A genomic wormhole – rapidly reorganised genomes likely helped species switch from the sea to the land

Posted on: 23 June 2025

We tend to think of evolution as a slow, gradual progress, with species accumulating small changes over time. But the fossil record often offers no missing links between apparent major jumps in the form and function of species. One such jump – a gargantuan leap in adaptation – is the transition from oceanic to terrestrial living that some species have made throughout history.

In a just-published study in leading journal Nature Ecology & Evolution, an international team of scientists focusing on worms, reports how they discovered evidence of rapid, massive genomic reorganisation, which likely played a huge role in the transition from a marine life to a land-based one some 200 million years ago.

This “genomic wormhole” may help explain why there is no obvious transitional form for some of these animals from an evolutionary perspective. Instead, it is as if an evolutionary spark shattered their genomes and then stuck them back together in a completely different way – giving rise to new forms and functions that enabled a sudden change in lifestyle.

Ultimately, the genetic mechanism identified could transform our concept of animal evolution and revolutionise the established laws of genome evolution.

An unprecedented invertebrate genomic library

The team sequenced for the first time the high-quality genome of various earthworms, and compared them to other closely related annelid species (leeches and bristle worms). The level of precision was the same as for sequencing human genomes, although in this case the team started from scratch, with no existing references for the studied species.

Until now, the lack of complete genomes had prevented the study of chromosomal-level patterns and characteristics for many species, limiting research to smaller-scale phenomena – population studies of a handful of genes, rather than macroevolutionary changes at the full-genome level.

Aoife McLysaght, Professor in Genetics in Trinity College Dublin’s School of Genetics and Microbiology, was a collaborator on the research. She said: “This exciting project allowed us to examine complete genome sequences from many very interesting worms for the first time. Not only are worms essential animals in a balanced ecosystem but they also have a fascinating evolutionary history having made the difficult transition from an aquatic life to one on dry land, with all the adaptations that that required.”

“This study revealed that their genomes endured radical changes around the same time as this dramatic habitat shift. The thorough evolutionary restructuring of their genomes may have created novel genetic opportunities for adaptation to the new niche, and reveals previously underappreciated possibilities in genome evolution.”

After putting together each of the genomic jigsaw puzzles, the team was able to travel back in time with great precision more than 200 million years, to when the ancestors of the sequenced species were alive.

“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,” comments Rosa Fernández, lead researcher of the Institute of Evolutionary Biology (IBE) Metazoa Phylogenomics and Genome Evolution Lab. The IBE is a mixed research centre belonging to the Spanish National Research Council (CSIC) and Pompeu Fabra University (UPF).

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

The reason why this drastic deconstruction did not lead to extinction could be in the 3D structure of the genome. The scientists discovered that the chromosomes of modern worms are much more flexible than those of vertebrates and other model organisms. Thanks to this flexibility, it is possible that genes in different parts of the genome could change places and continue working. 

Major changes in their DNA could have helped the worms adapt quickly to life on land, reorganising their genes to respond better to new challenges such as breathing air or being exposed to sunlight.

The study suggests that these adjustments not only moved genes around, but also joined fragments that had been separated, creating new “genetic chimeras” which would have driven their evolution.

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

Parallels with cancer in humans

This phenomenon of extreme genetic reorganisation has previously been observed in the progression of cancer in humans. The term chromoanagenesis covers several mechanisms which break down and reorganise chromosomes in cancerous cells, where we see similar changes to those observed in the earthworms.

The key difference is that while these genomic breakdowns and reorganisations are tolerated by the worms, in humans they lead to diseases. These findings thus open the door to a better understanding of the potency of this radical genomic mechanism, with wide-ranging and significant implications for human health.

The study involved the collaboration of research staff from the Universitat Autònoma de Barcelona, Trinity, the Universidad Complutense de Madrid, the University of Köln, and the Université Libre de Bruxelles. The study received support from SEA2LAND (Starting Grant funded by the European Research Council), and from the Catalan Biogenome Project, which funded the sequencing of one of the worm genomes.

The published journal article can be read on the publisher's website.

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