What do blind cavefish, dinosaurs, and sunburnt humans have in common? A lot more than you may realise, according to a thought-provoking new study.
New research published today in Current Biology shows that Somalian blind cavefish (Phreatichthys andruzzii) are missing an ancient DNA repair kit that protects many animals from the harmful effects of sunlight. This observation makes total sense, given that this cave-dwelling species has lived, and subsequently evolved, for millions of years in complete darkness. The lost system, called photoreactivation DNA repair function, uses energy from visible light to repair DNA damage caused by ultraviolet (UV) light, and it’s found in many organisms, including bacteria, fungi, plants, and many animals. This repair kit is one of the reasons why plants can bask in the sun all day without becoming riddled with mutated DNA, while humans risk getting skin cancer when we sunbathe.
Indeed, placental animals, a group that includes humans, do not have this special DNA system. An intriguing aspect of this new research is that it’s potential evidence for the “nocturnal bottleneck” theory—the idea that the ancient ancestors of modern mammals lived underground or were exclusively nocturnal in order to avoid being eaten by dinosaurs. Like the blind cavefish, these early mammals evolved in total darkness for a prolonged period, resulting in the gradual loss of the light-activated DNA repair function. It’s from this group of “bottlenecked” mammals that all placental mammals emerged, which may explain why modern placental mammals still lack this genetic trait. And why humans are now so dependent upon sunscreen.
Or at least that’s the prevailing theory. As some experts told Gizmodo, this new study is really interesting, but more work will be needed to strengthen the apparent connection between the lifestyles of our very ancient ancestors and our missing DNA repair kit.
Use it or lose it. It’s a simple phrase, but it eloquently explains an evolutionary process known as “relaxed selection.” It happens when the survival, or fitness, of a species is no longer dependent on a certain physical characteristic or behavioural trait. An unnecessary or superfluous trait will wither away in a species as the genetic code responsible for that trait degrades over time, or if mutations turn it into something else. This doesn’t happen overnight, and it often leads to vestigial traits. In humans, we see this in our wisdom teeth, tonsils, appendix, and coccyx, otherwise known as the tailbone. Eventually, these traits will likely disappear completely as the genetic code required to express these traits continue to worsen over time.
For the Somalian blind cavefish, relaxed selection resulted in the gradual loss of its photoreactivation DNA repair function. This feature likely appeared during the earliest stages of life on Earth as a protection against the harmful effects of sunlight. Nick Foulkes, the lead author of the new study and a researcher at the Karlsruhe Institute of Technology in Germany, said this repair mechanism is very efficient, which likely explains why most plants and animals have retained this function for millions of years.
Foulkes studies the effects of evolution on animals living in extreme environments and how it changes their DNA. This led him to the Somalian blind cavefish—a species that hasn’t had any exposure to UV or visible light for more than 3 million years. Genetic analysis showed that the DNA of Somalian blind cavefish underwent mutations that wrecked its light-activated DNA repair function. What’s more, the fish also lacks a D-box enhancer—a regulatory enhancer that coordinates and boosts DNA repair in response to sunlight by activating other genes. Interestingly, other cavefish species appear to have retained their DNA repair kits.
A Somalian blind cavefish.
Image: Luca Scapoli/University of Ferrara
“The Somalian cavefish has been living in complete darkness for millions of years while other cavefish that have been studied may have been isolated in the dark for a much shorter time, in some cases for less than 100,000 years,” Foulkes told Gizmodo. “So these other species may not have been isolated in the dark long enough to lose photoreactivation. But of course, it may well be that there are other cave animals where this has happened, but to date only a small number of cave animals have been studied in this detail.”
As noted, the only other group of animals known to have lost this function are placental mammals.
“Photoreactivation is found in all living things, from plants, fungi, and bacteria to fish, amphibians, reptiles, birds, and even mammals like marsupials—kangaroos, koalas, and opossums being good examples,” said Foulkes. “Only placental mammals like ourselves lack this. Precisely why has, for a long time, been a mystery. Now, our finding of a fish that has also lost this ancient genetic repair kit, comes as a big surprise. These fish will not have seen the sun or suffered the effects of UV radiation for millions of years. So photoreactivation, which depends on light, may serve no useful purpose. This may well explain why this ancient repair kit is lost in this particular cavefish and also raises the fascinating possibility that our ancestors may have shared a similar lifestyle with cave animals.”
