Unusual Fossil Discovery Rewrites the History of Freshwater Fish

New research finds that ocean-dwelling fish entered freshwater environments on several occasions, evolving enhanced hearing abilities in the process.

When ancient marine fish transitioned from saltwater to freshwater environments, many also developed more complex hearing systems, including middle ear bones that resemble those found in humans.

Today, about two-thirds of all freshwater fish — more than 10,000 species, ranging from catfish to aquarium favorites such as tetras and zebrafish — possess this specialized middle ear structure known as the Weberian apparatus. This system enables them to detect much higher-frequency sounds than most ocean-dwelling fish, with a hearing range similar to that of humans.

Juan Liu, a paleontologist at the University of California, Berkeley, has examined the structure of the Weberian apparatus in a newly identified fossil fish and used it to revise the evolutionary timeline for the origin of freshwater fish.

From ocean ancestors to freshwater innovators

Fish with a Weberian ear system, known as otophysan fish, were previously believed to have entered freshwater habitats around 180 million years ago, before the supercontinent Pangea began to fragment. However, Liu’s new analysis places their emergence later — roughly 154 million years ago, during the late Jurassic Period — after Pangea had started to break apart and modern oceans were beginning to form.

https://youtu.be/HC0MTmvpbw8
Juan Liu and her student used finite element analysis to create a computer model of the vibrational response of the Weberian ossicles of fish. This simulation shows the amplitude and vibrations of zebrafish ossicles at a frequency of 1,012 Hertz. The large, triangular ossicle is called the tripus and is a modification of the rib and third vertebra to amplify sound vibrations from the air bladder. Credit: Juan Liu & Zehua Zhou, UC Berkeley and UCMP

By combining fossil evidence with genomic data, Liu determined that the early versions of these hearing structures first appeared in marine species. It was only after two separate lineages moved into freshwater environments that the Weberian apparatus became fully functional. One lineage gave rise to modern catfish, knife fish, and African and South American tetras, while the other led to carps, suckers, minnows, and zebrafish — the largest order of freshwater fish alive today.

Fossil evidence reshapes evolutionary understanding

“The marine environment is the cradle of a lot of vertebrates,” said Liu, an assistant adjunct professor of integrative biology and an assistant curator in the UC Museum of Paleontology. “A long time consensus was that these bony fish had a single freshwater origin in the large continent Pangea and then dispersed with the separation of different continents. My team’s analysis of some fantastic fossils that shed new light on the evolutionary history of freshwater fish and found completely different results: the most recent common ancestor of otophysan fish was a marine lineage and there were at least two freshwater incursions after that lineage split up.”

This finding reshapes our understanding of the evolutionary history and intricate biogeography of the world’s most successful group of freshwater fish, she added. “These repeated incursions into freshwater at the early divergence stage likely accelerated speciation, and are key factors in explaining the extraordinary hyper-diversity of otophysans in modern freshwater faunas.”

Liu and her colleagues describe and name the 67-million-year-old fossil fish, Acronichthys maccagnoi, in a paper recently published in the journal Science. In that paper, the researchers analyze 3D scans of the fossil’s Weberian structure and the genomes and morphology of modern fish to revise the genealogy of freshwater fish, and also simulate the frequency response of the fossil fish’s middle ear structure.

A Rube Goldberg-like structure in the middle ear

Ears that work underwater require a different anatomy than ears that detect sound traveling through the air. Many land vertebrates evolved an eardrum-like structure that vibrates in response to sound waves. That eardrum moves a Rube Goldberg-like array of bones in the middle ear — in humans, the malleus, incus and stapes — that amplify the sound and poke the fluid-filled inner ear, which jiggles and eventually jostles hairs that send signals to the brain.

A 3D model of the head of the newly named 67 million-year-old fossil fish, Acronichthys maccagnoi, based on CT scans. The skull bones are brightly colored while the ribs and backbones of the spine are in gray. The small, bright red bones at the junction between the spine and head are ossicles of the Weberian apparatus. Credit: Juan Liu, UC Museum of Paleontology & Don Brinkman, Royal Tyrrell Museum

But sound waves in water go right through a fish, which has a similar density to the surrounding water. So fish developed a bladder filled with air — essentially a bubble — that vibrates in response to sounds passing through the fish. Those vibrations are transferred to the fish’s inner ear in a rudimentary way in most saltwater fish, which limits their hearing to bass notes below about 200 Hertz.

Otophysan fish, however, developed bony “ossicles” between the air bladder — often inaccurately referred to as the swim bladder — and the inner ear to amplify and extend the frequency range the ears can detect. Zebrafish, for example, can hear frequencies up to 15,000 Hz, not far from the 20,000 Hz limit of humans.

Why these fish need to hear high frequencies is a mystery, though it may be because they live in diverse and complicated environments, from rushing streams to static lakes.

Liu studies the Weberian apparatus in living and fossil fish, and last year published a computational simulation of how the apparatus works. That simulation allows her to predict the frequency response of the bony ossicles, and thus the hearing sensitivity of fish.

Fossils and digital imaging reveal ancient anatomy

Numerous specimens of the newly named fossil fish, a mere 2 inches long, were excavated and collected in Alberta, Canada, over six field seasons starting in 2009 by ichthyologist and co-author Michael Newbrey of Columbus State University in Georgia. The fossils are housed in the Royal Tyrrell Museum in Drumheller, Alberta. A couple of specimens were so well preserved that the bones in the middle ear were clearly Weberian. The fish is the oldest known North American fossil of an otophysan fish, or Otophysi, dating from the late Cretaceous Period, only a short time before the non-avian dinosaurs disappeared. Older specimens have been found elsewhere in the world, but none had a well-preserved Weberian apparatus, Liu said.

Technicians with the Canadian Light Source at the University of Saskatchewan in Saskatoon and at McGill University in Montreal captured 3D X-ray scans of the fish, and Liu modeled the ossicles of the Weberian apparatus in her laboratory. The model suggests that, even 67 million years ago, otophysan fish had nearly as sensitive hearing as zebrafish do today.

Hearing evolution and biodiversity

“We weren’t sure if this was a fully functional Weberian apparatus, but it turns out the simulation worked,” Liu said. “The Weberian apparatus has just a little bit lower output power, which means lower sensitivity, compared to a zebrafish. But the peak, the most sensitive frequency, is not too much lower than zebrafish — between 500 and 1,000 Hertz — which is not too bad at all and which means the higher frequency hearing should have been achieved in this old otophysan fish.”

She noted that the findings highlight a general pattern in evolution: sudden increases in new species can arise from repeated incursions into new habitats rather than a single dispersal event, especially when coupled with new innovations, such as more sensitive hearing.

“For a long time, we presumed that the Otophysi probably had a freshwater origin because this group consisted almost exclusively of freshwater fishes,” Newbrey said. “The new species provides crucial information for a new interpretation of the evolutionary pathways of the Otophysi with a marine origin. It just makes so much more sense.”

Reference: “Marine origins and freshwater radiations of the otophysan fishes” by Juan Liu, Donald B. Brinkman, Alison M. Murray, Michael G. Newbrey, Zehua Zhou, Lisa L. Van Loon and Neil R. Banerjee, 2 October 2025, Science.
DOI: 10.1126/science.adr4494

Liu was funded by a Franklin Research Grant from the American Philosophical Society.

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