An Inconvenient Hagfish

On the importance of intermediates.


We think of scientific progress as working like building blocks constantly being added to a growing structure, but sometimes a scientific discovery can actually lead us to realize that we know less than we thought we did. Take vision, for instance. Vertebrates (animals with backbones) have complex, highly-developed “camera” eyes, which include a lens and an image-forming retina, while our invertebrate evolutionary ancestors had only eye spots, which are comparatively very simple and can only sense changes in light level.

At some point between vertebrates and their invertebrate ancestors, primitive patches of light sensitive cells which served only to alert their owners to day/night cycles and perhaps the passing of dangerous shadows, evolved into an incredibly intricate organ capable of forming clear, sharp images; distinguishing minute movements; and detecting minor shifts in light intensity.

Schematic of how the vertebrate eye is hypothesized to have evolved, by Matticus78

In order for evolutionary biologists to fully understand when and how this massive leap in complexity was made, we need an intermediate stage. Intermediates usually come in the form of transitional fossils; that is, remains of organisms that are early examples of a new lineage, and don’t yet possess all of the features that would later evolve in that group. An intriguing and relatively recent example is Tiktaalik, a creature discovered on Ellesmere Island (Canada) in 2004, which appears to be an ancestor of all terrestrial vertebrates, and which possesses intermediate characteristics between fish and tetrapods (animals with four limbs, the earliest of which still lived in the water), such as wrist joints and primitive lungs. The discovery of this fossil has enabled biologists to see what key innovations allowed vertebrates to move onto land, and to precisely date when it happened.

There are also species which are referred to as “living fossils”, organisms which bear a striking resemblance to their ancient ancestors, and which are believed to have physically changed little since that time. (We’ve actually covered a number of interesting living fossils on this blog, including lungfish, Welwitschia, aardvarks, the platypus, and horseshoe crabs.) In the absence of the right fossil, or in the case of soft body parts that aren’t usually well-preserved in fossils, these species can sometimes answer important questions. While we can’t be certain that an ancient ancestor was similar in every respect to a living fossil, assuming so can be a good starting point until better (and possibly contradictory) evidence comes along.

So where does that leave us with the evolution of eyes? Well, eyes being made of soft tissue, they are rarely well preserved in the fossil record, so this was one case in which looking at a living fossil was both possible and made sense.

Hagfish, which look like a cross between a snake and an eel, sit at the base of the vertebrate family tree (although they are not quite vertebrates themselves), a sort of “proto-vertebrate.” Hagfish are considered to be a living fossil of their ancient, jawless fish ancestors, appearing remarkably similar to those examined from fossils. They also have primitive eyes. Assuming that contemporary hagfishes were representative of their ancient progenitors, this indicated that the first proto-vertebrates did not yet have complex eyes, and gave scientists an earliest possible date for the development of this feature. If proto-vertebrates didn’t have them, but all later, true vertebrates did, then complex eyes were no more than 530 million years old, corresponding to the time of the common ancestor of hagfish and vertebrates. Or so we believed.

The hagfish (ancestors) in question.  Taken from: Gabbott et al. (2016) Proc. R. Soc. B. 283: 20161151

This past summer, a new piece of research was published which upended our assumptions. A detailed electron microscope and spectral analysis of fossilized Mayomyzon (the hagfish ancestor) has indicated the presence of pigment-bearing organelles called melanosomes, which are themselves indicative of a retina. Previously, these melanosomes, which appear in the fossil as dark spots, had been interpreted as either microbes or a decay-resistant material such as cartilage.

This new finding suggests that the simple eyes of living hagfish are not a trait passed down unchanged through the ages, but the result of degeneration over time, perhaps due to their no longer being needed for survival (much like the sense of smell in primates). What’s more, science has now lost its anchor point for the beginning of vertebrate-type eyes. If an organism with pigmented cells and a retina existed 530 million years ago, then these structures must have begun to develop significantly earlier, although until a fossil is discovered that shows an intermediate stage between Mayomyzon and primitive invertebrate eyes, we can only speculate as to how much earlier.

This discovery is intriguing because it shows how new evidence can sometimes remove some of those already-placed building blocks of knowledge, and how something as apparently minor as tiny dark spots on a fossil can cause us to have to reevaluate long-held assumptions.


  • Gabbott et al. (2016) Proc. R. Soc. B. 283: 20161151
  • Lamb et al. (2007) Nature Rev. Neuroscience 8: 960-975

*The image at the top of the page is of Pacific hagfish at 150 m depth, California, Cordell Bank National Marine Sanctuary, taken and placed in the public domain by Linda Snook.

The Cost of Colour

or, the fading world at the tip of your nose.

