This Scrambled Genome May Explain Octopus Intelligence: Milky Way News

EARTH, Laniakea Supercluster—Octopuses are masters of disappearance. They slip into crevices, vanish into rocky seafloors, and improvise tools from nearby debris. Scientists have long been trying to understand what in their biology makes that kind of ingenuity possible. New research suggests one possibility may lie in how their DNA is folded and refolded in three dimensions.

Led by Thea Rogers of the University of Vienna, a study titled "Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods," published in Nature Communications on Oct. 9, 2026, maps how their genomes folding may relate to their complex nervous systems.

Octopuses, as well as squid and cuttlefish, belong to a group of soft-bodied cephalopods called coleoids. Unlike their distant cousin, the nautilus, they traded armor for agility. Along the way, they evolved the largest brains of any invertebrate.

The study compared 14 species' genomes in total. It mainly looked at one species of each kind of coleoid cephalopod: the Hawaiian bobtail squid (Euprymna scolopes), the common cuttlefish (Sepia officinalis), and the California two-spot octopus (Octopus bimaculoides).

"These three species let us compare the two main coleoid lineages," Rogers said in an email to Milky Way News. "The bobtail squid and the common cuttlefish represent the decapodiforms, which have eight arms and two tentacles, and the octopus represents the octopodiforms, which have eight arms. Because the two decapodiforms are more closely related to each other than either is to the octopus, we could ask which features are shared across all coleoids and which are specific to one lineage."

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One of the topics the study investigated was how chromatin shapes the 3D structure of the genome—the sum of an organism’s genetic material—in coleoids. In humans, the DNA in a single cell would stretch about two meters if pulled straight, yet it fits inside a nucleus far smaller than a grain of sand, so it has to fold. Chromatin consists of folded DNA strands and protein. Chromatin domains, which are larger folds in a genome, are relatively stable, but a smaller kind of chromatin structure behaves differently.

"There are also chromatin loops, which are specific contacts that bring two distant pieces of DNA together, sometimes millions of DNA letters apart. In our study, we found that these layers behave very differently in evolution. Large chromatin domains are broadly similar across squid, cuttlefish and octopus, whereas loops are much more variable between species, tissues and developmental stages," Rogers said.

Think of chromatin domains and loops as origami folds. Chromatin domains are the bigger folds that make a foundation, like a diamond base. You can then take that base and make (generally) smaller folds to create different animals like an angelfish or a crab. Chromatin loops are like those smaller folds that create more variation. Some of those small folds even tuck one corner against another from far across the paper.

While researchers need to investigate this further, this specific genome structure in coleoids may create more opportunities for genes to turn on and off, even as their core functions stay the same.

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Chromatin loops also often sit near genes that affect the development of a coleoid's nervous system. The study noted that this pattern could help explain why their nervous systems are so "large and elaborately structured." At the same time, the researchers note that their results don’t show these DNA changes directly caused cephalopod intelligence.

These genetic features likely trace back to a great genetic reshuffling in coleoids hundreds of millions of years ago.

"What makes cephalopods special is their evolutionary history: their genomes were dramatically reshuffled, so their 3D structures had to form and stabilize around a completely new arrangement of genes," Rogers said.

In addition to evidence of that genetic event, researchers found differences between how octopodiform and decapodiform genomes have changed over time. More study is necessary, however, to figure out how exactly their genomes organized themselves.

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The study also explored how something the research team called "regulatory entanglement" may have helped shape their genome. Factors like chromosomal rearrangement and spatial proximity can link distant regions of the DNA, making parts of the 3D genome interdependent. Each genome is like a big genetic web or network. When one part of a genome changes, it can have far-reaching evolutionary consequences for other parts.

Moving forward, this study opens up pathways for even more research and understanding. Coleoid cephalopods' genomes can help scientists further understand how genomes and evolution inform each other.

"All our data and code are openly available, so others can use our 3D genome maps to identify candidate regulatory regions, compare cephalopods with other animals, or design their own experiments," Rogers said.

Further study can also create more appreciation for these animals. According to the World Wildlife Fund, cephalopods are "canaries of the ocean." Because their growth responds quickly to changing conditions, they could serve as an early warning sign of how climate change is affecting the ocean. Cephalopods function as predators and prey, and some can even help the ocean store carbon in the deep sea.

While the jury's still out on what exactly gives octopuses their incredible intelligence, they'll keep doing amazing things for our environment—even when they're hiding in plain sight.