Extant and ancient cephalopods—including octopuses, squids, extinct ammonites, cuttlefish, and nautiluses—have all had to solve the problem of buoyancy, whether they have hard external shells or not.

Among ancient cephalopods, internal structures such as the siphuncle, chambers, septa, and septal necks were used to regulate buoyancy. The siphuncle—a tube running through the shell chambers—is central to this system since it can be filled with water or gas to control buoyancy. It is regarded as one of the key evolutionary innovations that distinguishes cephalopods from other mollusks. Unfortunately, due to the lack of a continuous fossil record, the detailed evolution of the siphuncle has been unclear.

Now, an international research team has discovered the earliest known siphuncle-bearing cephalopod from the early Cambrian of South China, providing new insights into the group’s early origin and evolutionary history.

Dr. PAN Bing of the Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, in collaboration with researchers from China, the United Kingdom, and the United States under the leadership of Prof. GUO Junfeng of Chang’an University, discovered a new fossil species, Eoceras shaanxiense, which was recovered from the approximately 520-million-year-old Shuijingtuo Formation in South China.

The findings were published in Nature on July 29.

The earliest accepted cephalopod, Plectronoceras cambria, dates to the late Cambrian period about 30 million of years younger than the divergence time of cephalopods estimated by molecular clocks during the Cambrian Explosion (early Cambrian). Thus, the researchers have been trying to find more earlier fossil records of cephalopods, especially in the early Cambrian. The abundant multi-phylum microfossils known as “small shelly fossils” including diverse mollusks and their close relative groups occurred and distributed worldwide in early Cambrian rocks, and may offer great potential for discovering the earliest cephalopods.

Targeting at the small shelly fossils of the early Cambrian Shuijingtuo Formation as a potential resource, the researchers identified 32 specimens of E. shaanxiense and concluded it is an early cephalopod.

Using scanning electron microscopy (SEM) and micro-computed tomography (micro-CT), the researchers examined the specimens—which were preserved through different types of phosphatization—to reconstruct the overall external morphology and internal anatomy of the new species.

Eoceras is millimeter in size, with an orthoconic shell, an oblique apertural margin, multiple septa, and a ventrally situated segmented tube that appears to bridge the septa via minute canals. After making a comprehensive comparison of its internal structures with those of typical siphuncle-bearing cephalopods, the researchers concluded that the segmented tube of Eoceras is indeed a siphuncle—making these fossils the earliest known examples of siphuncle-bearing cephalopods. The researchers argue that Eoceras represents an intermediate evolutionary stage between earlier species with chambered shells and later species with more developed buoyancy systems.

The researchers also outlined a general early evolutionary pathway for cephalopods: First, early cephalopods originated from a taxon characterized by orthoconic shells and multiple septa. Second, cephalopods evolved a sealed, segmented siphuncle within the orthoconic shell. Third, they evolved a true siphuncle with septal necks and connecting rings.

Due to its primitive and simple buoyancy regulation system, Eoceras likely had a mostly benthic lifestyle. However, the fossil lacks features observed in later cephalopods, and its soft-body anatomy is unclear. The researchers note that additional Cambrian fossil discoveries are essential to further resolve the earliest stages of cephalopod evolution and the origin of their distinctive shell architecture.

This study was supported by the National Natural Science Foundation of China, the National Key Research and Development Program of China, and the Opening Foundation of the State Key Laboratory of Continental Evolution and Early Life.

Journal

Nature

DOI

10.1038/s41586-026-10868-y

The team’s research focuses on decapodiform cephalopods, the ten-limbed group encompassing both squids and cuttlefish, whose evolutionary pathways have long been debated. The study leverages three newly sequenced squid genomes and integrates these with existing genomic repositories, marking the first time a near-complete genomic picture of decapodiform lineages has been assembled. This work, recently published in Nature Ecology & Evolution, reveals a complex and fascinating “long fuse” evolutionary model, characterized by a protracted period of evolutionary stasis followed by rapid diversification coinciding with the mid-Cretaceous period.

Central to this investigation is the examination of the internal shell structures that diverse squid and cuttlefish species exhibit. These range from the broad, buoyant cuttlebones unique to cuttlefish to the sleek, gladius-shaped shells seen in many oceanic squids, and the distinctive spiral shell of the elusive ram’s horn squid (Spirula spirula). Intriguingly, some shallow-water squid species have even lost their internal shells altogether. Past phylogenetic attempts, often constrained by limited morphological data and partial genetic sequences, yielded conflicting conclusions about these evolutionary relationships. However, whole genome sequencing now enables researchers to detect subtle genetic markers and evolutionary signals that paint a more consistent picture of lineage divergences.

