Cave fish evolution: how they did it in the dark

How long did it take cave fish to optimise to their environment?
01 June 2020

Interview with 

Helena Bilandžija, Ruđer Bošković Institute


A cave arch with light coming through the ceiling on the other side


In some flooded caves, despite the cold, total darkness and paucity of food, some fish species nevertheless thrive. And they’re well adapted to their environment: for instance, they’ve lost their eyes, and their metabolism is very different from non-cave dwellers. So how long did it take these optimisations to appear? As she explains to Chris Smith, Helena Bilandžija wondered the same thing and was very surprised by the results of her study…

Helena - I was always fascinated by how these cave adapted animals ever colonized caves because we consider it as an extreme environment where you've got constant darkness and you don't have a lot of food. And you know, a transition from a surface environment to caves must be a difficult endeavor. And so there is this general model that explains how all of the ancestors of cave dwellers lived on the surface. From there, they entered the caves and through successive generations they acquired a series of these adaptations that allow them to survive in this extreme environment. Many, many different traits: morphological, physiological, there are neuro changes, behavioural changes. However, the surface ancestor who entered the caves didn't have any of these adaptations. And so how did it manage to survive? And so this was something that was always bugging me.

Chris - Over what sort of timescale do we think that the original species adapted to become a cave dwelling equivalent?

Helena - Well, that's the thing. It was always considered that it took millions of years, and in recent years a number of studies came out that suggest how some of these cave dwellers have originated very recently. And the species that we worked with, Astyanax mexicanus, is a wonderful model species because you have both the cave form and the surface form still present. So you can do a direct comparison. And recent studies have dated the cave fish lineage anywhere between 30,000 and 200,000 years ago. So this is a very short timeframe for the evolution of all these different traits.

Chris - And you said it bugged you, that you wanted to know how so many of these changes could be accrued in such a short space of time. So what did you do to find out?

Helena - We took the ancestral form of Astyanax, which is a surface fish, and we exposed them to conditions that we thought these ancestors had when they first entered the caves. And the only environmental cue that is present in all different subterranean habitats is actually darkness. So we took our surface fish and we put them in the dark and asked, how were you able to survive once you were flushed into the caves?

Chris - How long did they have to live in the dark for?

Helena - Our fish were in the dark anywhere between seven months and a couple of years.

Chris - So you've got a group of fish that you keep as controls presumably, and they're just having normal day and night cycle. And then you've got this group of fish, you're simulating cave dwelling, and you've abruptly put them into complete darkness for up to two years. My mind is boggling slightly about how you actually do the experiment. Then how do you keep fish in total darkness and still be a scientist who needs light to see? How did you study them?

Helena - We had a separate room in which we maintained complete darkness and when we needed to study them we would enter with dim red light so that we were able to see.

Chris - So you go into a room, which is like a photographic dark room from the good old days, take a small sample of the fish that have been living in the dark, and then you basically are just asking are these guys any different than the ones that are in the room next door with the normal light cycle.

Helena - Yes.

Chris - And when you do that, how quickly do you start to see changes, if any?

Helena - We started seeing changes already in the first generation of the fish. So we put our surface fish in the dark already a couple of days after they were spawned. And a couple of months later we looked at different traits and already we saw a series of traits being changed just by putting the fish in the dark. Higher fat content, higher starvation resistance, lower metabolic rate, different hormone levels, a series of traits that we didn't expect. And what was really remarkable was that the direction of these changes mimicked the cave fish phenotype.

Chris - The difference between the fish that have evolved over a long period of time in caves is that many of those adaptations are fixed genetically, are they? Whereas your fish change very rapidly to start adopting some of these characteristics, but they can't change their genetic information in such a short time. They must've just changed how they're using their genes.

Helena - Yes, the changes that we saw in the surface fish when you put it in the dark, were basically phenotypic changes and this is called phenotypic plasticity where you have a change in the phenotype without change in the genotype. However, these changes, these adaptations in cave fish are genetically imprinted and there must have been something called genetic assimilation that allowed these phenotypic changes to somehow get imprinted into the genotype of cave fish. And now they are irreversible because when you put cave fish back into the light, you don't get reverse of these phenotypes back to the surface fish. They are fixed in their genomes.

Chris - Why is it a one way street then in the sense that, why is it easier for a non-cave dwelling fish to turn into a cave dwelling fish? But the adaptations can't be so readily undone?

Helena - It's because all these adaptations in cave fish are now genetically determined. There have been mutations in some of the genes that cause, I don't know, the loss of pigmentation or the increase in fat deposition and so on. So now, although there is still some plasticity in cave fish, we have discovered it never goes all the way back to the surface fish phenotype.


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