CTHULHU STUDIES

Vampires in the deep: An ancient link between octopuses and squids

A 'genomic living fossil' reveals how evolution of octopuses and squids diverged more than 300 million years ago

University of Vienna

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The vampire squid (Vampyroteuthis sp.) is one of the most enigmatic animals of the deep sea.

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Credit: Steven Haddock_MBARI

In a study now published in iScience, researchers from the University of Vienna (Austria), National Institute of Technology - Wakayama College (NITW; Japan), and Shimane University (Japan) present the largest cephalopod genome sequenced to date. Their analyses show that the vampire squid has retained parts of an ancient, squid-like chromosomal architecture, and thus revealing that modern octopuses evolved from squid-like ancestors.

The vampire squid (Vampyroteuthis sp.) is one of the most enigmatic animals of the deep sea. With its dark body, large eyes that can appear red or blue, and cloak-like webbing between its arms, it earned its dramatic name – although it does not suck blood, but feeds peacefully on organic detritus. "Interestingly, in Japanese, the vampire squid is called "kōmori-dako", which means 'bat-octopus'", says one of three lead PIs of this project, Masa-aki Yoshida, Shimane University. Yet its outward appearance hides an even deeper mystery: despite being classified among octopuses, it also shares characteristics with squids and cuttlefish. To understand this paradox, an international team led by Oleg Simakov from the University of Vienna, together with Davin Setiamarga (NITW) and Masa-aki Yoshida (Shimane University), has now decoded the vampire squid genome.

A glimpse into deep-sea evolution

By sequencing the genome of Vampyroteuthis sp., the researchers have reconstructed a key chapter in cephalopod evolution. "Modern" cephalopods (coleoids) – including squids, octopuses, and cuttlefish – split more than 300 million years ago into two major lineages: the ten-armed Decapodiformes (squids and cuttlefish) and the eight-armed Octopodiformes (octopuses and the vampire squid). Despite its name, the vampire squid has eight arms like an octopus but shares key genomic features with squids and cuttlefish. It occupies an intermediate position between these two lineages – a connection that its genome reveals for the first time at the chromosomal level. Although it belongs to the octopus lineage, it retains elements of a more ancestral, squid-like chromosomal organization, providing new insight into early cephalopod evolution.

An enormous genome with ancient architecture

At over 11 billion base pairs, the genome of the vampire squid is roughly four times larger than the human genome – the largest cephalopod genome ever analyzed. Despite this size, its chromosomes show a surprisingly conserved structure. Because of this, Vampyroteuthis is considered a "genomic living fossil" – a modern representative of an ancient lineage that preserves key features of its evolutionary past. The team found that it has preserved parts of a decapodiform-like karyotype while modern octopuses underwent extensive chromosomal fusions and rearrangements during evolution. This conserved genomic architecture provides new clues to how cephalopod lineages diverged. "The vampire squid sits right at the interface between octopuses and squids," says the senior author Oleg Simakov from the Department of Neurosciences and Developmental Biology at the University of Vienna. "Its genome reveals deep evolutionary secrets on how two strikingly different lineages could emerge from a shared ancestor."

Octopus genomes formed their own evolutionary highway

By comparing the vampire squid with other sequenced species, including the pelagic octopus Argonauta hians, the researchers were able to trace the direction of chromosomal changes over evolutionary time. The genome sequence of Argonauta hians ("paper nautilus"), a "weird" pelagic octopus whose females secondarily obtained a shell-like calcified structure, was also presented for the first time in this study. The analysis suggests that early coleoids had a squid-like chromosomal organization, which later fused and compacted into the modern octopus genome – a process known as fusion-with-mixing. These irreversible rearrangements likely drove key morphological innovations such as the specialization of arms and the loss of external shells. "Although it is classified as an octopus, the vampire squid retains a genetic heritage that predates both lineages," adds second author Emese Tóth, University of Vienna. "It gives us a direct look into the earliest stages of cephalopod evolution."

Revisiting cephalopod evolution

The study provides the clearest genetic evidence yet that the common ancestor of octopuses and squids was more squid-like than previously thought. It highlights that large-scale chromosomal reorganization, rather than the emergence of new genes, was the main driver behind the remarkable diversity of modern cephalopods. 

