How squid survived Earth’s biggest extinction and took over the oceans
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How squid survived Earth’s biggest extinction and took over the oceans
Squid and cuttlefish evolved in the deep sea and survived Earth’s biggest extinction by hiding in oxygen-rich refuges.
Date:
April 1, 2026
Source:
Okinawa Institute of Science and Technology (OIST) Graduate University
Summary:
Scientists have finally cracked a long-standing mystery about squid and cuttlefish evolution by analyzing newly sequenced genomes alongside global datasets. The research reveals that these bizarre, intelligent creatures likely originated deep in the ocean over 100 million years ago, surviving mass extinction events by retreating into oxygen-rich deep-sea refuges. For millions of years, their evolution barely changed—until a dramatic post-extinction boom sparked rapid diversification as they moved into new shallow-water habitats.
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Photo of a common cuttlefish (Sepia sp.) Credit: Keishu Asada
Squid and cuttlefish are among the ocean's most fascinating animals, known for their color-changing skin and jet-like movement. For decades, scientists have tried to understand how these unusual creatures evolved. Progress has been slow because their fossil record is limited and their genomes are complex. Now, new research is finally providing clearer answers.
A study published in Nature Ecology & Evolution by researchers at the Okinawa Institute of Science and Technology (OIST) combines large genomic datasets with three newly sequenced squid genomes. This work reveals a "long fuse" pattern that explains how squid and cuttlefish, together known as decapodiform (ten-limbed) cephalopods, evolved into the diverse group seen today.
Dr. Gustavo Sanchez, first author on the study and Staff Scientist in OIST's Molecular Genetics Unit, says, "Squid and cuttlefish are remarkable creatures, yet their evolution has been notoriously difficult to study. The question of their ancestry has been under investigation for decades, and many research groups have proposed different evolutionary hypotheses based on different morphological characteristics and molecular datasets. With our new genomic information, we have been able to resolve some of the mysteries surrounding their origins."
A Clearer Picture of Squid and Cuttlefish Evolution
Squid and cuttlefish live in environments ranging from deep ocean waters to shallow coastal regions. Despite their diversity, most share one feature: an internal shell. This structure varies widely, from the rounded cuttlebone in cuttlefish to the thin, blade-like gladius in many squid, as well as the spiral shell of the ram's horn squid. Some shallow-water species have even lost the shell entirely.
Understanding how these different forms are related has been challenging. Sanchez explains, "Earlier reconstructions of decapodiform evolution were built from datasets with limited resolution and were prone to biased signals, obscuring the true relationships between different species. Whole genome data now provide a cleaner, more consistent picture of how these animals evolved."
Sequencing squid genomes is no easy task. Their genomes are often up to twice the size of the human genome, which requires advanced technology and significant computing power to analyze. Collecting suitable samples is also difficult, since fresh DNA is needed and many species live in remote or hard-to-reach habitats. "Some lineages are only abundant and highly diverse in tropical reef systems like the Ryukyu Archipelago, while others are enigmatic and known only in the deep sea. We were fortunate to find some key species on our doorstep in Okinawa, and collaborate with colleagues with access to more challenging samples," says Sanchez.
Building the First Comprehensive Evolutionary Tree
The research team constructed the first evolutionary tree for decapodiformes based on genome sequences from nearly all major lineages. This achievement was made possible by a global collaboration over five years, including the Aquatic Symbiosis Genomics Project funded by the Wellcome Sanger Institute. The project aims to sequence genomes from a wide range of marine and freshwater species, including cephalopods. Sanchez led the Japanese branch of this effort.
"Within the symbiosis project, we've been steadily sequencing genomes for several years, but several key gaps remained. In this study, we were able to fill these missing puzzle pieces," confirms Sanchez.
One particularly important species was the rare ram's horn squid, Spirula spirula. Its unusual internal 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 ram's horn squid shell made some scientists wrongly conclude it was closely related to cuttlefishes.," says Fernández-Álvarez. "I believed this genome could hel