Sweeping gene survey reveals new facets of evolution

Who would have suspected that a handheld genetic test used to unmask sushi bars pawning off tilapia for tuna could deliver deep insights into evolution, including how new species emerge?

And who would have thought to trawl through five million of these gene snapshots—called "DNA barcodes"—collected from 100,000 animal species by hundreds of researchers around the world and deposited in the US government-run GenBank database?

That would be Mark Stoeckle from The Rockefeller University in New York and David Thaler at the University of Basel in Switzerland, who together published findings last week sure to jostle, if not overturn, more than one settled idea about how evolution unfolds.

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.

But is that true?

"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.

For the planet's 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity "is about the same," he told AFP.

The study's most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.

"This conclusion is very surprising, and I fought against it as hard as I could," Thaler told AFP.

That reaction is understandable: How does one explain the fact that 90 percent of animal life, genetically speaking, is roughly the same age?

Was there some catastrophic event 200,000 years ago that nearly wiped the slate clean?

Simpler, cheaper

To understand the answer, one has to understand DNA barcoding. Animals have two kinds of DNA.

The one we are most familiar with, nuclear DNA, is passed down in most animals by male and female parents and contains the genetic blueprint for each individual.

The genome—made up of DNA—is constructed with four types of molecules arranged in pairs. In humans, there are three billion of these pairs, grouped into about 20,000 genes.

But all animals also have DNA in their mitochondria, which are the tiny structures inside each cell that convert energy from food into a form that cells can use.

Mitochondria contain 37 genes, and one of them, known as COI, is used to do DNA barcoding.

Unlike the genes in nuclear DNA, which can differ greatly from species to species, all animals have the same set of mitochondrial DNA, providing a common basis for comparison.

Mitochondrial DNA is also a lot simpler, and cheaper, to isolate.

Around 2002, Canadian molecular biologist Paul Hebert—who coined the term "DNA barcode"—figured out a way to identify species by analysing the COI gene.

"The mitochondrial sequence has proved perfect for this all-animal approach because it has just the right balance of two conflicting properties," said Thaler.

'Neutral' mutations

On the one hand, the COI gene sequence is similar across all animals, making it easy to pick out and compare.

On the other hand, these mitochondrial snippets are different enough to be able to distinguish between each species.

"It coincides almost perfectly with species designations made by specialist experts in each animal domain," Thaler said.

In analysing the barcodes across 100,000 species, the researchers found a telltale sign showing that almost all the animals emerged about the same time as humans.

What they saw was a lack of variation in so-called "neutral" mutations, which are the slight changes in DNA across generations that neither help nor hurt an individual's chances of survival.

In other words, they were irrelevant in terms of the natural and sexual drivers of evolution.

How similar or not these "neutral" mutations are to each other is like tree rings—they reveal the approximate age of a species.

Which brings us back to our question: why did the overwhelming majority of species in existence today emerge at about the same time?

Darwin perplexed

Environmental trauma is one possibility, explained Jesse Ausubel, director of the Program for the Human Environment at The Rockefeller University.

"Viruses, ice ages, successful new competitors, loss of prey—all these may cause periods when the population of an animal drops sharply," he told AFP, commenting on the study.

"In these periods, it is easier for a genetic innovation to sweep the population and contribute to the emergence of a new species."

But the last true mass extinction event was 65.5 million years ago when a likely asteroid strike wiped out land-bound dinosaurs and half of all species on Earth. This means a population "bottleneck" is only a partial explanation at best.

"The simplest interpretation is that life is always evolving," said Stoeckle.

"It is more likely that—at all times in evolution—the animals alive at that point arose relatively recently."

In this view, a species only lasts a certain amount of time before it either evolves into something new or goes extinct.

And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there's nothing much in between.

"If individuals are stars, then species are galaxies," said Thaler. "They are compact clusters in the vastness of empty sequence space."

The absence of "in-between" species is something that also perplexed Darwin, he said.

© 2018 AFP