Living in the Dark

Hundreds of eyeless fish swim in tanks stacked to the ceiling in Richard Borowsky’s cramped Manhattan laboratory. Small, pale and sightless, these fish look like mutants from genetics experiments gone awry. The lab’s fluorescent lighting is a far cry from their natural habitat. These are blind cavefish — part of the curious menagerie of animals adapted to life in the dark, often underground, world of caves around the globe.

Though it may be intuitive that eyes are useless for fish living in the dark, what is less obvious to biologists like Borowsky at New York University is the evolutionary mechanism that causes these fish to lose their power of sight. The mystery of the blind cavefish illuminates evolution’s complexity — not always a unidirectional race to build bigger, more complex organisms, but sometimes regressive, involving the reduction of certain traits over time. Scientists since Darwin have debated the cause of this evolutionary enigma, and now Borowsky and his research team may be one step closer to cracking the case of the blind cavefish.

“We do indeed think of evolution as progress, but it isn’t always progress,” says Borowsky. The regression, or disappearance, of certain traits over time is essential to the development of new species. “Without it, we’d have cilia on the outsides of our bodies and tails and gills. We’d be burdened with all the things our ancestors had,” says Borowsky, who studies regressive evolution in the blind cavefish. Living in the dark has not only resulted in the loss of eyesight and, in some cases, the whole eye, but skin pigmentation as well, giving a pale or whitish coloring to cavefish and other cave-dwelling organisms.

Video: New York University researchers gather cavefish in the northeastern Mexican states of Tamaulipas and San Luis Potosi.

Regressive evolution can be seen across the animal kingdom. Modern birds evolved from toothed ancestors but, over time, lost their heavy teeth and developed beaks, which many biologists believe helped make them lighter for flight. Humans and higher primates carry a mark of regressive evolution as well: the tailbone, a remnant inherited from our tailed, tree-dwelling ancestors.

Though examples of regressive evolution abound, the blind cavefish is rare because, in many places, it still interbreeds with its nearest living relatives, the normal-eyed fish that swim around the mouth of the cave. When the blind cavefish mate with fish from the closely related surface populations, their offspring have small eyes — an intermediate between the normal and blind parent species. With these unique populations, scientists can study evolution in action. In fact, the cavefish has become a model organism for studying trait regression.

Borowsky and his colleagues are investigating two mechanisms for eye loss in the blind cavefish — natural selection and genetic drift. Darwin’s theory of natural selection, also known as survival of the fittest, is the process by which favorable traits become more common in a population because individuals with these traits are more likely to survive and reproduce.

Genetic drift, on the other hand, is the accumulation of random genetic mutations in a population over time. For instance, a fish born with a mutation causing poor eyesight in clear surface waters may not be able to survive and reproduce as well as a fish that can see normally. But put the two in a dark cave where neither fish can see, and the mutation is no longer detrimental. In the cave environment, that particular mutation becomes neutral; the blind fish may reproduce equally as well as the fish that can see.

If it was solely genetic drift at play for the cavefish, Borowsky would expect to see some mutants with bigger eyes and some with smaller eyes, since eyesight does not determine survival in a cave. But only fish with very small or nonexistent eyes persist in caves. The best explanation for the bias toward blindness, according to Borowsky, is natural selection. “The hypothesis is that the eye is an energetically expensive thing to grow and maintain. If you don’t need it, you are better off without it,” he says.

The fact that cavefish’s eyes only decrease in size suggests that natural selection is at work, agrees William Jeffery, a cavefish biologist at the University of Maryland. But, so far, current research has not disproved genetic drift’s contribution to the evolution of the cavefish eye. A scenario that could make genetic drift possible, explains Jeffery, is that a small number of fish were swept into a cave during a flood and separated from the larger breeding population. Such an event could have led to inbreeding in the isolated cave population, increasing the chances that a random genetic mutation causing poor eyesight could have occurred and been passed on to future generations. “My bottom line right now is that both [natural selection and genetic drift] may be involved,” says Jeffery.

To get to the bottom of the evolutionary mystery, Borowsky, along with his doctoral student Martina Bradic, gather cavefish from caves near each other in the northeastern Mexican states of Tamaulipas and San Luis Potosi.

After descending into Pachon cave, in northeastern Mexico, with climbing ropes, harnesses, helmets and headlamps, Bradic and Borowsky waded into the cave waters and waited quietly with their fishing nets. The blind cavefish swim slowly, making them easy targets, says Bradic. Because food is often scarce in the cave environment, they drift languidly through the water to conserve energy.

Once back in the lab, Bradic extracts DNA from the captured cavefish. She is looking for molecular markers, short sequences of genetic code that tend to mutate frequently. These fast-mutating fragments serve as clues to Bradic because they can vary between two closely related fish populations, such as the blind cavefish and their ancestors with normal eyes living just outside the caves. She can look at specific parts of the genome, such as genes responsible for eye size or skin pigmentation, to get an idea of whether they changed because of natural selection or genetic drift. This is the first step to understanding the underlying genetics of blindness in cave-dwellers and the evolutionary mechanisms that may have contributed to the makings of the pale, sightless fish found in many caves today.

“Until we really explore the genetic details, we don’t really have much hope for explaining from an evolutionary standpoint why it is that [regressive evolution] is happening,” says Josh Gross, a postdoctoral fellow in genetics at Harvard Medical School, who also studies cavefish evolution. Cave-dwelling critters across the board, from salamanders to spiders and crickets, exhibit loss of eyes and skin pigmentation. But hope for untangling the genetic mysteries of regressive evolution lies with the blind cavefish because the fish has something these other organisms don’t: populations of normal surface relatives with whom they still interbreed. Thus the blind cavefish has become the go-to organism for studying the effects of a cave environment on cave-residing creatures.

“The cavefish is an example of evolution happening in front of our eyes,” says Bradic. The fish populations she is examining come from several different caves, but they all have a common phenotype: small or no eyes and reduced skin pigmentation. For this reason, each cave with its own population of blind cavefish is like a separate, repeatable experiment, making this an ideal place to pin down the genetic mechanisms of regressive evolution. “You couldn’t design a more perfect set of experiments in the laboratory,” says Bradic. “For me, this is the most beautiful example of evolution in nature.”

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