Mysterious holes found on ocean floor have scientists ‘stumped’

These linear, peculiar-looking openings in the sand could be human made. But a more plausible explanation might be that they’re tracks left behind by an undiscovered species lurking in the deep sea. The depths of the Earth's oceans contain many secrets that often take researchers years of investigation to solve. A new mystery in the Atlantic Ocean is almost literally taking them down the rabbit hole. On July 23, along the seafloor off the coast of Portugal beneath the island chain of the Azores, scientists working with the National Oceanic and Atmospheric Administration (NOAA) found a dozen sets of small holes in the sand at a depth of nearly 2 miles, with no clues of how they got there. Two weeks later and 300 miles away, they found even more mysterious holes, exactly the same as the first.

A close look at the sets of holes along the floors of the Atlantic Ocean. The origins of the holes are unclear. (NOAA Ocean Exploration) From May to September 2022, NOAA is carrying out an expedition called Voyage to the Ridge 2022 in this relatively unexplored region of the Atlantic. NOAA scientists set off from Newport, Rhode Island, to Newfoundland, Canada, on the first leg of the trip and then left Norfolk, Virginia, for the Azores. They will finish up by traversing the Atlantic in the other direction, to Puerto Rico and the Caribbean. Their research vessel, called the Okeanos Explorer, is investigating the coral and sponge colonies on volcanic ridges. Finding the holes was more of a happy accident. This isn't the first time scientists encountered these strange-looking patterns. NOAA spokesperson Emily Crum told The New York Times that in 2004, right in the vicinity of this initial discovery, researchers recorded the first sighting of the holes. “The origin of the holes has scientists stumped,” NOAA's Ocean Exploration project tweeted. “The holes look human made, but the little piles of sediment around them suggest they were excavated by … something.” “There is something important going on there and we don’t know what it is,” NOAA deep-sea biologist Michael Vecchione told the Times. “This highlights the fact that there are still mysteries out there.” Hypotheses regarding the origins of the holes range from human-made causes to the tracks of an undiscovered species of animal or a gas vent blowing bubbles up through the sand. Vecchione co-authored a paper in 2022 discussing the gaps in current knowledge of the holes and what could be causing them. According to the paper, the holes appear to have been either excavated from the top or pierced up from underneath, meaning whatever created them could have been digging the holes or burrowed under the sediment and potentially used the holes as a breathing apparatus -- like a snorkel. There's no definitive evidence to say for sure, though, and it will take more time and investigations to find the truth.

NOAA scientists use this underwater drone, called Deep Discoverer, to examine features of the seafloor up to 19,000 feet below the ocean's surface. (NOAA Ocean Exploration) Vecchione, who was present for this latest run-in with the mysterious holes, said he was happy to see them again after nearly two decades but also expressed disappointment that there are still no answers. The Okeanos Explorer is currently docked in the Azores until Aug. 6, when the vessel will set out for its third Voyage to the Ridge expedition.

The mysterious, legendary giant squid's genome is revealed.

How did the monstrous giant squid -- reaching school-bus size, with eyes as big as dinner plates and tentacles that can snatch prey 10 yards away -- get so scarily big?

Today, important clues about the anatomy and evolution of the mysterious giant squid (Architeuthis dux) are revealed through publication of its full genome sequence by a University of Copenhagen-led team that includes scientist Caroline Albertin of the Marine Biological Laboratory (MBL), Woods Hole.

Giant squid are rarely sighted and have never been caught and kept alive, meaning their biology (even how they reproduce) is still largely a mystery. The genome sequence can provide important insight.

"In terms of their genes, we found the giant squid look a lot like other animals. This means we can study these truly bizarre animals to learn more about ourselves," says Albertin, who in 2015 led the team that sequenced the first genome of a cephalopod (the group that includes squid, octopus, cuttlefish, and nautilus).

Led by Rute da Fonseca at University of Copenhagen, the team discovered that the giant squid genome is big: with an estimated 2.7 billion DNA base pairs, it's about 90 percent the size of the human genome.

Albertin analyzed several ancient, well-known gene families in the giant squid, drawing comparisons with the four other cephalopod species that have been sequenced and with the human genome.

She found that important developmental genes in almost all animals (Hox and Wnt) were present in single copies only in the giant squid genome. That means this gigantic, invertebrate creature -- long a source of sea-monster lore -- did NOT get so big through whole-genome duplication, a strategy that evolution took long ago to increase the size of vertebrates.

So, knowing how this squid species got so giant awaits further probing of its genome.

"A genome is a first step for answering a lot of questions about the biology of these very weird animals," Albertin said, such as how they acquired the largest brain among the invertebrates, their sophisticated behaviors and agility, and their incredible skill at instantaneous camouflage.

"While cephalopods have many complex and elaborate features, they are thought to have evolved independently of the vertebrates. By comparing their genomes we can ask, 'Are cephalopods and vertebrates built the same way or are they built differently?'" Albertin says.

Albertin also identified more than 100 genes in the protocadherin family -- typically not found in abundance in invertebrates -- in the giant squid genome.

"Protocadherins are thought to be important in wiring up a complicated brain correctly," she says. "They were thought they were a vertebrate innovation, so we were really surprised when we found more than 100 of them in the octopus genome (in 2015). That seemed like a smoking gun to how you make a complicated brain. And we have found a similar expansion of protocadherins in the giant squid, as well."

Lastly, she analyzed a gene family that (so far) is unique to cephalopods, called reflectins. "Reflectins encode a protein that is involved in making iridescence. Color is an important part of camouflage, so we are trying to understand what this gene family is doing and how it works," Albertin says.

"Having this giant squid genome is an important node in helping us understand what makes a cephalopod a cephalopod. And it also can help us understand how new and novel genes arise in evolution and development."

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Materials provided by Marine Biological Laboratory. Original written by Diana Kenney. Note: Content may be edited for style and length.