Peering into the dark to shed new light on evolution

Aparna Agarwal, Kruttika Phalnikar and Deepa Agashe

This article originally appeared in the 2016 edition of IMPRINT, the science magazine of the Dept of Zoology, St. Xavier’s College, Mumbai. The issue focused on life in the dark, and we wrote about evolutionary adaptations to darkness. We thought we would share it with others.

Look into the deepest caves

Or remember the darkest hour you’ve seen

Float in the midnight zones of the sea

Or visit the deepest pits your mind has been…

Humans have a strange connection with darkness. Technically, darkness is just the absence of light; yet our language is strewn with examples of how we both fear and are fascinated by the dark at the same time. The parts of the universe that cannot be observed are composed of dark matter. The devil lurks in the dark, while heaven is the light at the end of a tunnel. What we do not understand are the dark arts, while discovering the truth brings facts to light. This obsession with the dark is not unreasonable. As humans – just like many other animals – we rely heavily on our visual system for information about the world we live in. However, many animals have moved away from such a visual bias, and understanding the evolutionary processes that drive this change has enriched our understanding of evolution itself. In the next page or two, we will highlight some of these patterns that dark-adapted organisms have revealed.

Darkness comes in many shapes and sizes, caves (or underground tunnels) representing just one example where physical obstacles allow very little or no light to penetrate. But darkness also shows up in the deep oceans, where sunlight is reflected and/or gets absorbed by the upper layers of the water column. This results in virtually no light reaching the lower parts of the ocean, which we call the “midnight zone”. Just as darkness takes many forms, so do the species that occupy it. Regardless, dark environments tend to enforce similar selection on organisms, and as they adapt to these pressures, they develop characters that are also very similar to each other. Evolutionary biologists call this phenomenon “convergent evolution”.

It’s a blind world out there

One of the most striking examples of convergent evolution in animals living in the dark is the recurrent loss of vision. Think about the Texas blind salamander, or the toothless blind cat in North America (which, incidentally is a fish). Or think about the phrase “blind as a bat”. Darwin thought that this was an example of Lamarckian adaptation. It sounds about right. Lamarck had proposed that continued use of a body part will strengthen it over time, and the strengthened part would be passed on to the next generation. On the other hand, parts that are not used will become weak and eventually regress. Since organisms that live in the dark do not use their eyes, the eyes degenerate and thus you have eyeless individuals. Unfortunately, just because something sounds right doesn’t make it so. What Darwin and Lamarck didn’t know – but we do – is that the key players involved in inheritance are stretches of DNA that we call genes. Genes are passed on to offspring through special cells called gametes, which are typically not modified by environmental stresses faced by the organism. Most of the changes that happen during an organisms’ lifetime affect non-gametic cells, called somatic cells. For instance, our skin cells acquire mutations – changes in the DNA sequence – after continuous exposure to UV radiation from the sun, but our gametes (housed in our reproductive system) are not affected. The key fact here is that somatic cells (e.g. cells from our eyes) do not get transferred to the next generation, so changes to these cells are not inherited by the offspring. Hence, although it is true that early cave colonizers would not have used their eyes, this fact alone is not sufficient to explain why subsequent generations of troglobionts lost their eyes.

How, then, do we account for the recurrent loss of eyes in organisms that live in the dark? Well, there are a few theories that might explain the convergence. One theory is that since troglobionts’ fitness is not affected by the presence or absence of functional eyes, the species accumulate mutations over generations. Typically, most mutations in genes encoding important functions (such as vision) are deleterious, i.e. they reduce the organism’s ability to survive or reproduce. Since organisms carrying such mutations would be less likely to pass on their genes, these mutations would eventually be lost from the population. However, in an environment such as a cave, mutations in genes that are essential to make functional eyes might be “tolerated”, being effectively neutral in terms of their impact on fitness. It’s how you would be much more tolerant of your cousin if he spilled coffee on an old shirt you don’t wear anyway, instead of one you absolutely love. So this is the proposition: due to relaxed selection on eyes, troglobionts accumulate neutral mutations that don’t affect their fitness, but that ultimately result in the degeneration of the eyes.

On the other hand, the loss of eyes might actually be beneficial for troglobionts; for instance, if they save energy that is normally spent on developing and maintaining functional eyes. If these cost savings are substantial, individuals carrying mutations that reduce eye function might produce more offspring, eventually replacing sighted individuals. However, to date there is no evidence for immediate benefits of eye loss, and it is unclear where there is indeed direct selection favouring the loss of eyes in these habitats.

