The world’s rarest fish

The world’s rarest fish

Swimming on the edge of existence

In the middle of the hottest desert on Earth lives the world’s rarest fish. It lives on the shallow shelf of an oxygen-deprived water basin measuring only 3 metres wide, 21 metres long and around 152 metres deep. Science communicator Alicia Robertson tells the remarkable story of the Devils Hole pupfish

Alicia Robertson

Devils Hole is a vast, water-filled cavern in the Mojave Desert, part of Death Valley National Park in Nevada, USA. The hole is an exposed opening to an aquifer that plunges more than 150 metres below the surface of the desert (see Figure 1). The underground cave system is so deep that earthquakes from as far away as Central America and Alaska can cause miniature tsunamis to roil its waters.

Devils Hole pupfish (Cyprinodon diabolis), so named for their playful, frolicking nature, are isolated from other pupfish populations in the Mojave Desert, and experience many challenges to their survival. With a brief, 12-month lifespan, and the lowest genetic diversity ever documented in the wild, their chances of surviving continuous threats from monsoonal floods, earthquakes and the desert’s changing climate are in doubt.

How did the Devils Hole pupfish get there?

Death Valley is currently the driest place in North America, but it was once a water-filled sanctuary. During the Pleistocene epoch, around 2.58 million to 11700 years ago, ice covered the surrounding mountain ranges and rivers flowed into the valley, feeding a large lake. Over time the climate of the valley changed, and the lake became a system of interconnected ponds and marshes, with the majority disappearing completely as the valley dried up.

The Devils Hole pupfish is one of several pupfish species that call the desert home (see Box 1), but it is the most distinctive. Death Valley pupfish are believed to have evolved less than 20000 years ago from a common ancestor, with small groups becoming isolated in desert springs. Scientists originally theorised that pupfish in Devils Hole were cut off from other populations around 10000 to 20000 years ago, but a new study of the mutation rate of pupfish genes suggests that they were breeding with related species in the region as recently as 105 to 830 years ago.

It is not known how pupfish made their way to Devils Hole. It is possible that Native Americans, who included pupfish in their diet, may have intentionally or unintentionally transferred fish and eggs between springs.

Adaptation in an extreme environment

The cave is an unlikely environment for the pupfish, with a constant temperature of 34°C, minimal direct sunlight during the winter, and dissolved oxygen concentrations near lethal limits of 2–3 ppm (most fish require 5–20 ppm). While the pupfish have been recorded swimming as deep as 20 metres, they forage and spawn on a shallow rock shelf near the water’s surface.

Their diet consists primarily of algae, with research directly linking pupfish population numbers to the quantity of algae present on the shelf. The growth of algae within the hole depends on the duration of sunlight reaching the shelf, as well as the concentration of nutrients within the water. Nutrients are at their highest concentration when local barn owls use the area for nesting, depositing nutrient-rich pellets and droppings into the water.

Isolated from other populations, pupfish in different waters have acquired different traits, resulting in a range of distinct species. Occasionally populations mix when seasonal flooding temporarily joins nearby ponds. Although Devils Hole is close to other pupfish habitats, it is especially isolated owing to its geological topography. The Devils Hole population is particularly small, with estimates ranging from 35 to 550 fish since official recordkeeping began in the 1970s.

The pupfish of Devils Hole have several unique features (see Figure 2). With an average length of 2cm, they are smaller and less aggressive than other pupfish species, which typically range from 3–10cm. C. diabolis has relatively larger eyes than other pupfish species, possibly linked to low-light vision, and darker scales, which could facilitate thermoregulation. They also have extended anaerobic respiration abilities, allowing them to convert energy without oxygen – an essential attribute in their oxygen-deficient habitat.

Curiously, they lack pelvic fins, which aid in stabilisation of other pupfish while swimming. In an attempt to mimic the morphological modifications of C. diabolis, studies were carried out on the Amargosa River pupfish, a close but non-threatened relative. A severely restricted diet, coupled with increased water temperature, led the Amargosa pupfish to develop physical traits similar to those of the inhabitants of Devils Hole – in just 126 days.

The researchers concluded that the very specific environmental constraints of Devils Hole reduce the thyroid hormone concentrations in the pupfish, resulting in their unique appearance. It has been proposed that such environmentally induced changes may be followed by adaptive evolution. Recent genomic analysis shows that C. diabolis is presenting signs of genetic evolution after being isolated for less than 1000 years, which, on an evolutionary timescale, is exceptionally fast.

