From the depths to discovery: a tiny limpet reveals big secrets of the deep sea

In the inky depths of the Central Pacific Ocean, nearly 2,400 meters below the surface, scientists have discovered a new species of deep-sea limpet clinging to a sunken log.

During a 2023 expedition aboard the E/V Nautilus, scientists using the remotely operated vehicle Hercules spotted a fragment of sunken wood resting off the remote Johnston Atoll. When they drew closer, they found a thriving community clinging to the timber. Among them was a large population of strange limpets — oval, pale, and thick-shelled, with a distinctive arched profile. It didn’t take long for Paula Rodríguez-Flores, postdoctoral researcher in the Department of Organismic and Evolutionary Biology (OEB) at Harvard who was aboard Nautilus when the wood fragment was collected, to realize they were looking at a new species.

In a new study published in Molluscan Research, researchers in OEB and the Harvard Museum of Comparative Zoology (MCZ) formally describe Pectinodonta nautilus, named in honor of the exploration vessel responsible for its discovery. The team led by Gonzalo Giribet, Professor in OEB and Director of the MCZ, and Postdoctoral Researcher Paula Rodríguez-Flores, used cutting-edge imaging and molecular techniques to fully examine the 79 individuals collected from the 35-centimeter-long piece of wood.

Belonging to a family of mollusks known as Pectinodontidae, P. nautilus is part of a rare group of limpets that make their homes on “wood falls”— sunken tree trunks and branches that drift down from the surface and settle on the seafloor. These decomposing logs become temporary islands of life in an otherwise barren environment, nourishing dense bacterial mats and specialized creatures that feed on them.

“Wood falls are fleeting ecosystems in the deep ocean, and yet they host remarkably specialized fauna,” said Rodríguez-Flores. “Unlike the well-studied ecosystems built around hydrothermal vents and methane seeps, wood falls remain elusive, less studied in their natural setting.” Yet, they are crucial patches of life in the deep ocean, delivering bursts of organic matter into what might otherwise be a biological desert.

Back in the lab with the samples, the team used high-resolution micro-CT scanning and 3D modeling to visualize the limpet’s anatomy without dissection. These limpets are large for their family – some more than three centimeters long – and they continue growing as the wood decays around them. Their off-white shells are sturdy, strongly arched, and unusually smooth. Scanning electron microscopy revealed a faint radial sculpture near the posterior dorsal surface. The smoothness, combined with thick concentric growth lines, set the species apart from its relatives.

Things got even more interesting inside the mouth. Like other wood-dwelling limpets, P. nautilus boasts oversized radular teeth – the chitinous scraping tools that function like conveyor-belt tongues. Each tooth resembles an inverted V studded with around 17 cusps. When compared with relatives like P. mazuae, the new species has nearly double the size in its radular structures, hinting at distinct feeding strategies or evolutionary pressures tied to its isolated nursery log.

DNA sequencing and mitochondrial genome analysis confirmed that P. nautilus represents a distinct lineage within Pectinodonta. Phylogenetic analyses revealed that P. nautilus is most closely linked with species from New Zealand and the Western Pacific, including P. Marinovichi and P. orientalis.

“Our findings suggest this lineage of wood-fall may be far more widespread across the Pacific than previously recognized,” said lead author Gonzalo Giribet, Professor in OEB and Director and Curator of Invertebrates in the MCZ.

The deeper evolutionary tree, however, remains hazy. Mitochondrial arrangements across related families showed intense gene shuffling, making lineage boundaries difficult to pin down. The researchers determined a need for full genome assemblies before confidently rewriting the family history. The findings also indicate that radular morphology, rather than shell shape, may be a more reliable way to distinguish among these cryptic species.

“The discovery underscores how little is known about life in the deep sea,” Rodríguez-Flores said. “Fewer than seven percent of described marine species come from below 1,000 meters, leaving vast stretches of ocean biodiversity unexplored.”

But the presence of individuals of many different sizes – juveniles to well-grown adults – indicates the wood fall supported multiple generations; suggesting that even tiny islands of habitat can sustain deep-sea communities long enough for population turnover and dispersal.

The team, which included Ph.D. candidate Arianna Lord and MCZ Curatorial Associate, Jennifer Winifred Trimble, took on no easy task studying these fragile organism. The team faced challenges in handling the delicate radulae – one disintegrated during cleaning – and in generating complete genome data from the limited tissue available. A shortage of comparative specimens from other oceans also made it difficult to test broader evolutionary and biogeographic patterns.

Still, the researchers say the discovery of Pectinodonta nautilus adds a crucial piece to the puzzle of how life persists in one of Earth’s harshest habitats. They hope to continue examining other deep-sea communities near Johnston Atoll, which have already yielded several new species of crustaceans and corals, including a previously unknown squat lobster species that the Nautilus team named Munidopsis giribeti, in honor of Professor Gonzalo Giribet and his passion and dedication to invertebrates.

“Every deep dive reveals that the ocean still holds countless surprises,” said Rodgríguez-Flores. “We’re only just beginning to understand the hidden biodiversity living on the seafloor.”

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