Recent studies do suggest, however, that there might be indirect selection favouring the loss of eyes in troglobionts. To understand how that might work, let us think about the abundance of taste buds in Slovenian cave salamanders (Proteus anguinus) or in the cave fish Mexican tetra (Astyanax mexicanus). An interesting fact is that the development of taste buds is encoded by the same genes that code for eye development. For instance, a gene called hedgehog is involved in many developmental processes including eyes and taste buds; such genes encoding multiple functions are called a “pleiotropic genes”. Why does that matter? The reason it matters is that mutations in these genes are responsible for an increase in the number of taste buds. In a dark environment, these mutations might be favored because they could increase the animal’s sensitivity to chemical cues in the environment, making it easier to find food or mates or avoid predators. However, those same mutations would probably also affect eye development, and hence we could end up with organisms that have defective eyes (the “hedgehog hypothesis”). Repeat this process for many generations, and you end up with fish that have flaps over their eyes and everyone calls them ‘wrecks of evolution’, even though they were just adapting to their environment by enhancing their sense of taste.

Apart from a convergent increase in the number of taste buds, cave animals have also repeatedly evolved a slower metabolic rate, increased jaw size, loss of pigmentation, and elongated limbs. Genes involved in eye development also encode many of these traits, and thus, pleiotropy might often underlie these beautiful examples of evolutionary convergence.

No free lunch

Another common feature of dark environments is that almost everything is in short supply – even something as basic as food. You know the one thing that you don’t get in a dark, desolate cave? Pizza deliveries. They just refuse to deliver there. You also don’t get many other options, especially if you are vegetarian. Plants cannot grow in the dark because they don’t get enough sunlight. Therefore, if you are stuck in a cave, all you are left with is water seeping through the crevices which brings in plant material from the outside. Or if you are lucky, you get bits of dead animals. Otherwise, you have to rely on bat poop (guano), which is probably not so tasty. This poses a serious survival challenge for organisms living in the dark. To combat this, they often turn to our trusty little friends – no, not dogs – microbes. There are many microorganisms (called chemo-autotrophs) that can synthesize carbohydrates in the absence of light. Instead of sunlight, they use chemicals such as minerals in the caves (or sulfur if they are near sulfur vents), acting as primary producers. Growing in large numbers, they can produce biofilms, which are then eaten by the other organisms in that habitat. Thus, the food webs in dark habitats are often simpler and rather different from what we are used to seeing out in bright sunlight.

Bacteria not only serve as food; but they can also help find food in the deep oceans. For example, the angler fish female traps bioluminescent bacteria in a beacon-like organ that hangs in front of and above her mouth. In the dark ocean, the prey sees is attracted to the beacon, and unwittingly swims into the wide-open mouth of the fish. These fish also have a distensible jaw and stomach, which allows them to eat very large prey. After all, if you do not know when your next meal is going to be, you better gobble whatever floats in. In fact, this strategy is common among dark-adapted predators: when uncertainty looms over the prospect of your next meal, you make sure you eat your fill when you find food. Thus, many dark-adapted animals have large jaws and distensible stomachs, which allow them to engulf prey that are (sometimes) even larger than they are. For instance, it is estimated that the black swallower fish can swallow prey up to four times its own size.

Funny business in the dark

Ironically, darkness also makes the sex lives of these creatures quite difficult. Pizza deliveries aside, another thing that you don’t find easily in these dark and in sparsely populated spaces places is a member of the opposite sex, especially when the space is as vast as an ocean. So when you do find one, you make sure you stick with them. Literally, just stick to them. That’s what the male angler fish do. When they find a female they bite into her body and secrete enzymes that fuse their jaws to the female body; over time their circulatory systems get linked. From that point onwards, the female sustains the male. This reduces the male to just a pair of gonads. Again, literally. After fusing with the female, the male loses his eyes, gut and other organs and just acts as a mobile sperm bank.

In contrast, the deep-sea squid Octopotheuthis deletron uses a different strategy to deal with the low mate-finding probability. It uses its prehensile penis to indiscriminately glue sticky packets of sperm (known as spermatangia) onto any member of its species that it encounters, regardless of whether it’s a male or a female. Some spermatangia might land on a female, and then a few lucky sperm might just get to fertilize the female’s eggs when she deposits them in the water.

In caves, the problem is not as severe since the relatively smaller space means that there is a higher probability of finding a mate. In fact, there is even evidence for mate choice in some species. For instance, Atlantic cave mollies (fishes) retain their ancestral preferences of mating with large bodied individuals. While their surface dwelling ancestors used visual cues to choose larger mates, the cave dwelling ones rely on non-visual cues to identify larger mates in the dark.

