Rosa Rubicondior: Creationism Refuted - 100 Million Years Of Cuttlefish and Squid Evolution

Monday, 30 March 2026

Creationism Refuted - 100 Million Years Of Cuttlefish and Squid Evolution

The intricate ram’s horn squid shell is only about the size of a fingernail. Compared to other cephalopod species, the shell structure has not degraded over time. As part of this study, researchers used transcriptomics which revealed genes supporting biomineralization and regeneration of the shell.

Credit: Catherine Hodges/OIST

100 million years ago, an ‘evolutionary fuse’ was lit in the deep ocean, sparking squid diversification | EurekAlert!

Another day, another gap in evolutionary history closed by scientists doing what scientists do: following the evidence wherever it leads. This time, the gap concerns the origins and diversification of squid and cuttlefish, the decapodiform cephalopods.

An international team led by the Okinawa Institute of Science and Technology (OIST) has now reconstructed a much clearer picture of their history, and their findings are published, open access, in Nature Ecology & Evolution. The study supports a rapid mid-Cretaceous diversification of the major decapodiform lineages around 100 million years ago, followed much later by expansion into coastal habitats after the K–Pg mass extinction. [1]

That is, of course, disastrous for creationism. Creationists need the history of life to be short, simple, and static: a few thousand years, separate acts of special creation, and only trivial shuffling of variation within rigidly defined “kinds”. What this study shows instead is exactly what evolutionary biology has long predicted - deep ancestry, branching descent, ecological change over immense spans of time, and major radiations triggered by changing environmental conditions. In other words, not magic, not fixity, and not “kinds”, but evolution. [1]

The researchers conclude that the ancestors of modern squid and cuttlefish probably originated in the deep ocean, where oxygenated refugia may have allowed them to survive while shallow marine environments became increasingly hostile. Ocean acidification in shallower waters would likely have damaged shell-bearing forms, and the later recovery of coastal ecosystems and coral reefs after the K–Pg event opened up new ecological opportunities. What followed was not the survival of a few immutable “created kinds”, but the adaptive expansion of lineages into newly available habitats. [2]

That matters because it gives the lie to one of creationism’s central evasions: the claim that organisms merely vary within fixed boundaries. The history uncovered here is not one of minor tinkering around the edges. It is one of common ancestry, divergence, persistence through catastrophe, and later radiation into new environments. It is precisely the sort of deep, branching history that creationists have to deny, ignore, or misrepresent because their belief system simply has no room for it. [1]

The team reconstructed this history using genome-scale data, including newly sequenced genomes that helped fill key phylogenetic gaps. Together with data from the Aquatic Symbiosis Genomics Project and other existing resources, this allowed the researchers to produce a robust evolutionary tree covering nearly all recognised decapodiform lineages. Because cephalopod genomes are often very large, this kind of work has only recently become practical with modern sequencing technology and computing power. [1]

So, once again, creationism is refuted not by some special anti-creationist project, but as an incidental consequence of real scientific research. Scientists set out to understand the evolutionary history of a fascinating group of animals, and in doing so they uncovered yet more evidence for common descent, ancient Earth history, and the power of evolution to generate biological diversity. Reality, as usual, has no respect for creationist dogma. [1]

Background information^ the evolution of squids and cuttlefish. Squids and cuttlefish are cephalopods, a molluscan group with a history stretching back more than 490 million years. Among living cephalopods, the two great surviving branches are the externally shelled nautiluses and the coleoids. The coleoids include octopuses, squid and cuttlefish, with squid and cuttlefish belonging to the ten-limbed decabrachian or decapodiform branch, while octopuses and vampire squid belong to the eight-armed octobrachian branch. [3]

The decapodiform cephalopods comprise 7 orders containing ~534 known species plus two extinct orders:[5]

Oegopsida (Oceanic squids): ~259 species.
Sepiida (Cuttlefish): ~120 species.
Sepiolida (Bobtail squids): ~89 species.
Myopsida (Coastal squids): ~48 species.
Idiosepida (Pygmy squids): ~5 species.
Bathyteuthida: ~3 species.
Spirulida (Ram's horn squid): 1 species (Spirula spirula).
Belamnitidia (belemnites) - extinct
Diplobelida - extinct.

The earliest history of the coleoids is still patchy because soft-bodied animals fossilise poorly, but unequivocal early coleoid fossils are known from the Carboniferous, and molecular studies generally place the origin of the crown-group somewhere around the Permian or Triassic. One of the key evolutionary steps was the internalisation of the shell. Instead of carrying a large external shell-like nautiluses, early coleoids evolved an internal shell and later added other innovations such as the ink sac. This shift seems to have been associated with greater manoeuvrability and more active swimming, helping to turn coleoids into agile predators. [4]

Modern squid and cuttlefish still retain traces of that ancestral shell, but in highly modified forms. In many squid it survives as a gladius or “pen”, a thin internal support rod. In cuttlefish it became the cuttlebone, a flattened chambered structure used for buoyancy control. Other decapodiform lineages show further reduction or modification, and some have lost the internal shell almost completely. This means that the various shell structures seen in living squid and cuttlefish are not separate creations but altered descendants of an ancestral chambered shell. [1]