Sobo_1906_324Try to imagine a colour you’ve never seen. Or a scent you’ve never smelled. Try to picture the mental image produced when a bat uses echolocation, or a dolphin uses electrolocation. It’s nearly impossible to do without referring to a previous experience, or one of our other senses. We tend to tacitly assume that what we perceive of the world is more or less all there is to perceive. It would be closer to the truth to say that what we perceive is what we need to perceive. Humans don’t require the extraordinary sense of smell that wild dogs do in order to get by in the world. But it wasn’t always this way.

Scent molecules are picked up and recognized in our noses by olfactory receptors. Each type of receptor recognizes a few related types of molecules, and each type of receptor is written into our DNA as an olfactory receptor (OR) gene. In mammals, OR genes make up the largest gene family in our genome. There are over a thousand of them. Sadly for us, over 60% of these genes have deteriorated to the point of being nonfunctional. Why? In what must be a hard piece of news for X-Men fans, extra evolutionary features tend not to hang around unless they’re actively helping us to survive longer and breed more. If a gene can develop a fault that makes it useless without causing its host a major competitive disadvantage, it’ll eventually do so, and an incredible number of these broken genes – called “pseudogenes” – have built up and continue to sit in our genome. This isn’t specific to humans; cows, dogs, rats, and mice all have about 20% of their OR genes nonfunctional. But that still works out to a difference of hundreds of different types of scents that we can’t detect. Even compared to our closest relatives, the apes and old world monkeys, we have twice as many OR pseudogenes, and are accumulating random mutations (the cause of pseudogenes) at a rate four times faster than they are. This is all quite logical, of course; humans have evolved in such a way that being able to smell prey or potential mates from a distance just isn’t key to our survival.

Phylo tree image
From: Gilad et al. (2004) PLoS Biology 2(1): 0120

What’s more interesting is that when scientists looked at the OR genes of apes and old world monkeys (OWMs), they found elevated rates of deterioration there, too… about 32%, compared to only 17% in our next closest group of relatives, the new world monkeys (NWMs). So what happened between the divergence of one group of primates and the next that made an acute sense of smell so much less crucial? The answer came with the one exception among the NWMs. The howler monkey, unlike the rest of its cohort, had a degree of OR gene deterioration similar to the apes and OWMs. The two groups had one other thing in common: full trichromatic vision. Nearly all other placental mammals, including the NWMs, are dichromats, or in common parlance, are colourblind. Using molecular methods that look at rates of change in genes over time to determine when a particular shift happened, scientists determined that in both instances of full colour vision evolving, the OR genes began to deteriorate at about the same time. It was an evolutionary trade-off; once our vision improved, our sense of smell lost its crucial role in survival and slowly faded away. In apes and monkeys, this deterioration process seems to have come to a halt – at a certain point, what remains is still necessary for survival – but in humans, it is ongoing. We know this because of the high number of OR genes for which some individuals carry functional copies, and some carry broken copies. This variability in a population, called polymorphism, amounts to a snapshot of genes in the process of decay, since the broken copies are not, presumably, causing premature death or an inability to breed amongst their carriers. So as we continue to pay the evolutionary price for the dazzling array of colours we are able to perceive in the world, our distant descendants may live in an even poorer scentscape than our current, relatively impoverished one. There may be scents we enjoy today that will be as unimaginable to them as the feel of a magnetic field is to us.

As a quick final point, it turns out humans aren’t the only animal group to have undergone a widescale loss of OR genes. Just as full colour vision made those genes unnecessary for us, so moving into the ocean made them unnecessary for marine mammals. In an even more severe deterioration than that seen in humans, some whales and porpoises have nearly 80% OR pseudogenes. As you may already know, whales, dolphins, and other marine mammals evolved from land-dwelling, or terrestrial mammals (want to know more about it? Read my post here). Using methods similar to those mentioned above for primates, researchers found that at about the same time they were adapting anew to life in the ocean, their scent repertoire was beginning to crumble. And since anatomical studies show that the actual physical structures used to perceive scent, such as the olfactory bulb in the brain, are becoming vestigial in whales, it’s likely the loss isn’t finished yet. Interestingly, the researchers behind this study also looked at a couple of semi-marine animals, the sea lion and the sea turtle, which spend part of their time on land, and found that they have a sense of smell comparable to fully terrestrial animals, with no increased gene loss.

The widescale and ongoing loss of the sense of smell in certain animals, particularly ourselves, is a nice illustration of an evolutionary principle which can be summarized as “use it or lose it”, or more accurately, “need it or lose it.” We tend to think of evolution as allowing us to accrue abilities and features that are useful to us. But unless they’re keeping us and our offspring alive, they’re not going to stick around in the long term. Which makes you wonder, with humans’ incredible success in survival and proliferation on this planet, which relies overwhelmingly on our cognitive, rather than physical abilities, what other senses or abilities could we eventually lose?


*The image at the top of the page comes from Sobotta’s Atlas and Text-book of Human Anatomy (1906 edition), now in the public domain.