Indeed, this could be an example of convergent evolution, in which similar or identical traits (or in this case, the disappearance of traits) appear in non-related species. The commonality here is prolonged exposure to darkness. But where Somalian blind cavefish were trapped in dark caves for millions of years, early mammals lived in the dark, either due to nocturnal living or subterranean lifestyles, to avoid being predated upon by dinosaurs. Mammals first evolved around 200 million years ago, spending around 130 million years amongst non-avian dinosaurs.
“The finding is fascinating as it is the first report of an organism outside of mammals that has lost UV-mediated DNA repair, and the fact that they apparently lost it because of their dark environment fits nicely with the hypotheses that humans have lost the same ability because of our nocturnal past in mammalian evolution,” Nicolas Rohner, a research scientist at the Stowers Institute and an expert on cavefish who was not involved in this study, told Gizmodo. “The findings are surprising because a related study in another cavefish species has found the opposite. In this study the authors found cavefish to have [functional] DNA repair. This means that different cavefish species use different strategies to survive under seemingly similar conditions.”
Aniket Gore, a scientist who works at the Laboratory of Molecular Genetics at the National Institute of Child Health and Human Development, said the new study is a “very well done, careful analysis.”
“Understanding the molecular mechanisms behind DNA repair systems are essential to developing effective therapeutic approaches for different diseases, including cancers,” Gore, who did not participate in the new research, told Gizmodo. “The study highlights that unique model organisms, such as the cavefish, reveal answers to fundamental questions related to human health and development.”
As for the claim that dinosaurs are the reason humans need sunscreen, Gore said that’s a bit of a stretch. He claims there are several other possibilities to explain why humans lost the light-induced DNA repair system, while retaining other DNA repair mechanisms, namely NER (nucleotide excision repair) and BER (base excision repair).
“One possibility is that NER and BER can fix changes in the DNA sequence independent of light and hence they can work even in the dark at night or in overcast conditions making them highly effective repair systems to fix mutations.”
In other words, perhaps mammals weren’t solely dependent on the photoreactivation repair kit, given the effectiveness of other DNA repair mechanisms.
Gizmodo also reached out David M. Grossnickle, an evolutionary biologist from the University of Chicago and an expert on early mammal evolution, to get his take on the new study.
“The apparent convergent evolution in placentals and Somalian blind cavefish is really interesting, and I think there’s exciting potential for future studies to expand on these results,” Grossnickle told Gizmodo. “The study provides indirect support for the hypothesis that placental mammals lost the photoreactivation DNA repair function because they were nocturnal and not exposed to sunlight.”
Grossnickle said this is a welcome addition to our growing knowledge of early mammal ecologies and behaviours, but it’s important to acknowledge that two other groups of living mammals—pouched marsupials, such as kangaroos, and egg-laying monotremes, like the duck-billed platypus—have retained the photoreactivation DNA repair function. In addition to these three living groups (placentals, marsupials, and monotremes), Grossnickle says there were numerous other early mammal groups that were very diverse in the Mesozoic era (the time of the dinosaurs), but are now extinct.
“Placentals did not show up on the scene until the very end of the Mesozoic,” explained Grossnickle. “So the study does have implications for placental mammal evolution, but it does not indicate that all mammals experienced a nocturnal bottleneck in the Mesozoic. I urge caution in applying what we learn about placental origins to our story of all mammals.”
The connection between blind cavefish and sunburnt skin may be a leap, but it’s not completely outrageous. The idea that some of our characteristics can be traced back to the time of dinosaurs is wholly plausible, given that mammals first emerged back then. What’s needed now is more evidence, both paleontological and genetic, to strengthen this extraordinary claim.
Until then, please pass the sunscreen.
Featured image: Luca Scapoli/University of Ferrara