How Snakes Lost Their Legs

A Chinese riddle invites on to guess the identity of runners without a leg, swimmers without a flipper, gliders without a wing. The answer, of course, is snakes. Today more than 3,000 species share a long, limbless body that can negotiate land, water and even the air between trees. Their ancient ancestors, however, had limbs of various shapes. How, scientists have wondered, did snakes lose their legs?

Special forms of appendages are often tied to certain habitats. Whales evolved flippers as adaptations to the aquatic realm. Birds evolved wings as they transitioned to life in the air. But for decades evolutionary biologists have struggled to ascertain what kind of environment helped to forge the distinctive body plan of snakes, in part because today's snakes are so widespread and because the fossil record of early snakes is sparse. Debate has centered on two competing hypotheses. One holds that snakes lost their legs on land while adapting to subterranean environments; the other posits that snakes evolved their telltale traits in the sea. Both these settings favor a streamlined body.

If only we could travel back in time to the Cretaceous period, between 145 million and 66 million years ago, when snakes got their start. Then we could observe ancestral snakes in their actual habitats and see whether they excelled at burrowing or swimming. In reality, we have only their fossilized remains to go on, and it can be difficult to reconstruct the ecology of an animal and how it behaved based on its bones alone, particularly when they are damaged or fragmentary, as fossils often are.

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Over the past 10 years, however, advances in imaging technology have enabled scientists to break through previous limits in understanding snake origins. High-energy x-ray imaging of fossil skulls has revealed hidden features that hint at the ecology of ancient snakes. Meanwhile studies of developmental biology have elucidated the genetic mechanisms underlying the loss of limbs, as well as the gain of vertebrae.

Our knowledge is far from complete. But these insights are at last allowing scientists to start piecing together the long-standing puzzle of how snakes underwent their extraordinary evolutionary transformation.

Evolutionary Experiments

Snakes did not lose functional limbs in one fell swoop. The fossil record indicates that the first snake with no legs, Dinilysia patagonica, emerged about 85 million years ago during the Late Cretaceous period, when dinosaurs reigned supreme. Researchers recovered the remarkably well-preserved remains of Dinilysia from rust-colored sandstones on the Patagonia plateau. The almost complete skeleton of this animal, which was about as long as a human adult, shows that not only did it not have legs, but it also lacked the shoulder or pelvic girdles to support such appendages. Because the fossil was found in terrestrial sedimentary deposits, we know it lived on land.

Yet other snakes from this time period retained legs. Najash rionegrina, a roughly 92-million-year-old terrestrial snake from Argentina that was only as long as a strand of spaghetti, possessed a pair of tiny hind limbs composed of bony elements from the hip to the ankle. Najash's limbs were far too small and delicate to bear the animal's weight. Instead they may have functioned as claspers during mating.

Other Late Cretaceous snakes with legs lived in the ocean. Fossils from marine deposits near what is now Jerusalem reveal sea snakes that swam among sharks. Two such creatures, Pachyrhachis and Haasiophis, display almost complete hind limbs made up of bones from the thigh, shin and foot. The function of these legs remains unclear. Both Pachyrhachis and Haasiophis lack a pelvic girdle to attach the leg to the trunk of the body, so their legs would have been of little use for swimming.

All told, these fossils indicate that by the Late Cretaceous snake evolution was already well under way. The long, sinuous body with highly reduced limbs was established, and snakes were undergoing an adaptive radiation, rapidly diversifying into a multitude of forms that could exploit a variety of ecological niches. To probe the origin of the snake's characteristic body plan, then, scientists need to look to even older fossils.

Until recently, researchers had few snake fossils predating the Late Cretaceous to study. But over the past five years several new candidates from the Early Cretaceous and the even earlier Jurassic period have come to light. The remains, which hail from terrestrial deposits in Europe and the U.S., are quite fragmentary and do not reveal much about the body proportions of these animals. If they are in fact snakes, however, these specimens would extend the fossil record of this group by another 70 million years and show that the oldest known members were small and lived on land, not in the sea.

