Vampires of 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.

In a study now published in iScience, researchers led equally by three Principal Investigators from the Shimane University (Japan), National Institute of Technology — Wakayama College (NITW; Japan), and University of Vienna (Austria), 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 suggesting that modern octopuses probably evolved from squid-like ancestors.

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 and instead feeds peacefully on organic detritus. 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 Masa-aki Yoshida (Shimane University), Davin Setiamarga (NITW), and Oleg Simakov (University of Vienna) has now decoded the vampire squid's genome.

The vampire squid's draft genome was sequenced by a team led by Atsushi Toyoda and Hideki Noguchi at the National Institute of Genetics, Japan, under the Platform for Advanced Genome Science (PAGS) program, which provides large-scale genome sequencing and bioinformatics support to selected KAKENHI (a Japanese federal research funding scheme) research projects.

A project led by Masa-aki Yoshida and Davin Setiamarga was selected for PAGS Support to sequence two cephalopod species, the vampire squid and the muddy argonaut (Argonauta hians). The muddy argonaut is another weird octopus, having a shell-like calcified eggcase but not a real shell. In 2022, a team led by Setiamarga and Yoshida reported the draft genome sequence of a congener of this species, the greater argonaut (A. argo), with genome sequencing also supported by PAGS (Yoshida et al., 2022). Yoshida and Setiamarga then invited their long-time friend and collaborator, Oleg Simakov, to expand the sequencing of the A. hians genome to chromosome-level resolution and to analyze together the karyotypic evolution of cephalopods.

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 250 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. "In Japanese, the vampire squid is called "kōmori-dako", which actually means "bat-octopus"," says Yoshida, one of three lead PIs of this project.

An enormous genome with ancient architecture

At around 12 billion base pairs, the genome of the vampire squid is roughly four times larger than the human genome — the largest cephalopod genome ever analyzed. However, interestingly, 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 Simakov, another lead PI of this project. "Its genome shows how two strikingly different lineages could emerge from a shared ancestor." "Therefore, you can probably say that octopuses are just bootleg squids," says Setiamarga, also another lead PI of the project.

From a common ancestor to two lineages

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, or the "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 Emese Tóth, an Evolutionary Genomics and Systems Biology Master student from the University of Vienna who is the second author on the manuscript. "It gives us a direct look into the earliest stages of cephalopod evolution." "It is really interesting though that, although the vampire squids are considered as ancestral among the octopuses, molecular clock suggests that the split between the lineage of the vampire squids and the common squids actually happens in a very short time — way before the split between the vampire squids and the octopuses," remarks Kazuki Hirota, a PhD Student of the Department of Earth and Planetary Sciences at the University of Tokyo and a technical staff of NITW, who was also involved in the study.

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.

Scientific contacts

Dr. Davin Setiamarga
Professor (Assoc.) of Molecular Biology
Department of Applied Chemistry and Biochemistry
National Institute of Technology (KOSEN) — Wakayama College (NIT-Wakayama)
77 Noshima, Nada, Wakayama 644-0023, Japan
TEL +81-738-29-8429
davin＠wakayama-nct.ac.jp

Dr. Oleg Simakov
Professor of Evolutionary Genomics
Department for Neurosciences and Developmental Biology
University of Vienna
Djerassiplatz 1, 1030 Vienna, Austria
TEL +43-1-4277-56501
oleg.simakov＠univie.ac.at

Dr. Masa-aki Yoshida
Professor of Marine Biology
Faculty of Life and Environmental Science, Shimane University
194 Kamo, Okinoshima-cho, Oki, Shimane 685-0024, Japan
TEL +81-8512-2-1814
mayoshida＠life.shimane-u.ac.jp

Journal Information
Publication: iScience
Title: Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes
DOI: 10.1016/j.isci.2025.113832