Earthworm DNA is changing how we understand evolution, possibly proving Darwin wrong

In 1859, Darwin proposed that evolution worked slowly – even for creatures like the worm. Tiny changes, stacked over time, led species to gradually become something new.

But even he had to admit the fossil record didn’t back that up. It was missing too many pieces – too many “in-between” species. He chalked it up to a broken archive: most of the story was lost.

Then, in 1972, scientists Stephen Jay Gould and Niles Eldredge made a bold claim. Maybe species don’t evolve slowly at all. Maybe they stay mostly the same for millions of years, and then – bang – something dramatic happens.

This idea, called “punctuated equilibrium,” could explain why so many transitional fossils are missing. But decades later, scientists still argue about whether it’s the rule or just a rare exception.

Now, researchers at the Institute of Evolutionary Biology (IBE) – a joint center between the Spanish National Research Council (CSIC) and Pompeu Fabra University (UPF) – have found compelling genomic evidence that supports the “bang” theory of evolution. And the evidence comes from a very unexpected place: worms.

Worms and evolution’s missing chapter

The team sequenced, for the first time, high-quality genomes of several earthworm species. They compared these to the genomes of other annelids like leeches and bristle worms.

The work was painstaking – done at a level of detail usually reserved for human genome studies. And it filled a major gap. Until now, scientists lacked complete genomes for many invertebrates, which made it hard to study evolution at the chromosomal level.

That changed with this study. The new genomes allowed the researchers to look back more than 200 million years.

Rosa Fernández is the lead researcher of the IBE’s Metazoa Phylogenomics and Genome Evolution Lab.

“This is an essential episode in the evolution of life on our planet, given that many species, such as worms and vertebrates, which had been living in the ocean, now ventured onto land for the first time,” she said. What the team found was not slow, steady change. It was upheaval.

Worms that broke all the rules

The worm genomes didn’t just shift gradually, as traditional Neo-Darwinian models would expect. They shattered. Then they reassembled in totally new ways.

“The enormous reorganization of the genomes we observed in the worms as they moved from the ocean to land cannot be explained with the parsimonious mechanism Darwin proposed; our observations chime much more with Gould and Eldredge’s theory of punctuated equilibrium,” Fernández said.

In simple terms: these marine worms broke their DNA into pieces, stitched it back together in a new order, and kept going. It wasn’t just odd – it was unheard of.

Across most species, including sponges, corals, and mammals, genomic structure tends to stay surprisingly stable. This was something else entirely.

“The entire genome of the marine worms was broken down and then reorganized in a completely random way, in a very short period on the evolutionary scale,” said Fernández. “I made my team repeat the analysis again and again, because I just couldn’t believe it.”

Surviving DNA chaos

Normally, that kind of chaos would spell extinction. But in this case, the worms didn’t just survive. They adapted.

The research team found that annelid genomes are much more structurally flexible than those of vertebrates. That flexibility could allow genes in different parts of the genome to change positions without losing function.

The shift to land was a massive environmental change. Suddenly, these animals had to breathe air, deal with sunlight, and navigate new terrains. The genomic rewiring may have helped them adapt quickly by creating new gene combinations.

“You could think that this chaos would mean the lineage would die out, but it’s possible that some species’ evolutionary success is based on that superpower,” said Fernández.

The study suggests that some genes didn’t just move – they fused with others. These new “genetic chimeras” may have played a role in helping the worms handle life on land.

Evolution isn’t orderly for worms

This finding also raises a bigger question: is genome stability really all that important?

“It seems from this study that conserving the genomic structure at the linear level – i.e., where the genes are more or less in the same place in different species – may not be as essential as had been thought,” said Fernández.

“In fact, stability could be the exception and not the rule in animals, which could benefit from a more fluid genome.”

That idea has serious implications. In humans, similar genomic breakdowns are seen in cancer. There’s even a term for it: chromoanagenesis. It refers to catastrophic chromosome reorganization in cancer cells. The difference? In humans, it’s a disease. In these worms, it was a survival strategy.

The comparison could open up new ways to study how genomes work – and how they break.

DNA evidence challenges Darwin

The debate between slow change and sudden leaps isn’t settled. But this study adds strong support for the idea that both models might be right, depending on the circumstances.

“Both visions, Darwin’s and Gould’s, are compatible and complementary,” Fernández said. “While Neo-Darwinism can explain the evolution of populations perfectly, it has not yet been able to explain some exceptional and crucial episodes in the history of life on Earth.”

“Those events included such as the initial explosion of animal life in the oceans over 500 million years ago, or the transition from the sea to land 200 million years ago in the case of earthworms. This is where the punctuated equilibrium theory could offer some answers.”

And this might just be the beginning. There are thousands of invertebrate species we know almost nothing about. Their genomes may hold more surprises – and more exceptions to the rules we thought we understood.

“There is a great diversity we know nothing about, hidden in the invertebrates, and studying them could bring new discoveries about the diversity and plasticity of genomic organization, and challenge dogmas on how we think genomes are organized,” Fernández concluded.

The full study was published in the journal Nature Ecology & Evolution.

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