Still, the mounting fossil evidence pointing to a terrestrial origin for snakes did not address the question of why they evolved a streamlined body. A subterranean way of life would benefit from limb reduction. Modern burrowing snakes and lizards simply push their head through soft earth to tunnel underground—legs would only get in the way. But establishing that any given fossil snake actually did burrow underground is tricky. The Jurassic and Early Cretaceous fossils are too scrappy to even guess their behavior. Najash might have been a burrower, judging from its short tail, which resembles those of living snakes that burrow. For its part, Dinilysia, the earliest known snake to lack legs altogether, was much larger than modern burrowing reptiles. Could it have burrowed anyway? I decided to find out.

Clues in the Ear

On Christmas Day 2014, I flew from Buenos Aires to New York City, carrying skulls of Dinilysia with me in a shoebox. It had taken almost a year for my Argentine colleagues and me to prepare the paperwork needed to borrow the specimens for computed tomographic scanning in the U.S.—all so that we could study the animal's ear.

Why the ear? Working with Mark A. Norell at the American Museum of Natural History, I had developed a method to distinguish modern burrowing snakes from marine species based on that anatomical region, and we wanted to try it on Dinilysia.

Using a state-of-the-art imaging technique, we had obtained high-resolution x-ray images of the skulls of dozens of modern-day snakes and lizards. We then stacked these images to create three-dimensional virtual models of their inner ears. We focused on a structure called the vestibule, which holds lymphatic fluid and the so-called ear stones that aid in sensing gravity and movement.

Statistical shape analyses of the virtual models revealed significant differences in the vestibules of burrowing specialists, terrestrial generalists and aquatic forms. In marine snakes and lizards, the vestibule has shrunk to nearly nothing. In burrowers, however—particularly those that do their own digging, as opposed to taking another animal's burrow for shelter—the vestibule has blown up like a balloon, enabling better hearing underground. This trend holds true regardless of the size and limb structure of the burrower: we observed vestibular expansion in a three-foot sand boa and a 10-inch Asian pipe snake, as well as in the bizarre burrowing lizard Bipes, which has a pair of front limbs but no hind limbs.

I had reason to suspect that Dinilysia would align with the burrowers: a study published in 2012 presented an x-ray image of its skull, in which a large vestibule was visible. But no one knew what the vestibule looked like in three dimensions. I was confident that subjecting the fossil to our method would settle the question of this ancient snake's locomotor behavior.

Our study confirmed that Dinilysia's vestibule is indeed large, with the same balloonlike shape seen in today's burrowers. In fact, it is nearly indistinguishable from that of the modern sunbeam snake, a large burrower from Southeast Asia that eats mainly small rodents and smaller snakes. Our model predicted Dinilysia to be a burrower with nearly 95 percent probability. We speculate that it lived much like the sunbeam snake, hunting on the ground surface and digging into loose soil for shelter.

When mapped onto an evolutionary tree, these findings illuminate the role of habitat shift in the transition from lizard to snakes. Dinilysia was not among the first lineages to split off from lizards. Instead it is closely related to the ancestor of today's snakes—more advanced than Najash, with its functional hind limbs, but more ancestral than modern species. The revelation that Dinilysia was a burrower strengthens the hypothesis that the lineages leading to modern snakes lost their limbs while adapting to life underground.

The fact that burrowing, rather than swimming, became the predominant modus operandi in the ancestors of present-day snakes does not imply that in the Cretaceous, a group of lizards decided to live underground and gradually lost their limbs to become snakes. Rather evolution works in a stochastic fashion. Going subterranean was one of many influential events that took place in the millions of years over which the unique body plan of snakes took shape. This new way of life probably lifted certain constraints on the genomes of primitive snakes that had previously been essential for survival. Freed from these limitations, the limbs and trunk could change. Hence, a wide array of limb types and body lengths is evident in the fossil record of snakes.