Inbreeding to extinction

While inbreeding among pupfish is common, the genomes of other species are only 10–30% identical. High levels of inbreeding tend to increase the frequency of damaging mutations, which could potentially doom a species to extinction. Due to the fragility of the population of C. diabolis, previous testing could only be carried out on other pupfish species. However, a recent boom in the population allowed biologists to collect samples from live C. diabolis specimens for DNA sequencing. These genomic tests revealed that C. diabolis is so inbred that, on average, 58% of the fish have identical genomes – the equivalent of five or six generations of full sibling couplings.

The study also examined loss-of-function SNPs to determine whether detrimental genetic variants could explain historic population decline. This research revealed that 15 presumed essential genes have disappeared entirely from the Devils Hole pupfish genome. Five of these missing genes are involved in adapting to living in a low-oxygen environment – a surprising finding given that the habitat of Devils Hole is highly hypoxic.

Another missing gene, one that normally involves the production of sperm, has scientists perplexed. Genomic studies of other species have shown that this type of deletion causes infertility, leaving biologists to wonder how the pupfish are able to reproduce at all. The plan now is to study the genomic results in greater detail, to determine what each gene is doing and how the fish are compensating for genetic losses.

External threats

While severe inbreeding has likely contributed to lower fitness and past population declines, a multitude of external threats have exacerbated the perilous state of the Devils Hole pupfish. Small-population dynamics are particularly sensitive to environmental and random events, which can lead to extinction vortices.

During the late 1960s to early 1970s there was a marked recession of the water level within Devils Hole, which threatened to expose the shallow shelf that serves as the main spawning and feeding habitat for the population. Nearby farms were siphoning water from the aquifer. In response to this the Desert Fishes Council – an organisation dedicated to the study and preservation of desert aquatic ecosystems – was created. Its work ultimately underpinned extensive legal protection for Devils Hole through a water-rights case, with the US Supreme Court ruling in 1976 in favour of the pupfish.

In July 2021 the habitat was hit by two rare environmental events within a few days of each other. First, a sudden flash flood deposited mud and rocky debris into the habitat, and raised water levels within the hole. Then, 2 days later, a magnitude 8.2 earthquake struck the Alaskan peninsula, causing a seiche within the hole, which redistributed the still settling flood debris and removed a significant amount of algal growth.

While the increasing frequency of these disturbance events has scientists concerned, there is an argument to be made that such events, on rare occasions, are important contributors to the environment’s ecosystem. While the fish do spawn year-round, scientists have noticed increases in egg laying after events such as these, leading biologists to study the links between environmental disturbances and reproduction.

Refuge from extinction?

Since C. diabolis was one of the first species to be listed – in 1967– as endangered under the US Endangered Species Act, conservationists have made several attempts to ensure that these tiny fish are protected from extinction. Over the years, several efforts have been made to breed populations of C. diabolis in artificial refuges, all of which have failed. Most refuges simply could not simulate the natural habitat of Devils Hole, leading to the pupfish populations showing significant morphological deviations within as little as 5 years.

Fortunately, the most recent refuge attempt is showing promise. In 2013 the Ash Meadows Fish Conservation Facility was opened. This state-of-the-art conservation centre is dedicated to building a self-sustaining population of Devils Hole pupfish. The centre consists of a 450000dm3 refuge tank, with a 3D-printed replica of the hole’s spawning shelf, a propagation room, wet laboratory and equipment that helps to maintain specific environmental parameters. With eggs, aquatic invertebrates and algae transferred directly from Devils Hole, the current population of the refuge is thriving and, remarkably, retaining its original morphological traits.

While its future remains uncertain, one thing is for sure – the Devils Hole pupfish cannot survive in its current habitat forever. Will it be lost due to extreme climate change or its ever-diminishing gene pool? Will scientists be able to save this species from an isolated environment while keeping its unique traits intact? The road ahead is long, but there is hope that these tiny fish can swim their way back from the brink.

Topic for discussion

■ An enormous amount of resources is being expended on these little fish. Is their survival as a species worth the effort?

Alicia Robertson is a science communicator at Glasgow Science Centre. She investigates a wide variety of scientific topics, and finds ways to make science interesting and accessible to everyone.