About the University of Vienna: 

For over 650 years the University of Vienna has stood for education, research and innovation. Today, it is ranked among the top 100 and thus the top four per cent of all universities worldwide and is globally connected. With degree programmes covering over 180 disciplines, and more than 10,000 employees we are one of the largest academic institutions in Europe. Here, people from a broad spectrum of disciplines come together to carry out research at the highest level and develop solutions for current and future challenges. Its students and graduates develop reflected and sustainable solutions to complex challenges using innovative spirit and curiosity.

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Journal

iScience

DOI

10.1016/j.isci.2025.113832 

Article Title

Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes

Article Publication Date

21-Nov-2025

CTHULHU STUDIES

Ancient cephalopod, new insight: Nautilus reveals unexpected sex chromosome system

Harvard University

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Nautilus pompilius in its natural environment

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Credit: Marjorie Awai

Nautiloids—a lineage of ancient, externally-shelled cephalopods that diverged from their octopus and squid relatives over 400 million years ago—once dominated our oceans. Today, this living fossil is restricted to a handful of species in the Southern Indo-Pacific, making it one of the few marine invertebrates listed under CITES appendix II of species in need of protection from over-exploitation..

Although no one had previously investigated sex determination systems in cephalopods, recent research suggested a ZZ/Z0 system, where males are homozygous (having two identical sex chromosomes) and females are hemizygous (having only one sex chromosome). This system was believed to have originated approximately 480 million years ago in the last common ancestor of all cephalopods, thus making it one of the oldest conserved sex determination systems known in animals.

However, a new study published in Current Biology, challenges this in modern cephalopods. Instead, researchers discovered the first evidence of an XX/XY system in chambered nautiluses. This genetic mechanism is more similar to that found in humans, mammals and many other animals, where males are the heterogametic sex (XY).

The international team of researchers led by Professor David Combosch of the Marine Laboratory at the University of Guam, with co-author Professor Gonzalo Giribet in the Department of Organismic and Evolutionary Biology and Director of the Museum of Comparative Zoology at Harvard, analyzed three distinct genomic datasets. These included 28 low-coverage whole genomes and 63 restriction-site associated DNA sequencing (RAD-seq) datasets sourced from six species and nine populations of nautiloids.

Using Bayesian analyses, sex-specific differences in genome coverage, and patterns of heterozygosity, they identified one DNA segment as an X chromosome and pinpointed five additional DNA segments as likely Y-linked regions. These five Y-scaffolds contain 36 genes, most of which were either male-specific or significantly enriched in males.

“This is the first time anyone has identified X- or Y-linked sequences in a cephalopod,” Giribet noted. “Our findings suggest that sex chromosomes in mollusks are far more dynamic and lineage-specific than previously assumed.”

To investigate the biological relevance of these genes, the researchers performed functional annotation and BLAST protein searches using a stringent e-value threshold. Many genes showed homology to human genes with known expression in reproductive tissues or links to sex-related traits, as documented in genome-wide association studies. Further Gene Ontology enrichment analysis supported the idea that these genes are involved in sex-specific functions. The team also identified chromosome #4 as the X chromosome rather than Z chromosome as previously assumed.

Despite the breakthrough, the study faced key limitations. The lack of a chromosome-level genome for male nautiluses limited the researchers’ ability to fully characterize the structure and evolution of the sex chromosomes. Still, this work lays the foundation for further genomic exploration across other cephalopod lineages and has broader implication for cephalopod biology and conservation. Several nautilus species are currently listed as vulnerable due to overharvesting and habitat loss. A better understanding of their genetics, including sex determination mechanisms, could directly inform future conservation and management efforts.

By revealing that nautiluses possess an XX/XY sex determination system, this research not only revises assumptions about cephalopod genetics, but also contributes a critical piece to the broader puzzle of sex chromosome evolution in animals.

“Our results rewrite our understanding of cephalopod sex determination and help clarify the evolutionary history of these fascinating animals,” Combosch said. “It reminds us that, in the natural world, even the most fundamental biological systems can evolve quickly and in unexpected ways.”

