Claw gene remnants point to legs in snake ancestors

Nonfunctional remnants of genes (pseudogenes) can often provide evidence of the evolutionary history of life. I once wondered if snakes have any pseudogenes that pointed to a time when they once had legs, a conclusion suggested by comparative genetics and the fossil record. but I had trouble imagining what kinds of genes would provide a record of this hypothetical history. After all, there aren’t ‘leg’ genes or ‘arm’ genes, as the genes involved in making limbs participate in the development of a number of body structures.

However, I was excited to learn that there are indeed some genes that appear to be specific to a portion of the limbs: the claws. These genes, known as keratins, seemed like good candidates for investigation, and led to me to study the evolutionary history of snakes. But first, let me share a few details about keratins to give you some context

Keratins are known as structural proteins, meaning they form physical structures that are often visible to the naked eye. Though proteins are involved a wide variety of functions, ranging from vision to carrying oxygen to tissues throughout your body, most do not clump together in large enough quantities to be visible to the naked eye. Keratins, on the other hand, are often quite visible, and include things as different as hair, nails, feathers, porcupine quills and rhino horns.

Claws are also made of keratin, just like your nails, and a pair of studies found that at least two of these keratins appear to be localized almost entirely in the claws of lizards [1,2].

In addition to showing that these keratin genes, HA1 and HA2, are turned on in the fingers and toes of lizards, and staining techniques demonstrated that HA1 is produced at the base of lizard claws, the researchers showed that the HA1 gene is present and intact in every lizard that they looked at, except for one. The exception? A legless, and therefore clawless, lizard, known as the slow worm [3]. They didn’t find the gene completely absent in this animal, however, but present in the genome with two mutations that lead to a nonfunctional keratin. This points to a time when legless lizards and limbs and claws, consistent with studies of DNA and developmental biology.

Furthermore, they tried to look for the gene in snakes, but to no avail. I, on the other hand, benefit from working in the world of genomics. Since this initial paper was published, multiple snake genomes have been sequenced and assembled, so I made an effort to look for both claw keratin genes, HA1 and HA2, in eight species of snakes.

Whereas I could not find HA2 in the snakes, no matter how hard I looked, I found a degraded portion of HA1 in the genomes of six of the snake species [4]. What was perhaps even more exciting, is that all of these species, which included species as different as a python, vipers, rattlesnakes, and a cobra, all shared the exact same disabling mutation: an eight letter (base pair) insertion in the first portion of the gene. This suggests that these snakes share a common ancestor that once possessed a functional claw keratin gene, along with claws, digits and limbs.

This provides another exciting example where DNA and fossils tell the same story: one where a group of lizards evolved into the legless snakes that we love (or loathe) today.

Question for Creationists

Why would the Creator create a broken claw keratin gene in legless snakes and a legless lizard? Wouldn’t it make more sense to simply create them without a broken gene? If these animals evolved from ancestors with claws and legs after the flood, why and how did they lose their legs so quickly? Why do they all share the same mutation, even though they are different ‘kinds’? Is it just a coincidence that snakes have remnants of a claw gene, show DNA evidence of descending from legged lizards and also have fossil evidence of formerly possessing legs?


1. Eckhart, L., Dalla Valle, L., Jaeger, K., Ballaun, C., Szabo, S., Nardi, A., … & Tschachler, E. (2008). Identification of reptilian genes encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair. Proceedings of the National Academy of Sciences, 105(47), 18419-18423.

2. Alibardi, L., Jaeger, K., Valle, L. D., & Eckhart, L. (2011). Ultrastructural localization of hair keratin homologs in the claw of the lizard Anolis carolinensis. Journal of morphology, 272(3), 363-370.

3. Dalla Valle, L., Benato, F., Rossi, C., Alibardi, L., Tschachler, E., & Eckhart, L. (2011). Deleterious mutations of a claw keratin in multiple taxa of reptiles. Journal of molecular evolution, 72(3), 265-273.

4. Emerling, C. A. (2017). Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes. Molecular phylogenetics and evolution, 115, 40-49.

2 thoughts on “Claw gene remnants point to legs in snake ancestors

  1. God did not create without. Reference in Genesis where God curses the snake.
    Genesis 3:14
    The Lord God said to the serpent,
    “Because you have done this,
    cursed are you above all livestock
    and above all beasts of the field;
    on your belly you shall go,
    and dust you shall eat
    all the days of your life.

    1. Hi rdlafleur: thanks for your comment!

      It is an interesting connection, but it’s also a bit confounding from both a religious and biological perspective.

      So in this instance, the Lord God curses a single serpent. I suppose I agree with you that the implication is that maybe it had legs before, but at the same time, it doesn’t explicitly mention this. Being on its belly presumably is implying this, but… well, I suppose it could have been more explicit about legs being lost! A lot of lizards spending a lot of time on their bellies, and certainly “eat” the dust of a lot of other animals (in a metaphorical sense). Certainly snakes don’t literally eat dust, so perhaps this was more of a poetic comment.

      But let’s discuss the religious side of things. I believe that most Christians, and possibly Jews (?), equate this serpent with Satan. So, if true, does that not mean that God was just cursing Satan? Not snakes as a whole? And if He was cursing snakes as a whole, why would He? The snakes aren’t responsible for what Satan did! If it’s not Satan, then we have a whole other question about how this snake is able to speak…

      But let’s ignore all of these theological bits and focus on your thought that perhaps God took the snake, cursed it to lose its legs, and that is why snakes don’t have legs.

      Question 1: does this apply to all snakes? Or just this particular snake? It doesn’t say anything about all snakes, but perhaps somehow we can read it that way?

      Question 2: if it applies to all snakes, why did all the snakes that I looked at in my research have that exact same mutation? Perhaps God thought it was effective, so what the heck, why not? Couldn’t He have just deleted the gene altogether?

      Question 3: perhaps, this was the ancestor to all snakes, so maybe it was cursed and received this mutation that breaks its claw gene. This then means that all other snakes received this mutation because they descended from this initial cursed ancestor. But then doesn’t that imply that thousands of snakes evolved from this single ancestor in simply 6,000–10,000 years? (depending on your dating scheme) Pythons, rattlesnakes and cobras, while all snakes, have very distinct anatomy, physiology, behavior, etc. so that’s an awful lot of evolution in such a very short time! Evolutionary biologists don’t even think such a thing is possible (I certainly don’t!).

      Question 4: How does this relate to the other “legless lizards”? There’s evidence that many lizards independently lost their legs, using genetics, developmental biology and anatomy. Did God curse them too?

      So while this particular passage in Genesis seems to (maybe) imply that snakes formerly had legs and then lost them, if true, it raises a whole lot of questions both theological and biologically that seem quite difficult to answer!

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