A crucial point is that “squid” is not a single neat evolutionary category in the same way that cuttlefish are. Cuttlefish form one order, Sepiida, but the animals commonly called squid are spread across several decapodiform orders. Recent phylogenomic work using new genome sequences has helped clarify these relationships and shows that nearly all recognised modern decapodiform orders were already diverging rapidly in the mid-Cretaceous, about 100 million years ago. [1]

The new picture suggests a deep-ocean origin for the major modern squid and cuttlefish lineages. According to this model, the first major splits happened in the open ocean during the mid-Cretaceous, but much of the later expansion into shallow seas and coastal habitats happened only after the K–Pg mass extinction 66 million years ago. In other words, there was a long interval between the first branching of the main lineages and their later ecological radiation - an evolutionary “long fuse” before the modern diversity of squid and cuttlefish really took off. [1]

The work of the OIST-led team is the subject of an OIST news release published via EurekAlert!

100 million years ago, an ‘evolutionary fuse’ was lit in the deep ocean, sparking squid diversification
New evolutionary mapping suggests deep sea origins and mass extinction-triggered diversification of modern squid and cuttlefish
From color-changing skin to jet-propelled motion, squid and cuttlefish have long fascinated scientists. To understand the origins of their unique characteristics, many attempts have been made to define their evolutionary history. However, the limited fossil record and incomplete genomic information have made it impossible to confidently order the evolution of these enigmatic creatures, until now.

Published in Nature Ecology & Evolution, a new study from the Okinawa Institute of Science and Technology (OIST) combines existing databases with three newly sequenced squid genomes to identify the ‘long fuse’ that led to today’s diversity of squid and cuttlefish, which together make up the decapodiform (ten-limbed) cephalopods.

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.

Dr. Gustavo Sanchez, first author
Molecular Genetics Unit
Okinawa Institute of Science and Technology
Onna, Japan.

Demystifying the decapodiformes

Squid and cuttlefish are found in a wide variety of habitats across the globe, from deep seas to shallow coastlines. One of the few characteristics linking most of these diverse creatures is their internal shell. But even this takes a variety of forms, from the smooth, rounded cuttlebones of cuttlefish, the thin, sword-like gladius of oceanic and coastal squid, and the spiral-shaped shell of ram’s horn squids, to a complete loss in shallow water species.

Past attempts to order the evolution of these animals have been limited by a lack of data.

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.

Dr. Gustavo Sanchez.

Because most squid and cuttlefish genomes are large, typically reaching up to twice the size of human genomes, generating and analyzing them requires state-of-the-art sequencing facilities and considerable computational power. Researchers also need fresh DNA for sequencing, which is a challenge when sourcing specimens at sea.

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.

Dr. Gustavo Sanchez.

The paper presents the first-ever evolutionary tree for decapodiformes that is based on sequenced genomes from nearly all decapodiform lineages. This was made possible due to a global collaboration spanning the last five years, with the Aquatic Symbiosis Genomics Project funded by the Wellcome Sanger Institute aiming to sequence some cephalopod genomes among other marine and freshwater species. Sanchez headed the Japanese branch of the cephalopod hub of this project.
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.

Dr. Gustavo Sanchez.

Co-author Dr. Fernando Á. Fernández-Álvarez of the Spanish Institute of Oceanography was especially enthusiastic to study the enigmatic ram’s horn squid, Spirula spirula, a rarely encountered species whose unusual internal shell has long puzzled biologists. From the moment he had it in hand, he saw its genomic potential.

In the past, the structure of the ram’s horn squid shell made some scientists wrongly conclude it was closely related to cuttlefishes. I believed this genome could help close a key gap and bring clarity to the broader evolutionary questions of cephalopods.

Fernando Ángel Fernández-Álvarez, co-author
Centro Oceanográfico de Gijón (IEO, CSIC)
Spanish Institute of Oceanography
Gijón, Spain.

A long fuse model of evolution

Using a combination of genomic data and recently discovered fossils, the researchers were able to map out an evolutionary timeline and ecological scenario for the origin and diversification of squid and cuttlefish.

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

Dr. Gustavo Sanchez.

The model shows that the different decapodiform orders first split rapidly around 100 million years ago, putting their origins firmly in the mid-Cretaceous period. However, 66 million years ago, a catastrophic mass extinction event known as the Cretaceous-Paleogene (K-Pg) wiped out three-quarters of the plant and animal species on Earth. This same event famously led to the extinction of dinosaurs and the rise of mammals. So how did squid survive?

The researchers believe that ancient cephalopods were able to find refugia within tiny deep-sea microcosms which harbored an abundance of oxygen.

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.

Dr. Gustavo Sanchez.

After the K-Pg event, coral reefs started to rebuild along coastlines. This created more habitable shallow water ecosystems, to which many of the ancient 10-limbed cephalopod lineages migrated.

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.

Dr. Gustavo Sanchez.

