Paradoxically, however, the omissions suggest that the Devils Hole pupfish could be ill-equipped to physiologically handle the stress of a low-oxygen environment. This could explain why they don’t reproduce as successfully as other pupfish.

The authors warn that it would be hasty to immediately start fighting these harmful variants. First, we need to link these genetic changes to declines in survival or reproduction.

The study suggests that the Devil’s Hole pupfish is still in serious danger. Climate change will increase the danger by shortening the seasonal period when conditions are optimal for spawning on the shallow shelf where the Devils Hole pupfish spawns. Because environmental stress often exacerbates the problems caused by inbreeding, we know that the Devils Hole pupfish faces interacting threats that make survival a more difficult prospect. Like many of the other threats predicted to wipe out these thumb-sized creatures, it seems that the Devils Hole pupfish have been following their genetic situation closely. No one can ignore how their population has continued to grow.

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Maybe we can even help. Integrating genome sampling with conservation efforts is a new and promising scientific endeavor. Once we link a mutation to a change in survival or fertility, we can closely monitor that gene and spot mutations as they happen. This foresight gives scientists a better chance of using captive breeding programs to improve genetic diversity before populations plummet below recoverable levels.

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That’s the essence of endangered species management – you have to prevent a species from crossing that finish line. There is no turning back once a species has gone extinct.

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