As its name suggests, the devil cave killifish lives in a truly hellish environment.
Confined to a deep limestone cave in Nevada’s Mojave Desert, 263 of them live in water that hovers around 93 degrees Fahrenheit year-round, with food resources so scarce that they are always on the brink of starvation, oxygen The levels are so low that most other fish die instantly. Catfish, devil fishliving in the smallest habitat of any known vertebrate.
New research now documents the extreme impact these harsh and isolated conditions have on the fish’s genetic diversity.
In a paper published this week in the journal Proceedings of the Royal Society B, UC Berkeley biologists report the first complete genome sequences of eight pupfish species from the southwestern United States — a total of 30 individuals, including eight Devils Hole pupfish. Surprisingly, the inbred lineages of the devil’s cave juveniles were so close that, on average, the eight individuals’ genomes were 58 percent identical.
“High levels of inbreeding are associated with a higher risk of extinction, and inbreeding in devil’s cave juveniles is comparable to or more severe than levels reported to date in other isolated natural populations, such as Michigan’s Isle Royale wolf, mountain gorilla Tigers in Africa and India,” said lead researcher Christopher Martin, associate professor of integrative biology at UC Berkeley and curator of ichthyology at the campus’ Museum of Vertebrate Science. “While we cannot measure fitness directly, the increase in inbreeding in these pupfish may have resulted in a substantial decrease in fitness.”
The researchers found that other pupfish species were also inbred, but shared only 10 to 30 percent of their genomes.
The study’s lead author, graduate student David Tian, said the level of inbreeding in Devil’s Cave juveniles is equivalent to what would happen when four to five generations of siblings mate with each other. This tends to burn or repair, rather than remove, harmful mutations, potentially dooming a population to extinction due to mutational collapse. Devils Hole pupfish species are currently doing well in the wild and in captive or “refuge” populations, but such low genetic diversity could spell trouble as climate change and human impacts become greater.
In the face of these potential threats, the new genome sequences will help scientists and conservationists assess the health of native pupfish populations and potentially intervene in refugee populations to increase the genetic diversity of these species—especially Devils Hole pupfish.
“With this new genomic data, there is a lot of potential to study not only genetic diversity and how these species are phylogenetically related to each other, but also inbreeding and mutational load to understand what their current state is and how they have evolved history. may have influenced their current genetic variation and consider where the population is going and what we should be doing to protect these species,” Tian said.
Depopulation and Rescue
Pupfish species are scattered across the globe and tend to prefer isolated lakes and springs, often in extreme conditions where most fish cannot survive. About 30 species inhabit the warm, salty desert springs and streams of California and Nevada. Martin studied various pupfish populations, including several on the island of San Salvador in the Bahamas, to understand the genetics behind their adaptation to extreme conditions and unusual ecological niches.
However, Martin said the devil’s cave juvenile is unique in its small size and dangerous presence, making its fluctuating numbers in the wild a concern to conservationists.
“Part of the question about these declines is whether they might be due to the genetic health of the population,” Martin said. “Maybe the decline is because the deleterious mutation has been fixed because the population is so small.”
Part of the reason for the low numbers, Martin points out, is that humans have invaded their habitats. In the 1960s and 1970s, local ranchers and developers pumped groundwater in the area, which greatly lowered the water level in Devil’s Hole, causing population levels to drop. A 1976 Supreme Court ruling that allowed the federal government to limit groundwater pumping saved Devil’s Hole and its inhabitants, while captive breeding in a 100,000-gallon pond at the nearby Gray Meadows National Wildlife Refuge saved the species. Still, declines in the 1990s led to the wild population reaching its lowest point in 2013: 35 individuals. The wild population has since recovered, and the sanctuary population has ballooned to about 400 people, twice the size of the wild population.
Humans, however, cannot entirely blame the lack of genetic diversity in devil cave juveniles. UC Berkeley researchers also sequenced the genome of a juvenile fish collected in 1980 and preserved at the University of Michigan. It showed similar inbreeding and lack of genetic diversity to recently collected individuals, most of whom died of natural causes. This means that pupfish may have frequent population bottlenecks for hundreds if not thousands of years.
One consequence of this, Martin and Tian found, was that 15 genes had completely disappeared from the Devils Hole pupfish genome. Five of these appear to be related to adaptation to living in a hypoxic or hypoxic environment.
“These absences are a paradox because this is a habitat where you are most exposed to lack of oxygen,” Martin said. “Over time, it could be related to habitat stability. But in our view, the hypoxia pathway is disrupted. Once you disrupt one gene, whether you disrupt other genes in that regulatory pathway doesn’t matter. Important. “Our future work is to really investigate the role of these deletions. Do they increase tolerance to hypoxia? Do they reduce tolerance to hypoxia? I think both cases are equally plausible at the moment. “
Selective breeding in captive devil’s cave juvenile populations could help increase diversity and potentially save the species from eventual extinction, he said. To restore lost genes, CRISPR genome editing can add them back in.
The genomes of fish collected in 1980 were about as inbred as today’s, Martin said, which “may be good news because historically the population has been highly inbred with very low genetic diversity, suggesting that the recent 90 s, with only 35 fish in 2013 and 38 in 2007, the population bottleneck doesn’t seem to have much impact.”
Tian is currently analyzing approximately 150 complete genome sequences of nine American pupfish species to gain a more complete picture of deleterious mutations and gene deletions in different populations in the Southwest. He sees the research as an example of what conservation genomics can do for endangered and potentially inbred populations around the world.
“We’re on the cusp of a really cool wave when it comes to using genomic data and applying it to conservation, especially at a time when this problem is likely to only get worse with climate change and habitat fragmentation and anthropogenic changes, ” He says.
Tian, however, is skeptical of genetic interventions because little is known about how genes affect a species’ physical and behavioral traits and how this relates to fitness and adaptation to specific environments. Protection should remain a priority.
“The answer remains to increase funding for these populations, protect habitat, legal ways to protect these species, and figure out ways for humans and these endangered species to coexist on this planet,” he said.
Martin and Tian are co-authors Austin Patton of UC Berkeley and Bruce Turner of Virginia Tech in Blacksburg. This work was funded by the US Fish and Wildlife Service, the National Park Service, the National Science Foundation (1749764), and the National Institutes of Health (5R01DE027052-02).