How squid survived Earth’s greatest extinction and took over the oceans

A research revealed in Nature Ecology & Evolution by researchers on the Okinawa Institute of Science and Technology (OIST) combines massive genomic datasets with three newly sequenced squid genomes. This work reveals a “long fuse” sample that explains how squid and cuttlefish, collectively generally known as decapodiform (ten-limbed) cephalopods, developed into the various group seen at the moment.

Dr. Gustavo Sanchez, first creator on the research 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 stay in environments starting from deep ocean waters to shallow coastal areas. Despite their variety, most share one characteristic: an inside shell. This construction varies broadly, from the rounded cuttlebone in cuttlefish to the skinny, blade-like gladius in lots of squid, in addition to the spiral shell of the ram’s horn squid. Some shallow-water species have even misplaced the shell solely.

Understanding how these completely different varieties are associated has been difficult. 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 isn’t any simple activity. Their genomes are sometimes as much as twice the scale of the human genome, which requires superior know-how and vital computing energy to research. Collecting appropriate samples can also be troublesome, since recent DNA is required and plenty of species stay in distant 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 analysis group constructed the primary evolutionary tree for decapodiformes primarily based on genome sequences from almost all main lineages. This achievement was made potential by a worldwide collaboration over 5 years, together with the Aquatic Symbiosis Genomics Project funded by the Wellcome Sanger Institute. The challenge goals to sequence genomes from a variety of marine and freshwater species, together with cephalopods. Sanchez led the Japanese department 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 notably vital species was the uncommon ram’s horn squid, Spirula spirula. Its uncommon inside shell has lengthy confused scientists. Co-author Dr. Fernando Á. Fernández-Álvarez of the Spanish Institute of Oceanography acknowledged its significance 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 help close a key gap and bring clarity to the broader evolutionary questions of cephalopods.”

A Deep-Sea Origin and a “Long Fuse” Evolution

By combining genomic information with fossil proof, the researchers reconstructed each the timeline and environmental context of squid and cuttlefish evolution.

“Our analysis shows that these animals originated in the deep ocean, a habitat which still harbors species like the ram’s horn squid,” says Sanchez.

The research signifies that main decapodiform teams first break up about 100 million years in the past through the mid-Cretaceous interval. Later, round 66 million years in the past, the Cretaceous-Paleogene (Okay-Pg) mass extinction eradicated about three-quarters of Earth’s species, together with the dinosaurs. Despite this catastrophic occasion, squid ancestors survived.

Scientists imagine these early cephalopods discovered refuge in small, oxygen-rich pockets of the deep ocean. Sanchez explains, “The sea surface would have been a very harsh environment for cephalopods. Around that time, very few suitable oxygen-rich habitats would have been found near the shores. Intense ocean acidification in shallower waters would also likely have degraded their shells, so the fact that some form of this feature has been retained throughout their evolutionary history is evidence of their deeper oceanic origins.”

As the planet recovered, coral reefs regularly returned, creating new shallow-water ecosystems. Many squid and cuttlefish lineages then expanded into these environments.

“Following the initial lineage splits in the Cretaceous, we don’t see much branching for many tens of millions of years. However, in the K-Pg recovery period, we suddenly see rapid diversification, as species adapt and evolve to new and changing ecosystems. This is an example of a ‘long fuse’ model; a period of limited change followed by an explosion of diversity,” says Sanchez.

What These Genomes Reveal About Cephalopod Innovation

The researchers imagine this work offers a powerful basis for future research on the distinctive traits of squid and cuttlefish.

“Squids and cuttlefish have so many unique features compared to other animal groups, making them an endless source of inspiration for scientists,” says Prof. Daniel Rokhsar, head of the Molecular Genetics Unit. “With these genomes and with a clear picture of their evolutionary relationships, we can make meaningful comparisons to uncover the molecular changes associated with major cephalopod innovations, from the emergence of novel organs and dynamic camouflage to the neural complexity that supports their remarkable behavior.”