In snake genes, study finds they evolved 3x faster than other reptiles

The sci-fi writer David Brin built his fictitious ‘Uplift Universe’ in a series of novels for two decades from 1980. In the series, a patron race uplifts species of a future universe to a higher order of life.

Something similar happened in the earth’s distant past when many species went through bursts of evolutionary innovation, taking giant leaps and incorporating extraordinary diversity in their population, while others were left behind.

Unexplained bursts of change

The question of how some species become capable of taking these quantum leaps has been an enduring mystery in evolutionary biology.

The popular Darwinian theory of evolution states that all organisms evolve through the process of natural selection. In other words, organisms inherit small changes over many generations and these changes collectively enhance the organism’s ability to compete, survive, and reproduce. However, the earth’s fossil records tell a more complex, in fact different story: in addition to a constant rate of transformation, organisms also evolved at different speeds and through varying degrees of complexity.

Our planet’s evolutionary history is dotted with numerous instances of such unexplained bursts of evolutionary changes, leading to the emergence of new species or the extinction of old ones.

A tree of snakes and lizards

One such evolutionary explosion happened about 100-150 million years ago, when dinosaurs roamed the planet’s surface. An extraordinary evolutionary transformation happened at this time: the nondescript lizards lost their legs to become one of the most highly adapted predators in history, capturing almost every environmental niche on the planet. We know them today as snakes.

Through a series of remarkable adaptations, snakes acquired legless bodies that could slither across diverse terrains, developed complex chemical sensory systems to track prey, incorporated flexible jaws to swallow large animals, and evolved an assortment of attack mechanisms, including the production of lethal venoms.

In a study published on February 22 in the journal Science, an international team of scientists, led by researchers at the University of Michigan, worked together to unravel the genetic sequence of more than 1,018 snake and lizard species. The result was the largest and most comprehensive evolutionary tree of snakes and lizards. They analysed the genetic sequence data together with previous studies, and revealed that snakes have been evolving much faster than their reptilian cousins.

Specifically, the team estimated snakes evolved almost three-times faster than lizards and other reptiles, allowing them to take advantage of the new environmental niches that rapidly emerged after the extinction of the dinosaurs. 

A clock in the body’s molecules

DNA and protein sequences evolve at a relatively constant rate over time, irrespective of the organism. This allows scientists to use genetic differences between two species to estimate the time that has passed since these species last shared a common ancestor. This is then used to calculate the relative pace of evolution of the organism. In a way, genetic sequences serve as a molecular clock using which scientists can determine the ‘evolutionary distances’ between various organisms.

Along with snakes, many lizards also adapted to these rapid changes and developed snake-like traits, including losing their limbs and elongating their bodies. The Australian scincid lizard (Lerista), a member of the clade Squamata (which includes lizards and snakes), provides perhaps the best example of such evolution.

Lerista comprises more than 75 closely related species that display a wide variety of digit (finger) layout: from five digits to being entirely limbless. Such extraordinary malleability of limb-count in this lizard is the result of at least 10 independent evolutionary limb-reduction events over a few million years.

But while the lizards made desperate attempts to evolve, snakes easily outpaced them, leading to a burst of diversification. Researchers have attributed this surge to a phenomenon they call the “singularity of snakes”. This is akin to the Big Bang theory of cosmology, which postulates that our entire universe emerged from a singular event around 14 billion years ago. In the case of the evolution of snakes, the singularity emerged in a series of rapid changes in form and function, but which occurred so close together that they appeared to be a single, unified event on the evolutionary time-scale.

Availability of prey

The eventual result is that we have about 4,000 living species of snakes flourishing in a variety of geographical conditions. Today, snakes are terrestrial dwellers, tree-climbers, burrowers, swimmers, etc., sporting a bevy of hunting strategies and dietary preferences.

As part of the new study, scientists also painstakingly collected information about snakes’ dietary preferences by studying the stomach contents of more than 60,000 snakes and lizards, mostly from field observations and natural-history museum specimens. They found that snakes largely consumed small vertebrates while lizards preferred insects and invertebrates – meaning snakes specialised their food selection whereas lizards have tended to be non-specific.

However, the availability of prey alone is insufficient to explain snake diversity. The researchers also admitted the ultimate cause of the “singularity” remains hidden from view.

The Sonic hedgehog gene

The hallmark of a snake is the elegant manner in which it glides over land or water. Snakes can move this way thanks to their long spinal column and specially designed vertebrae. They have over 300 vertebrae versus about 65 in lizards and 33 in humans. Also, all three organisms have a backbone and almost the same genetic blueprint – yet varied body plans.

In a previous study of snake genomes, researchers were able to identify snake-specific changes in a vertebrate limb-enhancer of the Sonic hedgehog gene (named for the videogame character). This limb-enhancer sequence has also been found in primitive snakes, such as pythons and boa, but not in modern snakes. When they replaced the mouse-specific limb-enhancer gene with the snake-specific one in mice, the researchers observed severe limb reduction.

Scientists suspect such evolutionary bursts in some species may have happened multiple times, not just once, and are certain that understanding them is key to understanding the earth’s ecological future.

The authors are senior consultants at the Vishwanath Cancer Care Foundation and adjunct professors at Indian Institute of Technology, Kanpur.