Stretch the Body

Whole-genome sequencing and experimental gene editing of modern snakes have further enhanced scientists' understanding of snake evolution. All vertebrate species share a great number of genes. The dramatic differences in the body plans of creatures ranging from birds to fish actually stem from mutations in just a small portion of the genome. In theory, the evolution of the snake's long, limbless body from a lizard's short, sprawling form may have involved changes in just a handful of key regions of the genome.

A closer look at the embryonic development of vertebrates hints at the steps needed to evolve one of the snake's hallmark traits: its long spinal column, which is made up of more than 300 vertebrae compared with 33 in humans and 65 in a typical lizard. The head and trunk of limbed vertebrates form from blocks of cells called somites. Each somite gives rise to one vertebra. Somites initially appear similar, then differentiate to create the neck, chest, waist, hip and tail regions of the spine.

A gene whimsically dubbed Lunatic Fringe helps to increase the number of vertebrae in snakes. It works with other so-called somite-generating genes to create clusters of cells at the tail end of the embryo. Once a certain number of cells accumulate, a somite forms and moves up the body, like a bead on a string. Together the somite-generating genes are known as the somitogenesis clock because they turn on and off at regular intervals to make the somites. The faster the clock ticks, the more somites are produced from the same number of cells. Céline Gomez, now at the Wellcome Trust Sanger Institute in England, and her colleagues showed that the Lunatic Fringe gene is expressed more frequently in corn snakes, whose somitogenesis clock ticks far faster than that of lizards.

The vertebrae are not the only bones that have gone wild in snakes. The ribs have, too. Consider the mouse and alligator, for example. In these creatures, only the chest (thoracic) vertebrae bear ribs. No ribs attach to the neck (cervical) and waist (lumbar) vertebrae because a gene called Hox10 suppresses rib formation in these regions. In snakes, however, all the vertebrae except for the first three closest to the head and those in the tail bear ribs.

Researchers have long assumed that the mouse and alligator are good models for what the trunk skeleton of ancestral limbed animals looked like, with neck and waist vertebrae that are distinct from the chest vertebrae. The conventional wisdom was that snakes evolved their homogenized vertebral column from that ancestral form, a specialization possibly associated with limb loss. Scientists suspected that the Hox genes that typically govern the differentiation of vertebrae in other animals had somehow gotten disrupted in snakes.

A recent fossil analysis points to a different scenario. In 2015 Jason J. Head, then at the University of Nebraska–Lincoln, and P. David Polly of Indiana University Bloomington modeled the evolution of the trunk skeleton in four-limbed animals, also known as tetrapods. First, they predicted statistically that snakes actually have just as many distinct regions in the vertebral column as lizards do. The snake's Hox genes may simply be directing subtler changes in shape to the various types of vertebrae. Second, the researchers determined that contrary to the conventional wisdom, ancestral tetrapods actually had ribs associated with most of the vertebrae above the hip. Fossils of ancient relatives of mammals and alligators exhibit ribs attached to vertebrae of the neck and waist. Thus, the absence or reduction of ribs in these regions in modern alligators, birds and mammals evolved independently rather than being inherited from their ancient common ancestor.

Looking at fossils and recent species together has revealed which aspect of the trunk skeleton snakes inherited from their limbed ancestors (the rib distribution) and which is truly unique (the extremely elongate body).

Ditch the Legs

Recently scientists have made new inroads into understanding the genetic mechanisms underlying limb loss. In 2016 Evgeny Z. Kvon of Lawrence Berkeley National Laboratory and his colleagues reported that they had identified a genetic “switch” for limb development in the snake and mouse. In their study, the researchers stitched a piece of a snake gene into the genome of a lab mouse. What emerged from the experiment was a science-fiction animal: a “serpentized” mouse, which had a normal mouse body and truncated limbs.

