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.

“You are more microbes than human.”

It is possible you have had this factoid thrown at you, with the thrower claiming that the microbes in our bodies outnumber our own cells 10 to one.

But according to an assessment published in Nature Microbiology, this is a myth. In a 2016 study the assessment’s authors cited, researchers from Israel and Canada estimated a 70 kg “reference man” to have 38 trillion bacterial cells and 30 trillion human cells. Most current estimates of the size of the gut microbiome are also based on adults living in the urban areas of high-income countries, they added.

The authors, Alan Walker, senior research fellow at the Rowett Institute, University of Aberdeen, and Lesly Hoyles, professor of microbiome and systems biology, Nottingham Trent University, poked holes into this and 11 other popular claims that assail the human microbiome – the community of microbes living in the human body.

In the last two decades, microbiome research has gone from a “niche subject area” to “one of the hottest topics in all of science,” Dr. Hoyles said. The flip side of this is “hype and a temptation to over-simplify the really complex microbial interactions and activities occurring in our guts”.

Varun Aggarwala, assistant professor of biomedical and life sciences at Jio Institute, Navi Mumbai, who studies microbiome therapeutics, described the assessment as a “timely intervention that can bring nuance to the field of microbiomes.”

Here are the 11 other claims the article checked:

1. The age of the field

One of the more benign misconceptions the assessment takes aim at is that microbiome research is a new field. But according to the authors, scientists had described bacteria inhabiting the gut, such as Escerichia coli and Bifidobacteria, and speculated on their benefits in the late 19th and early 20th centuries itself.

2. Who named the field?

Many have credited Joshua Lederberg, a medicine Nobel laureate, with naming the field in 2001. But researchers had used the term in its modern form more than a decade earlier. According to a June 2017 paper that the authors cite, Whipps J.M., Lewis K., and Cooke R.C. used the term in 1988 to describe a community of microbes in a book.

3. The real number of microbes

Some of the more prevalent and more harmful myths concern the size of the microbiome. The absolute microbial cell numbers in one gram of human faeces have been exaggerated 10- to 100-fold. The actual number is around 10¹⁰-10¹², according to the authors.

4. The mass of the microbiome

Many research articles have stated that the human microbiota weigh 1-2 kg, but it only weighs about half a kg or less, the authors wrote. The 2016 study by Israeli and Canadian researchers estimated that it weighed about 200 grams.

5. From mother to child

Contrary to some opinions, mothers don’t pass their microbiomes to their children at birth. Some microorganisms are directly transferred during birth but they constitute a small fraction of the human microbiota. A smaller fraction of these microbes also survives and persists through the child’s life. “Every adult ends up with a unique microbiota configuration, even identical twins that are raised in the same household,” the authors noted.

6. Good or bad?

Some researchers have suggested (see here, here, and here, e.g.) that diseases are caused by undesirable interactions between microbial communities and our cells. But the authors wrote that whether a microbe and its metabolite are ‘good’ or ‘bad’ depends on the context. For example, most humans carry a species of bacteria called Clostridium difficile without any diseases for life. It causes problems only in the elderly or in people with compromised immune systems.

They acknowledged that diseases have been correlated with changes in the composition of the microbiome and that such changes could exacerbate some diseases (like inflammatory bowel disease). But they added that it is “extremely difficult” to implicate a specific profile of microbes, or changes to them, in a disease.

7. The firmicutes-bacteroidetes ratio

One myth correlates obesity with the ratio of two phyla of bacteria, firmicutes and bacteroidetes. The problem: the level of phyla is too broad to comment on effects with confidence. A phylum is a group within a kingdom. In the descending order of classifying organisms, a kingdom comprises different phyla; a phylum comprises classes; then there are orders, families, genuses, and, finally, species. Even within a bacterial species, several strains behave differently, causing the host to manifest different clinical symptoms. 

8. Not redundant

Some researchers have swung the other way, claiming that different microbes are actually functionally redundant. But the authors wrote that while different bacteria in the human microbiome perform some common important functions, many functions are the preserve of a few species.

9. Sequencing is not necessarily unbiased

The authors noted that the notion that “sequencing is unbiased” is a misconception – that biases can be introduced at various stages of studies based on the microbes’ genetic material, from collecting samples to storing them, even in the choice of software to analyse sequence data.

10. The standards question

According to the authors, there is a common opinion in microbiome research that researchers need standardised methods so that they can compare the findings of different studies. But the assessment stressed that no methodology is perfect and that adopting one universal methodology would come at the cost of turning a blind eye to the limitations of the chosen method.

11. The culturable microbiome

Is it difficult to grow microbes from the human microbiome in the lab? Yes, many say, but the authors pointed to work in the 1970s when scientists cultured diverse microbiome species from the gut. “So current gaps in culture collections are at least in part attributable to a lack of previous effort rather than an inherent ‘unculturability’,” they noted.

Joel P. Joseph is a freelance science journalist and researcher.