From gene evolution to gene editing

The team hopes this research can provide a framework for future investigations into the origins of decapodiformes’ unique characteristics.
Squids and cuttlefish have so many unique features compared to other animal groups, making them an endless source of inspiration for scientists. 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.

Professor Daniel S. Rokhsar, Co-corresponding author
Molecular Genetics Unit
Okinawa Institute of Science and Technology
Onna, Japan.

Publication:
Sanchez, G., Fernández-Álvarez, F.Á., Bernal, A. et al.
Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches.
Nat Ecol Evol (2026). https://doi.org/10.1038/s41559-026-03009-1

Abstract
The evolutionary relationships among decapodiform lineages (cuttlefish and diverse types of squid) remain uncertain, with implications for the origin of internalized structures (for example, gladius, cuttlebone and coiled shell) derived from the ancestral chambered shell as well as the ecological shifts between the deep ocean and shallow coastal habitats. To address these questions, we adopted a phylogenomic approach that integrated three new high-quality genome sequences with available genomic and transcriptomic datasets. Our analyses support a novel topology that separates a clade of open-ocean lineages (Oegopsida and Spirulida, together Acorneata) from a clade comprising the remaining coastal and shallow-water orders (Sepiida, Myopsida, Idiosepiida and Sepiolida, together Corneata). Molecular clock estimates suggest a rapid cladogenesis of modern decapodiform orders in the deep open ocean during the mid-Cretaceous, consistent with fossil data. This early diversification set a ‘long fuse’ that led to the explosive radiation of squid and cuttlefish into coastal and shallow-water environments as they recovered from the Cretaceous–Palaeogene extinction event.

a, Representative morphological characters of decapodiform lineages mapped to an unresolved decapodiform tree. RO, rostrum; SIPH, siphuncle; PROS, primordial rostrum; PRO, proostracum; PHR, phragmocone; ANG, accessory nidamental gland; COR, cornea; TP, tentacle pockets; OVD, oviduct; BC, branchial canal. The asterisk next to Spirulida and Oegopsida indicates that these two orders appear as sister early branching clades in our phylogeny. References cited in brackets for Idiosepiida, Sepiolida and Sepiida refer to prior studies that place these lineages as the earliest diverging decapodiform. In Bathyteuthida, the ANG is present in one family but absent in another, as indicated by the mixed presence/absence code. PROS, PRO and PHR are marked as ‘derived’ or ‘vestigial’ in most taxa based on the presence of homologous structures (for example, cuttlebone in Sepiida) that originate from the chambered shell of ancestral decapodiform. In this context, derived refers to functionally elaborated structures that evolved from ancestral components, whereas vestigial refers to highly reduced, non-functional remnants (for example, septa-like elements of the phragmocone in Oegopsida gladius). Only Spirulida retains a fully mineralized, chambered form with two out of three ancestral components. The shell diagram represents ancestral decapodiform characters. Some of the morphological traits were previously reported by Lindgren et al.¹⁴. The habitat category provides a summarized classification; more detailed ecological distributions are shown in Supplementary Table 1. b, Species with newly sequenced genomes presented in this study. Shell illustration in aadapted from ref. ¹⁴² under a Creative Commons License CC BY 4.0. Silhouettes in a adapted from PhyloPic under a Creative Commons License CC0 1.0. Credit for S. spirula photo in b: Victor Tuset. Bathyteuthis abyssicola silhouette in a adapted from ref. ¹⁴³, Neill.

Sanchez, G., Fernández-Álvarez, F.Á., Bernal, A. et al.
Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches.
Nat Ecol Evol (2026). https://doi.org/10.1038/s41559-026-03009-1

Copyright: © 2026 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What this study shows, yet again, is that the history of life is not the childishly simple tale creationism needs it to be. Squid and cuttlefish did not appear suddenly as fully formed “kinds” a few thousand years ago; they emerged from a branching evolutionary history stretching back into the Cretaceous, with major lineages diverging around 100 million years ago and later radiating into new habitats after the K–Pg mass extinction. That is a story of common ancestry, deep time and adaptive diversification — precisely the things creationists are forced to deny.

It also demolishes the old creationist fallback that organisms only vary within fixed limits. The evolutionary pattern here is not trivial shuffling within some imaginary boundary, but the splitting of ancestral lineages, the modification of inherited structures such as the internal shell, and the expansion of descendants into very different ecological niches. In other words, exactly what evolutionary theory predicts, and exactly what creationist dogma says cannot happen.

And once again, this refutation of creationism is entirely incidental. The researchers were not trying to disprove Bronze Age mythology; they were using genome-scale evidence to understand the real history of a remarkable group of animals. But reality has a habit of doing that. Every time science fills another gap, reconstructs another lineage, or uncovers another deep chapter in the history of life, creationism is left looking not merely wrong, but hopelessly detached from the world as it actually is.

Far from undermining evolution, studies like this show just how powerful it is as an explanatory framework. It enabled scientists to make sense of the relationships among living squids and cuttlefish, their modified shells, their deep-ocean ancestry and their later ecological expansion. Creationism, by contrast, contributes nothing beyond denial, distortion and the endless repetition of claims that the evidence keeps refuting.

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