A newly published genome study in the journal Nature Ecology and Evolution provides the first systematic overview of the evolutionary history of squid and cuttlefish, the "decabrachiocephalopods", revealing that they originated in the deep sea, rapidly diversified about 100 million years ago, and completed a diversification explosion along the "long lead" pattern during the long recovery period after the extinction of the dinosaurs.
Squids and cuttlefish are famous for their bizarre abilities such as instant color-changing camouflage and jet propulsion, but for a long time, scientists have had difficulty reconstructing their evolutionary lineage due to sparse fossil records and scattered genome data. New research led by Okinawa Institute of Science and Technology University (OIST) integrated existing databases and added three newly sequenced squid genomes for the first time to draw the most comprehensive evolutionary tree of decabrachiocephalopod genomes to date.
Gustavo Sanchez, the first author of the paper and a researcher at the OIST Molecular Genetics Unit, said that the ancestry of squid and cuttlefish has been debated for decades, with different studies proposing conflicting hypotheses based on morphological characteristics or limited molecular data. High-resolution whole-genome data has significantly reduced bias signals, allowing true genetic relationships to emerge. Research shows that most brachiopods have internal shell structures, but the shapes vary greatly: cuttlefish have round calcareous cuttlebones, many squids have thin, sword-like "feather shells", and the spiral shell of "little spiral squid", and some shallow-sea species have even lost this structure completely.
Large-scale whole-genome sequencing is technically very challenging, because the genome size of squid and cuttlefish can be twice that of humans. It not only requires high sequencing platforms and computing resources, but also requires the acquisition of fresh samples, which is not easy for species distributed in tropical coral reefs and even deep seas. Sanchez pointed out that some lineages are extremely abundant in tropical reef areas such as the Ryukyu Islands, while others only exist in mysterious forms in the deep sea. This study was able to rely on local resources in Okinawa and international cooperation to collect samples of key species.
The research is one of the key results of a five-year international collaboration under the Aquatic Symbiosis Genome Project, supported by the Wellcome Sanger Institute in the UK. The research team used the decabrachiocephalopod genome covering almost all major lineages to construct the first high-resolution evolutionary tree, filling many previous key gaps. Co-author Fernando Fernandez-Alvarez of the Spanish Institute of Marine Research focuses on the study of the "Spirula spirula". This unique inner shell structure once led some scientists to mistakenly believe that it is more closely related to squid. However, genomic evidence has corrected this misclassification and brought new clues to the overall evolution of the entire cephalopod.
By combining genomic information with the limited fossil record, the team reconstructed the evolutionary timeline of squid and cuttlefish. The results show that this group originated from the deep-sea environment, and species such as the spiny squid that still live in the deep sea today are likely to retain characteristics close to their early forms. Research infers that the main branches of the ten-brachiocephalopods rapidly diverged in the middle of the Cretaceous of the Mesozoic Era about 100 million years ago. Afterwards, about 66 million years ago, the Cretaceous-Paleogene (K-Pg) mass extinction event broke out, and about three-quarters of the animal and plant species on the earth disappeared together with non-avian dinosaurs.
The research team proposed that the key reason why early decabrachiopods were able to survive this catastrophe was that they retreated to a few oxygen-rich refuges in the deep sea. Sanchez explained that the sea surface environment at that time was extremely harsh for cephalopods, and there were very few oxygen-rich habitats for breathing in shallow coastal waters. At the same time, extreme ocean acidification would accelerate the dissolution and destruction of shells of shallow-sea species. In this context, the fact that decabrachiocephalopods still retained some form of internal shell throughout their evolutionary history is regarded as important evidence of deep-sea origins.
Over time, global ecosystems have gradually recovered and coastal coral reefs have been re-established, providing rich new ecological niches for decabrachiocephalopods and prompting many species to spread into shallow seas again. The evolutionary tree shows that after the emergence of early branches, lineage differentiation was very limited for tens of millions of years. However, during the post-K-Pg recovery period, the number of branches suddenly surged, showing that species evolved in multiple directions to adapt to the rapidly changing ecosystem. This is a typical "long lead" model: after a long incubation period, there is an explosion of diversification.
At the microscopic level, the study also used transcriptomics to analyze spiral shells the size of the delicate fingernails of the spiny squid and found that they have specific gene expression characteristics in biomineralization and shell regeneration. Compared with other cephalopod species, this kind of shell structure has not significantly degraded over the long geological time.
Researchers believe that this new genomic framework lays the foundation for understanding the evolution mechanism of unique traits in squid and cuttlefish. Professor Daniel Roxal, head of the Molecular Genetics Unit of OIST, pointed out that compared with other animal groups, decabrachiopods have a large number of unique organs and behaviors, from dynamic camouflage to complex nervous systems, which are a source of continuous inspiration for scientists. Now, with high-quality genomes and clear genetic relationships, researchers can compare the molecular changes behind these innovations in a more targeted manner.
The related paper is titled "Rapid diversification of squid and cuttlefish in the mid-Cretaceous preceded their radiation to coastal niches", written by Gustavo Sanchez and others, and published online on March 30, 2026. The research was supported by Okinawa Institute of Science and Technology Graduate University, Japan Society for the Promotion of Science, Chan Zuckerberg Biohub, and several scientific research funding agencies in Spain.