Squids and cuttlefish are some of the ocean’s most fascinating animals, known for their discolored skin and jet-like movements. For decades, scientists have been trying to understand how these unusual creatures evolved. Their limited fossil record and complex genomes have slowed progress. Now, new research finally has a clear answer.
Research published in natural ecology and evolution Researchers at Okinawa Institute of Science and Technology Graduate University (OIST) combined a large genomic dataset with three newly sequenced squid genomes. The study reveals a “long fusion” pattern that explains how squid and cuttlefish, together known as decapod (deca-limbed) cephalopods, evolved into the diverse group seen today.
“Squids and cuttlefish are remarkable creatures, but their evolution is notoriously difficult to study,” said Dr. Gustavo Sánchez, lead author of the study and a staff researcher in the OIST Molecular Genetics Unit. “It has been studied extensively, and many research groups have proposed different evolutionary hypotheses based on different morphological features and molecular datasets. With our new genomic information, we have been able to solve some of the mysteries surrounding it.” their origin. ”
A clearer picture of the evolution of squid and cuttlefish
Squid and cuttlefish live in a wide range of environments, from the deep sea to shallow coastal areas. Despite their diversity, most share one feature: an internal shell. This structure varies widely, from the round cuttlefish bones of the cuttlefish to the thin blade-like gladius of many squids, and even the spiral shell of the horned squid. Some shallow-water species have lost their shells entirely.
It was difficult to understand how these different formats were related. Professor Sánchez explains: “Early reconstructions of decapod evolution were built from datasets with limited resolution, prone to biased signals and obscuring the true relationships between different species. Whole-genome data now provide a clearer, more consistent picture of how these animals evolved.”
Sequencing the squid genome is not an easy task. Their genomes are often up to twice the size of the human genome and require advanced technology and large amounts of computing power to analyze. Collecting adequate samples is also difficult because fresh DNA is required and many species live in remote or hard-to-reach habitats. “Some lineages are abundant and diverse only in tropical reef systems like the Ryukyu Islands, while others are mysterious and only known from the deep ocean. We were fortunate to find some important species in the immediate vicinity of Okinawa and collaborated with colleagues who had access to more difficult samples,” says Sanchez.
Building the first comprehensive evolutionary tree
The research team has constructed the first evolutionary tree of Decapoda based on the genome sequences of nearly all major lineages. This achievement was made possible through five years of global collaboration, including the Wellcome Sanger Institute-funded Aquatic Symbiotic Genomics Project. The project aims to sequence the genomes of a wide range of marine and freshwater species, including cephalopods. Mr. Sanchez led the Japanese branch of this effort.
“While we have steadily sequenced the genome over several years in the Symbiosis Project, some important gaps remained. This study fills in these missing pieces of the puzzle,” Sanchez asserts.
One species of particular importance was the rare sheep squid, Spirula spirula. Its unusual inner shell has long confused scientists. Co-author Dr. Fernando Á. Fernández Álvarez of the Spanish Institute of Oceanography recognized its importance early on. “In the past, the structure of the sheep squid’s shell led some scientists to incorrectly conclude that it was closely related to squid,” Fernández Álvarez said. “I believed this genome would fill an important gap and help clarify broader evolutionary issues in cephalopods.”
Origin of the deep sea and evolution of the “long fuse”
By combining genomic data and fossil evidence, researchers reconstructed both the evolutionary timeline and environmental context of squid and cuttlefish.
“Our analysis shows that these animals originated in the deep sea, where species like the horned squid still live today,” Sánchez said.
This study shows that the major decapod group first split about 100 million years ago during the mid-Cretaceous period. Then, about 66 million years ago, the Cretaceous-Paleogene (K-Pg) mass extinction wiped out about three-quarters of Earth’s species, including the dinosaurs. Despite this catastrophe, the squid’s ancestors survived.
Scientists believe that these early cephalopods found refuge in small, oxygen-rich pockets of the deep sea. Professor Sánchez explains: “The ocean surface would have been a very harsh environment for cephalopods, as few suitable oxygen-rich habitats would have been found near the coast at the time. Severe ocean acidification in shallow waters likely also degraded cephalopod shells. Therefore, the fact that some form of this feature has been retained throughout evolutionary history is evidence of a deep-sea origin for cephalopods.”
As the Earth healed, coral reefs gradually returned and new shallow-sea ecosystems formed. Many squid and cuttlefish lineages subsequently expanded into these environments.
“After the first lineage split in the Cretaceous, we don’t see major divergence for tens of millions of years. However, during the K-Pg recovery period, we suddenly see rapid diversification as species adapt and evolve to newly changing ecosystems. This is an example of the ‘long fusion’ model, where limited change is followed by an explosion of diversity,” Sánchez says.
What these genomes reveal about cephalopod innovation
The researchers believe this study provides a strong foundation for future research into squid and squid’s unique properties.
Professor Daniel Roxard, Head of the Molecular Genetics Unit, said: “Squids and cuttlefish have so many unique characteristics compared to other groups of animals that they are an endless source of inspiration for scientists.” “Having a clear picture of these genomes and their evolutionary relationships will enable meaningful comparisons to reveal the molecular changes associated with major innovations in cephalopods, from the emergence of new organs and dynamic camouflage to the neural complexity that underpins their surprising behaviors.”