The snake gene in the serpentized mouse consists of a DNA segment referred to as the ZRS regulatory sequence. Active ZRS is critical for normal hind-limb formation in a mouse, yet it takes only a single mutation in this gene to cause limb abnormality. Because it is so important for survival, the ZRS regulatory sequence has remained mostly unchanged over the course of tetrapod evolution, but it is highly variable in snakes.

The ZRS variants found in snakes are consistent with the morphological diversity of their limb development. Primitive modern snakes, including the python and boa, retain a ZRS limb-enhancer sequence, albeit one that is shorter than that in other limbed vertebrates. Correspondingly, both species possess rudimentary, spurlike hind limbs. In contrast, advanced serpents such as the corn snake have lost the ZRS segment entirely and have no limb bones whatsoever.

Finding genetic variants that align with variations in limb development provides new understanding of fossil snakes. Najash preserves a pelvic girdle, femur, truncated tibia and fibula, but no toe bones. Pachyrhachis lacks toes, too. Najash and Pachyrhachis indicate that in the transition from lizard to snake, limb-specific regulatory genes were modified yet still functional in several ancestral snakes. For its part, Dinilysia had no limb bones or pelvic girdle at all, which marks the first complete loss of function in the evolution of a snake limb-enhancer sequence.

In the last chapter of the dinosaur era—the Late Cretaceous—snakes underwent dramatic change in their body plan and perhaps rapid evolution in their genome. We have only just begun to probe the genetic basis of the traits seen in the fossil record. Haasiophis had no pelvic girdle, but it did possess a complete femur and well-developed tibia and fibula, along with anklebones and foot bones. No living snake exhibits such an arrangement, but its existence in the fossil record hints at the interplay of multiple limb-regulatory sequences similar to the ZRS in the ancient past.

Missing Links

New clues to the origins of snakes continue to surface. In 2015 researchers led by David M. Martill of the University of Portsmouth in England announced their discovery of a 120-million-year-old four-legged snake from Brazil. Tetrapodophis amplectus had four complete limbs preserving digits and toes. The limbs would have been strong enough to function as claspers during mating. Though shorter than a chopstick from head to tail, this animal has more than 200 vertebrae. The creature's long trunk and short tail suggest it was a burrower, supporting the hypothesis that snakes originated on land. Given its geologic age, ecology and the state of its legs, Tetrapodophis seems to have all the characteristics paleontologists have been searching for in their quest for transitional snakes.

But at a meeting of the Society of Vertebrate Paleontology in Salt Lake City, Utah, in 2016, some researchers questioned the discovery team's description of the fossil. These critics suggested that Tetrapodophis is not a snake but rather a marine lizard. The specimen could rekindle the debate over whether snakes originated on land or in the sea. At that same meeting, however, a group of scientists reported that the private owner of Tetrapodophis removed it from the public museum where the fossils were housed, violating the convention that all named species, fossil or extant, should be available to other researchers and the public for further study. The debate over Tetrapodophis ground to a halt as a result.

Tetrapodophis aside, scientists are currently investigating unsolved mysteries of snake evolution. We are eager to determine, for instance, whether snakes first appeared on the northern continents or in the south and whether the founding members of this group were nocturnal or diurnal. We also want to know how snakes evolved jaws large enough to swallow prey larger than their head and how they acquired venom.

Answers to these questions will enhance an already riveting tale. Popular cultures and religions have offered up all manner of stories to explain how certain parts of the body can be lost or otherwise transformed. The biblical account of snakes holds that God cursed the serpent to crawl on its belly for leading Adam and Eve to eat the apple in the Garden of Eden. In Chinese legend, the heavenly Jade Emperor punished the snake for hurting humans by ordering its legs to be cut off and given to the frog. But as the fossil and genetic evidence from snakes underscores, natural selection is not goal-oriented. Evolutionary novelties do not originate by design. They emerge from never-ending interactions between animals and their world.