'Vampire Squid From Hell' Reveals The Ancient Origins of Octopuses

The so-called "vampire squid from hell" has produced the biggest cephalopod genome ever sequenced: a behemoth measuring more than 11 billion base pairs, which is over twice the size of the largest squid genomes known so far.

Within that vast arrangement of A, T, G and C sits an unexpectedly rich evolutionary narrative. Although Vampyroteuthis infernalis is not a true squid, it has retained a remarkably squid-like chromosomal architecture-a configuration once shared with the common ancestor of today’s octopuses and squids.

What the vampire squid (Vampyroteuthis infernalis) is - and why it matters

The vampire squid occupies an unusual position on the cephalopod family tree: a stubborn little branch that has endured while its close relatives disappeared. It is neither a squid nor an octopus (and, despite the name, not a vampire), but instead the last surviving representative of an ancient lineage whose other members are long gone.

In certain respects, many researchers regard it as a living fossil-dating back roughly 183 million years-because it retains numerous ancestral features alongside the adaptations that allow it to persist as a deep-sea scavenger in perpetual darkness.

Vestigial hints of body structures and traits shared with squids, octopuses and cuttlefish had already led scientists to suspect it might also preserve genetic clues about the origins of these animals, before they diverged around 300 million years ago.

"The vampire squid sits right at the interface between octopuses and squids," says genomicist Oleg Simakov of the University of Vienna. "Its genome reveals deep evolutionary secrets on how two strikingly different lineages could emerge from a shared ancestor."

A rare specimen from more than 600 metres down

Because the vampire squid is both elusive and timid-and lives in conditions profoundly hostile to humans at depths greater than 600 metres (2,000 feet)-obtaining suitable material is difficult. In this case, the team had a stroke of luck: a specimen was unintentionally collected as bycatch by the Tokai University research vessel T/V Hokuto during work in Suruga Bay.

The largest cephalopod genome ever sequenced

When the researchers sequenced its DNA, the scale of the genome surprised them: 11 to 14 gigabases. By comparison, the genome of the longfin inshore squid (Doryteuthis pealeii) is 4.4 gigabases, the Hawaiian bobtail squid (Euprymna scolopes) is 4.9 gigabases, and the previous record-holder for the largest known cephalopod genome-the common cuttlefish (Sepia officinalis)-is 5.5 gigabases.

Octopus genomes, meanwhile, are smaller still: the California two-spot octopus (Octopus bimaculoides) has 2.2 gigabases, the East Asian common octopus (Octopus sinensis) has 2.6 gigabases, and the common octopus (Octopus vulgaris) has 2.7 gigabases.

Taken together, this means the vampire squid genome can be several times larger than those of both squids and octopuses.

A notable feature of this genome is how repetitive it is: about 62 percent consists of repetitive elements-DNA sequences that recur again and again-swelling the total size without contributing additional coding sequences.

Chromosomal architecture links octopodiformes and decapodiformes

Next, the team set the vampire squid genome against previously sequenced cephalopod genomes, including those of ten-armed squids and cuttlefish (decapodiformes), eight-armed octopuses (octopodiformes), a nautilus, and several other molluscs.

They also sequenced the genome of the distinctly odd muddy argonaut (Argonauta hians), an octopus species in which females carry an external shell.

From these comparisons, a clear pattern emerged. Although the vampire squid is an eight-armed octopodiform, it still preserves portions of the chromosomal organisation seen in its ten-armed relatives, the decapodiformes. Separately, analyses of different octopus genomes indicate that early octopuses likewise possessed a squid-like chromosomal structure.

Over evolutionary time, that arrangement became compacted and fused with octopus-like chromosomal elements through an irreversible process known as fusion-with-mixing, which may have contributed to specialised octopus adaptations.

The results imply that octopuses experienced an early period of rapid chromosomal mixing, whereas vampire squid chromosomes stayed largely stable even while their genome expanded dramatically.

A Rosetta Stone for cephalopod evolution

Altogether, the findings place the vampire squid as a potential Rosetta Stone for decoding and interpreting cephalopod evolution.

"The vampire squid retains a genetic heritage that predates both [squid and octopus] lineages," says genomicist Emese Tóth of the University of Vienna. "It gives us a direct look into the earliest stages of cephalopod evolution."

The research has been published in iScience.