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The female is on the left and the male is on the right, with its spadix (arrow) protruding towards the female

Credit

Marjorie Awai

Journal

Current Biology

DOI

10.1016/j.cub.2025.07.047 

Article Title

Nautilus sex determination is unique among cephalopods

Article Publication Date

14-Aug-2025

 CTHULHU STUDIES

Octopus arms have segmented nervous systems to power extraordinary movements

The large nerve cord running down each octopus arm is separated into segments, giving it precise control over movements and creating a spatial map of its suckers.

University of Chicago

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Octopus arms move with incredible dexterity, bending, twisting, and curling with nearly infinite degrees of freedom.

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Credit: Cassady Olson

Octopus arms move with incredible dexterity, bending, twisting, and curling with nearly infinite degrees of freedom. New research from the University of Chicago revealed that the nervous system circuitry that controls arm movement in octopuses is segmented, giving these extraordinary creatures precise control across all eight arms and hundreds of suckers to explore their environment, grasp objects, and capture prey.

“If you're going to have a nervous system that's controlling such dynamic movement, that's a good way to set it up,” said Clifton Ragsdale, PhD, Professor of Neurobiology at UChicago and senior author of the study. “We think it’s a feature that specifically evolved in soft-bodied cephalopods with suckers to carry out these worm-like movements.”

The study, “Neuronal segmentation in cephalopod arms,” was published January 15, 2025, in Nature Communications.

Each octopus arm has a massive nervous system, with more neurons combined across the eight arms than in the animal’s brain. These neurons are concentrated in a large axial nerve cord (ANC), which snakes back and forth as it travels down the arm, every bend forming an enlargement over each sucker.

Cassady Olson, a graduate student in Computational Neuroscience who led the study, wanted to analyze the structure of the ANC and its connections to musculature in the arms of the California two-spot octopus (Octopus bimaculoides), a small species native to the Pacific Ocean off the coast of California. She and her co-author Grace Schulz, a graduate student in Development, Regeneration and Stem Cell Biology, were trying to look at thin, circular cross-sections of the arms under a microscope, but the samples kept falling off the slides. They tried lengthwise strips of the arms and had better luck, which led to an unexpected discovery.

Using cellular markers and imaging tools to trace the structure and connections from the ANC, they saw that neuronal cell bodies were packed into columns that formed segments, like a corrugated pipe. These segments are separated by gaps called septa, where nerves and blood vessels exit to nearby muscles. Nerves from multiple segments connect to different regions of muscles, suggesting the segments work together to control movement.

“Thinking about this from a modeling perspective, the best way to set up a control system for this very long, flexible arm would be to divide it into segments,” Olson said. “There has to be some sort of communication between the segments, which you can imagine would help smooth out the movements.”

Nerves for the suckers also exited from the ANC through these septa, systematically connecting to the outer edge of each sucker. This indicates that the nervous system sets up a spatial, or topographical, map of each sucker. Octopuses can move and change the shape of their suckers independently. The suckers are also packed with sensory receptors that allow the octopus to taste and smell things that they touch—like combining a hand with a tongue and a nose. The researchers believe the “suckeroptopy,” as they called the map, facilitates this complex sensory-motor ability.

To see if this kind of structure is common to other soft-bodied cephalopods, Olson also studied longfin inshore squid (Doryteuthis pealeii), which are common in the Atlantic Ocean. These squid have eight arms with muscles and suckers like an octopus, plus two tentacles. The tentacles have a long stalk with no suckers, with a club at the end that does have suckers. While hunting, the squid can shoot the tentacles out and grab prey with the sucker-equipped clubs.

Using the same process to study long strips of the squid tentacles, Olson saw that the ANC in the stalks with no suckers are not segmented, but the clubs at the end are segmented the same way as the octopus. This suggests that a segmented ANC is specifically built for controlling any type of dexterous, sucker-laden appendage in cephalopods. The squid tentacle clubs have fewer segments per sucker, however, likely because they do not use the suckers for sensation the same way octopuses do. Squid rely more on their vision to hunt in the open water, whereas octopuses prowl the ocean floor and use their sensitive arms as tools for exploration.

