Blind Somali Cavefish Reveals That First Mammal Survived Dinosaurs by Hiding in the Dark

A genetic repair system activated by light turns out to exist in everything from germs to animals – except for mammals and eyeless cavefish in Somalia

A Somalian blind cavefish. After evolving for millions of years in darkness, it has lost the capacity to harness light for repairing DNA.
Luca Scapoli at the University o

Eyeless fish that evolved for three million years inside caves in Somalia are an unlikely crutch for the theory that early mammals weathered the dinosaur age by going nocturnal. But that is the conclusion from a groundbreaking study of Phreatichthys andruzzii. Alternatively, our earliest ancestors may have burrowed to evade predation.

In either case, our diminutive and very distant forefathers lived in the dark, suggest Haiyu Zhao and colleagues in Current Biology, based on the genetic analysis of cave-dwelling fish.

What do long-isolated fish have to do with early mammals? The first mammals were a rat-like bunch: tiny and defenseless, except perhaps against marauding miniature millipedes. The “age of mammals” only began after dinosaurs almost died out around 65 million years ago (they didn’t go extinct), but in fact mammals and dinosaurs evolved almost in tandem during the Triassic.

So early mammals were already scuttling about some 200 million years ago. They just didn’t go far until the dinosaurs mostly disappeared. Paleontologists have always wondered how the tiny furry little things weathered the dinosaur age.

One mammalian strategy to avoid being eaten by the smaller predatory dinosaurs – assuming that T. rex and its ilk wouldn’t lower themselves to eat proto-rats – might have been to adopt a subterranean or exclusively nocturnal existence. Proto-mammal, the denizen of the night, has long been postulated; now a strange fish has strengthened the theory’s case.

Case of the missing genes

How many millions of years the pinkish, whiskered Phreatichthys lived in the lightless caves of Somalia is unclear – but it’s more than three, say the scientists. And while they were living there, the fish lost a specific system of DNA repair that harnesses visible light energy to fix damaged genetic material, Zhao and the team realized after sequencing it.

“DNA repair systems” are enzymes that fix DNA that gets damaged, for instance by radiation or toxins.

Other fish have this light-driven system; the most primitive of life-forms, bacteria and fungi, have it; reptiles have it; birds have it; worms and geckos have it. But placental mammals, and this fish, do not have it.

Since this DNA repair system lost by Phreatichthys exists in everything from germs to whale sharks, evidently it evolved very early in the scheme of life, and was kept as the single-celled animals evolved into multi-cellular animals. But it was evidently lost in this dark-dwelling fish – and the ancestor of all mammals.

This in turn indicates that its loss was no loss to them. Which in turn indicates that they lived in the dark.

The researchers say that discovering the piscine anomaly in the Somalian cave supports the “nocturnal bottleneck” theory: that ancestral mammals lived a subterranean or exclusively nocturnal existence as a strategy to avoid being eaten.

“We have revealed in a species of blind cavefish the loss of an ancient DNA repair system that is highly conserved,” says Nicholas Foulkes of Karlsruhe Institute of Technology, Germany. “Curiously, the only other animals previously known to lack photoreactivation DNA repair are placental mammals. So, what we see in this species of cavefish may be the first stages in a process that happened before in our ancestors in the Mesozoic era.”

Foulkes’ team, including first author Zhao, in collaboration with Cristiano Bertolucci at Italy’s University of Ferrara, had set out to study evolution in extreme environmental conditions, particularly the evolution of DNA repair systems. They note that Phreatichthys was a fantastic subject for them because the wee fish lived without any exposure to UV or visible light from the sun for more than 3 million years.

By the way, other species of fish discovered living in isolation in cave environments – but not as long as Phreatichthys – have normal, or even enhanced, photoreactivation mechanisms, says the team. But it had a long time to lose those genes.

Among other indications that the earliest mammals were nocturnal are the eyes. A 2012 paper in the National Center for Biotechnology Information journal finds support for the “nocturnal bottleneck” theory in mammalian eye structure.

Night-living vertebrates have big corneas relative to eye size, to enhance their visual sensitivity. Diurnal vertebrates have smaller corneas.

After examining 266 species, the paper concluded that the eye shapes of most diurnal and cathemeral mammals (the latter living by day or night, they don’t care) have eye shapes akin to nocturnal birds and lizards.

Humans are an exception to that rule, says that paper: Our eye shapes are like diurnal birds and lizards. That’s good to know. (It’s a case of convergent evolution.)

“Many features of modern mammals, such as the anatomy and function of the eye, show telltale features of a nocturnal life style,” Foulkes says. “It means we can now more confidently predict that mammalian ancestors experienced a prolonged period of evolution in complete darkness.”