The sheer size of cephalopod genomes presents a formidable technical challenge. With genome sizes up to twice that of humans, sequencing and analyzing these complex genomes require state-of-the-art techniques and immense computational resources. Additionally, accumulating fresh, high-quality DNA samples necessitates collecting specimens from a range of habitats, including deep-sea environments and tropical reefs where some species are both highly diverse and harder to access. Researchers at OIST were fortunate to access key species locally in Okinawa and collaborated internationally to secure samples from more remote conditions, allowing a comprehensive dataset to be created.

The monumental effort culminated in the construction of the first evolutionary tree for decapodiformes rooted in genomic data spanning nearly all major lineages. This achievement was enabled by the global Aquatic Symbiosis Genomics Project, funded by the Wellcome Sanger Institute. Within this international research framework, the Japanese team spearheaded the sequencing of previously underrepresented cephalopod genomes, effectively filling in critical gaps that hindered past evolutionary reconstructions. This database now forms a cornerstone resource for cephalopod evolutionary biology.

Among the most compelling insights is the genomic study of the ram’s horn squid, a rare species that biologists have long misclassified due to its unique shell form. For years, its shell’s similarity to cuttlebone structures led scientists to erroneously place Spirula spirula close to cuttlefish. The new genomic evidence upends this view, clarifying its true phylogenetic position and sharpening evolutionary narratives about cephalopods. The fresh data shine light on the diverse evolutionary paths that have produced the remarkable forms and adaptations vital to modern squid and cuttlefish.

Interlacing fossil discoveries with genomic timelines, the study proposes that modern decapodiform cephalopods originated around 100 million years ago during the mid-Cretaceous epoch—a period marked by rapid lineage divergence. Yet, a profound evolutionary bottleneck occurred approximately 66 million years ago during the catastrophic Cretaceous-Paleogene (K-Pg) extinction event, which famously led to dinosaur extinction and massive ecosystem upheavals. Cephalopods managed to endure, likely due to refuge in oxygen-rich microhabitats in the deep ocean where harsh surface conditions and ocean acidification were less severe.

The K-Pg event imposed a severe bottleneck that was followed by a prolonged period of minimal evolutionary change, consistent with a “long fuse” model of diversification. During this interval, deep-sea cephalopod lineages persisted, retaining features like internal shells adapted for their environments. Only after the gradual recovery of coastal ecosystems and the re-establishment of coral reefs did these animals explode in diversity and undergo extensive ecological radiation into shallower niches. This pattern—an initial rapid divergence, a prolonged stasis, then an explosive diversification—reflects a complex interplay between environmental pressures and evolutionary innovation.

Beyond reconstructing evolutionary history, this research lays the groundwork for probing the molecular underpinnings of cephalopod innovation. Squid and cuttlefish possess a suite of biological novelties that distinguish them from all other animal groups: elaborate camouflage systems, novel organogenesis, and extraordinary neural architectures underpinning their sophisticated behavior. With the advent of comprehensive genomes linked to a resolved phylogeny, scientists can now explore the genomic changes and regulatory networks driving these highly specialized traits. Such studies promise to revolutionize our understanding of cephalopod biology and evolution.

Professor Daniel Rokhsar, leading the Molecular Genetics Unit at OIST, underscores the transformative potential of these genomic resources. They enable comparative analyses that connect evolutionary events to genetic mechanisms, from the emergence of dynamic skin chromatophores controlling color and pattern to the development of advanced nervous systems managing complex behaviors. This research not only demystifies cephalopod origins but also provides a rich model for evolutionary developmental biology and genomics.

The implications extend beyond academic interest into biotechnology and evolutionary medicine, where the molecular strategies cephalopods use for adaptation might inspire new materials and neurological research. Given their evolutionary success and ecological importance, understanding how squid and cuttlefish adapted to changing oceans over millions of years also informs studies on resilience to current and future environmental changes, including ocean acidification and habitat degradation.

This landmark study exemplifies the power of international scientific collaboration, cutting-edge genomic technology, and integrative evolutionary biology. By resolving one of marine biology’s most enduring mysteries, it opens new frontiers for inquiry into the deep history and remarkable diversity of cephalopods. Unraveling the evolutionary “long fuse” that preceded the spectacular radiation of squid and cuttlefish enriches our appreciation not only of these enigmatic animals but also of the dynamic processes sculpting marine biodiversity.

As squid and cuttlefish continue to captivate with their luminous displays and rapid movements, scientists now stand equipped with the genetic blueprints to decode their remarkable adaptations. This confluence of paleontology, genomics, and marine biology heralds a new era of understanding, revealing how life in the ocean’s depths has shaped some of the most fascinating creatures on Earth.

Subject of Research: Animals

Article Title: Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches.

News Publication Date: 30-Mar-2026

Web References:
https://doi.org/10.1038/s41559-026-03009-1

Image Credits: Keishu Asada

Keywords: Cephalopods, Evolution, History of life, Evolutionary genetics, Evolutionary developmental biology, Aquatic animals, Marine biology