While octopuses and squid diverged from each other more than 270 million years ago, the commonalities in how they control parts of their appendages with suckers—and differences in the parts that don’t—show how evolution always manages to find the best solution.

“Organisms with these sucker-laden appendages that have worm-like movements need the right kind of nervous system,” Ragsdale said. “Different cephalopods have come up with a segmental structure, the details of which vary according to the demands of their environments and the pressures of hundreds of millions of years of evolution.”

University of Chicago

Octopus bimaculoides

Octopus bimaculoides

Octopus bimaculoides

Octopus bimaculoides

Octopus bimaculoides

Credit

Cassady Olson

Journal

Nature Communications

DOI

10.1038/s41467-024-55475-5 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Neuronal segmentation in cephalopod arms

Article Publication Date

15-Jan-2025

CTHULHU STUDIES

Octopuses and their relatives are a new animal welfare frontier

Photo by Masaaki Komori on Unsplash

The Conversation

December 27, 2024

We named him Squirt – not because he was the smallest of the 16 cuttlefish in the pool, but because anyone with the audacity to scoop him into a separate tank to study him was likely to get soaked. Squirt had notoriously accurate aim.


As a comparative psychologist, I’m used to assaults from my experimental subjects. I’ve been stung by bees, pinched by crayfish and battered by indignant pigeons. But, somehow, with Squirt it felt different. As he eyed us with his W-shaped pupils, he seemed clearly to be plotting against us

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A common cuttlefish (Sepia officinalis) in Portugal’s Arrábida Natural Park.

Diego Delso/Wikipedia, CC BY-SA

Of course, I’m being anthropomorphic. Science does not yet have the tools to confirm whether cuttlefish have emotional states, or whether they are capable of conscious experience, much less sinister plots. But there’s undeniably something special about cephalopods – the class of ocean-dwelling invertebrates that includes cuttlefish, squid and octopus.

As researchers learn more about cehpalopods’ cognitive skills, there are calls to treat them in ways better aligned with their level of intelligence. California and Washington state both approved bans on octopus farming in 2024. Hawaii is considering similar action, and a ban on farming octopus or importing farmed octopus meat has been introduced in Congress. A planned octopus farm in Spain’s Canary Islands is attracting opposition from scientists and animal welfare advocates.

Critics offer many arguments against raising octopuses for food, including possible releases of waste, antibiotics or pathogens from aquaculture facilities. But as a psychologist, I see intelligence as the most intriguing part of the equation. Just how smart are cephalopods, really? After all, it’s legal to farm chickens and cows. Is an octopus smarter than, say, a turkey? 

A deepwater octopus investigates the port manipulator arm of the ALVIN submersible research vessel. NOAA, CC BY

A big, diverse group

Cephalopods are a broad class of mollusks that includes the coleoids – cuttlefish, octopus and squid – as well as the chambered nautilus. Coleoids range in size from adult squid only a few millimeters long (Idiosepius) to the largest living invertebrates, the giant squid (Architeuthis) and colossal squid (Mesonychoteuthis) which can grow to over 40 feet in length and weigh over 1,000 pounds.

Some of these species live alone in the nearly featureless darkness of the deep ocean; others live socially on active, sunny coral reefs. Many are skilled hunters, but some feed passively on floating debris. Because of this enormous diversity, the size and complexity of cephalopod brains and behaviors also varies tremendously.

Almost everything that’s known about cephalopod cognition comes from intensive study of just a few species. When considering the welfare of a designated species of captive octopus, it’s important to be careful about using data collected from a distant evolutionary relative. 

Marine biologist Roger Hanlon explains the distributed structure of cephalopod brains and how they use that neural power.

Can we even measure alien intelligence?

Intelligence is fiendishly hard to define and measure, even in humans. The challenge grows exponentially in studying animals with sensory, motivational and problem-solving skills that differ profoundly from ours.

Historically, researchers have tended to focus on whether animals think like humans, ignoring the abilities that animals may have that humans lack. To avoid this problem, scientists have tried to find more objective measures of cognitive abilities.