Death visits the dark but rarely

Typically, dark habitats are dreary places with low oxygen, food and mates. Survival in this bleakness has thus required the evolution of drastically reduced rates of metabolism and extreme resistance to starvation. Yet, these environments are home to many species blessed with a freakishly long lifespan. ​The cave salamander holds the record for the longest living amphibian, with individuals living over 100 years (and counting). On deep ocean floors, the tubeworm Lamellibrachia luymesi lives for as long as 250 years. Closer home, naked mole rats that live in underground tunnels have lifespans exceeding 30 years: the longest living rodents. What makes them even more fascinating is that unlike humans, their mortality does not change with age and they reproduce successfully right until they die.

How do these species live so long, with few signs of ageing? Not surprisingly, naked mole rats are a favourite model species to understand the biology of longevity. Scientists speculate that their long lifespan could be a product of the same characteristics that allow them to colonize the dark habitats – slow metabolism and extreme resistance to starvation. In addition, the scarcity of resources, low population densities and simple food webs in these environments might reduce competition and predation, both of which are major causes of mortality outside. Life might not be so bad for these creatures after all.

 We have showcased some of the bizarre, crazy, and “regressive” adaptations found in the creatures of the dark. However, to use a cliché, if there is any rule in biology, it is that there are exceptions to every pattern. The loss of eyes is one end of the spectrum, but darkness also houses creatures with extraordinary sensitivity to light, enormous eyes, and other unique adaptations to utilize every photon that filters in. We have shown you a glimpse of the fascinating world that lies just out of our sight, and yet there is so much more that we could not get to. We did not talk about colossal squids with plate-sized pupils. Nor did we mention the octopi that incubate their eggs for four years. The fact is, we talked about altered food webs, and yet we know very little of the ecological dynamics in these environments. Biologists have barely begun to understand organisms in dark habitats, and there is plenty more novelty to explore. In this era of searching for life in space, we still have very little idea of what inhabits the dark corners of our own planet.

If this article has piqued your curiosity about dark dwellers and the biology behind, here are few places where you can find more details.

  1. Rétaux, Sylvie, and Didier Casane. “Evolution of eye development in the darkness of caves: adaptation, drift, or both.” EvoDevo 4.1 (2013): 26.
  1. Tebo, Bradley M., et al. “Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica.” Frontiers in microbiology 6 (2015).
  1. Niven, Jeremy E. “Evolution: convergent eye losses in fishy circumstances.” Current Biology 18.1 (2008): R27-R29.
  1. Simon, K. S., E. F. Benfield, and S. A. Macko. “Food web structure and the role of epilithic biofilms in cave streams.” Ecology 84.9 (2003): 2395-2406.
  1. Paoletti, Maurizio G., et al. “A New foodweb based on microbes in calcitic caves: The Cansiliella (Beetles) case in Northern Italy.” International Journal of Speleology 40.1 (2011): 6.
  1. Hoving, Hendrik JT, Stephanie L. Bush, and Bruce H. Robison. “A shot in the dark: same-sex sexual behaviour in a deep-sea squid.” Biology letters (2011): rsbl20110680.
  1. Pipan, Tanja, and David C. Culver. “Convergence and divergence in the subterranean realm: a reassessment.” Biological Journal of the Linnean Society 107.1 (2012): 1-14.
  1. Regan, Charles Tate, and Ethelwynn Trewavas. “Deep-sea angler-fishes (Ceratioidea).” (1932).
  1. O’Connor, Timothy P., et al. “Prolonged longevity in naked mole-rats: age-related changes in metabolism, body composition and gastrointestinal function.” Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 133.3 (2002): 835-842.
  1. Plath, Martin, et al. “Sexual selection in darkness? Female mating preferences in surface-and cave-dwelling Atlantic mollies, Poecilia mexicana (Poeciliidae, Teleostei).” Behavioral Ecology and Sociobiology 55.6 (2004): 596-601.
  1. Bergquist, Derk C., Frederick M. Williams, and Charles R. Fisher. “Longevity record for deep-sea invertebrate.” Nature6769 (2000) Bergquist, Derk C., Frederick M. Williams, and Charles R. Fisher. “Longevity record for deep-sea invertebrate.” Nature 403.6769 (2000): 499-500.

One thought on “Peering into the dark to shed new light on evolution

Add yours

  1. Excellent write up .Thought provoking and informative .What about darkness in the outer space or universe ? Life evolved from hydrogen and carbon available in abundance .

Leave a note

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

Create a website or blog at

Up ↑