Devils Hole pupfish may not have been so isolated for so long

The alarmingly rare Devils Hole pupfish — known from only one pool in a Nevada desert —might not be the long-isolated species it has seemed.  

The small, bluish Cyprinodon diabolis fish inhabits Devils Hole, a collapsed cavern filled with water in the Mojave Desert. To explain how fish got into such hostile terrain, biologists have speculated that C. diabolis and some related local pupfishes in the area descend from residents of ancient bodies of water that disappeared from the region more than 10,000 years ago. As those waters receded, fishes took refuge where they could, the idea goes. By now, descendants have adapted to odd remnant habitats of wetter days.

That intuitively appealing story, however, does not fit with hints from new genetic evidence, says Christopher Martin of the University of North Carolina at Chapel Hill. The Devils Hole pupfish appears to have recently shared genes with desert pupfishes that live in springs or other watery places — perhaps between 105 and 850 years ago. So the Devils Hole pupfish may not have been really isolated as a species as long as once thought. And it may not even have moved in to its watery hole in the desert recently, Martin and colleagues say January 27 in Proceedings of the Royal Society B.

Martin cautions that to give a firmer answer on the isolation time, he needs more information. He would have to measure directly the rate at which pupfish genes mutate, and research material is not abundant for these endangered species. The DNA he worked with came from a pupfish found dead in the water, and he and his colleagues scrutinized the species with modern equipment that processes high volumes of DNA. There were distinct signs, he says, that the Devils Hole species was somehow exchanging genes with related species in the region, suggesting that the species is more recent than relict.

C. diabolis’ entire range as a species is the deep pool of Devils Hole, with an opening only 3.5 meters by 22 meters. Steep sides keep sunlight from reaching the water for two months of the year, starving algae that fish need for food. Water temperatures stay about 32°Celsius, a temperature warm enough to kill most other fish within an hour, Martin says. “It’s one of the most ridiculous fish habitats I’ve ever seen.”

For years, the prevailing estimate for the age of the pupfish species was roughly 10,000 to 20,000 years, says Craig Stockwell of North Dakota State University in Fargo. That was roughly the end of the Pleistocene epoch, when bodies of water in western North America dried up.

The much more recent date is “plausible but suspect,” says Andrew Martin of the University of Colorado Boulder, who has studied pupfish for decades.

The new paper calibrated its timing based on well-studied mutation rates of pupfishes in Mexico’s Lake Chichancanab. But Andrew Martin argues that some of the Mexican species probably arose before the lake formed, so the mutation rate would be slower than thought and the age estimate different. Therefore, the new, low age for pupfish isolation, he concludes, “is as plausible to my mind as estimates that extend into the late Pleistocene.”   

Despite the study’s drawbacks, Stockwell is more open to the new, recent timing because of what conservation biology has learned about the perils of small populations. In 2014, he and Michael Reed of Tufts University in Medford, Mass., used decades of monitoring information about the ups and downs of the Devils Hole pupfish numbers to estimate the population’s powers of persistence. The chances of it surviving 10,000 years were just 2.1 percent, the pair concluded. A long-ago origin didn’t look likely. And looking at some repetitive sequences of DNA in pupfish cells, Stockwell and Reed saw some evidence for recent sharing of genes with other pupfish species. The Devils Hole fish probably were isolated “within the last few hundred to few thousand years,” they concluded.

Now that Christopher Martin’s study, with a different approach, has also come up with a recent age, Stockwell feels more confidence in the notion. The improbable history of the Devils Hole pupfish may have had some overlooked recent chapters.