One option is a relative measure of brain to body size. The best-studied species of octopus, Octopus vulgaris, has about 500 million neurons; that’s relatively large for its small body size and similar to a starling, rabbit or turkey.

More accurate measures may include the size, neuron count or surface area of specific brain structures thought to be important for learning. While this is useful in mammals, the nervous system of an octopus is built completely differently.

Over half of the neurons in Octopus vulgaris, about 300 million, are not in the brain at all, but distributed in “mini-brains,” or ganglia, in the arms. Within the central brain, most of the remaining neurons are dedicated to visual processing, leaving less than a quarter of its neurons for other processes such as learning and memory.

In other species of octopus, the general structure is similar, but complexity varies. Wrinkles and folds in the brain increase its surface area and may enhance neural connections and communication. Some species of octopus, notably those living in reef habitats, have more wrinkled brains than those living in the deep sea, suggesting that these species may possess a higher degree of intelligence.

Holding out for a better snack

Because brain structure is not a foolproof measure of intelligence, behavioral tests may provide better evidence. One of the highly complex behaviors that many cephalopods show is visual camouflage. They can open and close tiny sacs just below their skin that contain colored pigments and reflectors, revealing specific colors. Octopus vulgaris has up to 150,000 chromatophores, or pigment sacs, in a single square inch of skin.

Like many cephalopods, the common cuttlefish (Sepia officinalis) is thought to be colorblind. But it can use its excellent vision to produce a dizzying array of patterns across its body as camouflage. The Australian giant cuttlefish, Sepia apama, uses its chromatophores to communicate, creating patterns that attract mates and warn off aggressors. This ability can also come in handy for hunting; many cephalopods are ambush predators that blend into the background or even lure their prey.

The hallmark of intelligent behavior, however, is learning and memory – and there is plenty of evidence that some octopuses and cuttlefish learn in a way that is comparable to learning in vertebrates. The common cuttlefish (Sepia officinalis), as well as the common octopus (Octopus vulgaris) and the day octopus (Octopus cyanea), can all form simple associations, such as learning which image on a screen predicts that food will appear.

Some cephalopods may be capable of more complicated forms of learning, such as reversal learning – learning to flexibly adjust behavior when different stimuli signal reward. They may also be able to inhibit impulsive responses. In a 2021 study that gave common cuttlefish a choice between a less desirable but immediate snack of crab and a preferred treat of live shrimp after a delay, many of the cuttlefish chose to wait for the shrimp.

Cuttlefish perform in an experiment adapted from the Stanford “marshmallow test,” which was designed to see whether children could practice delayed gratification.

A new frontier for animal welfare

Considering what’s known about their brain structures, sensory systems and learning capacity, it appears that cephalopods as a group may be similar in intelligence to vertebrates as a group. Since many societies have animal welfare standards for mice, rats, chickens and other vertebrates, logic would suggest that there’s an equal case for regulations enforcing humane treatment of cephalopods.

Such rules generally specify that when a species is held in captivity, its housing conditions should support the animal’s welfare and natural behavior. This view has led some U.S. states to outlaw confined cages for egg-laying hens and crates too narrow for pregnant sows to turn around.

Animal welfare regulations say little about invertebrates, but guidelines for the care and use of captive cephalopods have started to appear over the past decade. In 2010, the European Union required considering ethical issues when using cephalopods for research. And in 2015, AAALAC International, an international accreditation organization for ethical animal research, and the Federation of European Laboratory Animal Science Associations promoted guidelines for the care and use of cephalopods in research. The U.S. National Institutes of Health is currently considering similar guidelines.

The “alien” minds of octopuses and their relatives are fascinating, not the least because they provide a mirror through which we can reflect on more familiar forms of intelligence. Deciding which species deserve moral consideration requires selecting criteria, such as neuron count or learning capacity, to inform those choices.

Once these criteria are set, it may be well to also consider how they apply to the rodents, birds and fish that occupy more familiar roles in our lives.

Rachel Blaser, Professor of Neuroscience, Cognition and Behavior, University of San Diego

This article is republished from The Conversation under a Creative Commons license. Read the original article.