Endangered Devils Hole pupfish is one of the most inbred animals known
A curious, captive-raised Devils Hole pupfish at the Ash Meadows Fish Conservation Facility in Nevada. The facility maintains a refuge population of pupfish as a backup to the wild population, which fluctuates over decades and once dipped to a mere 35 individuals. Credit: Olin Feuerbacher/USFWS

The Devil's Hole pupfish lives in a really bad place.

263 of them live in the water of a single deep limestone cave in Nevada's Mojave Desert, with food resources so scarce that they are always on the edge of starvation. The smallest habitat of any known animal is occupied by the pupfish.

The fish's genetic diversity has been severely affected by the harsh conditions.

The first complete genomes of eight pupfish species from the American Southwest were reported in a paper published this week. Almost half of the genomes of the eight individuals are the same.

The Isle Royale wolves in Michigan, mountain gorillas in Africa and Indian tigers have all been found to have high levels of inbreeding. The increased inbreeding in these pupfish may result in a reduction in fitness.

Only between 10% and 30% of the pupfish's genomes are the same, according to the researchers.

The author of the study said that the level of inbreeding in the pupfish is equivalent to what would happen if four to five generations of siblings were to marry. This tends to burn in or fix rather than weed out the bad stuff, which could doom a population to extinction. The low genetic diversity of the Devils Hole pupfish could pose a problem as the climate changes.

The new genome sequence will allow scientists to assess the health of native pupfish populations and possibly intervene in refuge populations to increase the genetic diversity of these species.

There's a lot of potential to look at not just genetic diversity and how these species are related to each other, but also look at inbreeding and mutations load to get an idea of what their current status is.

Endangered Devils Hole pupfish is one of the most inbred animals known
Chris Martin of UC Berkeley standing near Devils Hole, the sole residence of the Devils Hole pupfish. The pool gets direct sun only nine months of the year, and the pupfish rely for food on algae growing on the rock shelf visible in the photo. Credit: Jennifer Gumm

The population is declining and rescue is needed.

Most fish would find unsurvivable isolated lakes and springs, which is why pupfish species are often found around the globe. There are many species of desert springs and streams in California and Nevada. Martin has studied various pupfish populations to understand the genetics behind their adaptation to extreme conditions.

Martin said that the Devils Hole pupfish is unique in its small range and perilous existence.

The genetics of the population may be a factor in the declines. The population is so small that there are harmful genes that have been fixed.

Human incursions into their habitat are to blame for the small population. In the 1960's and 70's, local ranchers and developers pumped water out of the ground in order to reduce the water level in the area. The species was saved by a Supreme Court ruling that allowed the federal government to limit the amount of water pumped into the ground. The wild population declined in the 1990s and reached its nadir in the year 2013). The refuge population has doubled that of the wild population.

The lack of genetic diversity in the pupfish is not solely the fault of humans. A pupfish collected in 1980 and held at the University of Michigan was the subject of the UC Berkeley research. It showed a lack of genetic diversity like that found in individuals that died a natural death. This means that the pupfish has seen a lot of population problems over a long period of time.

There are 15 genes that have vanished from the pupfish genome. adaptation to living in low-oxygen or hypoxic environments seems to be involved in five of them.

This is a place where you're most exposed to hypoxia. Something could be related to the stability of the habitat. The hypoxia pathway seems to be broken. It doesn't matter if you break more genes in the regulatory pathway. We are going to look at what these deletions do. Is it possible that they increase tolerance of hypoxic conditions? Hypoxic tolerance may be decreased by them. I think those two scenarios are realistic.

He said that captive breeding could help increase the diversity and possibly save the species from extinction. It's possible to add genes back to them.

The population of fish has historically been highly inbred with very low genetic diversity, suggesting that the recent decline in the '90s is related to this.

The complete genomes of nine species of American pupfish are being analyzed by Tian to get a more complete picture of the deleterious changes and deletions. He sees the study as an example of what can be done with the use of genetics.

"We're on a really cool cusp when it comes to using genomic data and applying it to conserve, especially at a time when it's a problem that is likely only going to get worse with climate change and increased habitat fragmentation and just human activity," he said.

Since little is known about how genes affect the physical and behavioral characteristics of a species and how this relates to fitness and adaptation to a specific environment, Tian is leery of genetic interventions. It's still important to conserve.

Increased funding for these populations, protecting habitats, legal avenues for protecting these species and figuring out ways for humans and these extinct species to coexist on this planet is the answer.

Two of the co-authors are from UC Berkeley and Virginia Tech.

In the Proceedings of the Royal Society B: Biological Sciences, there is information on severe inbreeding, increased mutation load and gene loss-of-function. rspb.2022.1561 is a book.

Journal information: Proceedings of the Royal Society B