Natural history museums have entered a new stage of discovery and accessibility — one where scientists around the globe and curious folks at home to study, learn or just be amazed. This new era follows the completion of , or oVert, a five-year collaborative project among 18 institutions to create 3D reconstructions of vertebrate specimens and make them freely available online.

The team behind this endeavor, which includes scientists at the 91̽�� and its , published a March 6 in the journal BioScience, offering a glimpse of how the data can be used to ask new questions and spur the development of innovative technology.

Natural history museums have become valuable resources for the public, with exhibits highlighting biodiversity, evolution and conservation. But most museum collections remain behind closed doors, accessible only to scientists who must either travel to see them or ask that a small number of specimens be transported on loan. The oVert team wanted to change that.

“If you require someone to get on a plane and travel to you to collaborate, that’s prohibitive in a lot of ways,” said , head of the oVert project and curator of herpetology at the Florida Museum of Natural History. “Now we have scientists, teachers, students and artists around the world using these data remotely.”

Between 2017 and 2023, oVert project members took CT scans of more than 13,000 vertebrate specimens. For the project, a team at the UW’s scanned more than 7,200 specimens — mostly fish, but also reptiles, amphibians and mammals — using the facility’s micro-CT scanner. Many of the specimens scanned at Friday Harbor came from the Burke Museum’s permanent collection. The 91̽��team also trained more than 150 researchers, students and educators from around the world on how to CT scan specimens and analyze them for study purposes.

Since CT scanners use high-energy X-rays to peer past an organism’s exterior and view the dense bone structure beneath, most oVert reconstructions are skeletons. But, for some specimens, researchers took extra steps to visualize soft tissues, such as skin, muscle and other organs. The models give an intimate look at internal portions of a specimen that could previously only be observed through destructive dissection and tissue sampling.

“oVert is a way of reducing the wear and tear on samples while also increasing access, and it’s the next logical step in the mission of museum collections,” said Blackburn.

The project initially sought to scan only specimens preserved in ethyl alcohol, which represent the bulk of fish, reptile and amphibian collections. But researchers were reluctant to leave out larger specimens and came up with creative solutions. Project members at the Idaho Museum of Natural History, for example, painstakingly took apart a humpback whale skeleton to produce 3D models of each individual bone and digitally reassemble the whole skeleton. To scan mummified tortoises from the California Academy of Sciences’ collection, researchers had to pose them on top of inflatable swimming tubes.

Scientists have already used data from the project to gain new insights. One study of more than , for example, revealed that frogs have lost and regained teeth more than 20 times throughout their evolutionary history. A separate study concluded that , a massive dinosaur that was larger than Tyrannosaurus rex and thought to be aquatic, would have actually been a poor swimmer, and thus likely stayed on land. UW’s contributions to oVert have to date resulted in more than 40 peer-reviewed publications.

“It is so exciting to deposit the skeletal data for a new species in a repository where any scientist can access it,” said oVert team member , a 91̽��professor of biology and of aquatic and fishery sciences, who is based at Friday Harbor Labs.

Artists have used the 3D models to create realistic animal replicas, and photographs of oVert specimens have been displayed in museums, including the Burke. Specimens have been incorporated into virtual reality headsets that give users the chance to interact with and manipulate them.

oVert models have also been used by educators in both K-12 and university settings, including in 91̽��courses taken by hundreds of students.

“Digital 3D models of fish skeletons were incredibly useful during the COVID-19 pandemic, when remote labs meant 91̽��students couldn’t access physical specimens,” said oVert team member , a 91̽��associate professor of aquatic and fishery sciences and curator of fishes at the Burke Museum. “And now, we continue to use them as invaluable educational tools even though we’re back in the lab in person.”

The biggest challenge will be creating tools that are sophisticated enough to analyze the data, researchers say. This is the largest number of 3D natural history specimens released for public use, and it will take further developments in machine learning and supercomputing to use them to their full potential.

“In fact, the 91̽��has a collaborative NSF grant to do just that — develop free, open-source software to look at all these new data and quantify their shapes,” said Summers.

Katherine Maslenikov, collections manager of fishes at the Burke, is also a member of the oVert team and a co-author on the new paper. oVert was funded by the National Science Foundation.

For more information, contact Tornabene at ltorna1@uw.edu and Summers at fishguy@uw.edu.

Adapted from a by the University of Florida.

The deep sea contains more than 90% of the water in our oceans, but only about a third of all fish species. Scientists have long thought the explanation for this was intuitive — shallow ocean waters are warm and full of resources, making them a prime location for new species to evolve and thrive. But a new 91̽�� led by reports that throughout Earth’s ancient history, there were several periods of time when many fish actually favored the cold, dark, barren waters of the deep sea.

“It’s easy to look at shallow habitats like coral reefs, which are very diverse and exciting, and assume that they’ve always been that way,” said Miller, who completed the study as a postdoctoral researcher in the 91̽�� and is now a postdoctoral fellow at the University of Oklahoma. “These results really challenge that assumption, and help us understand how fish species have adapted to major changes to the climate.”

The deep sea is typically defined as anything below about 650 feet, the depth at which there is no longer enough sunlight for photosynthesis to occur. That means there is far less food and warmth than in the shallows, making it a difficult place to live. But by analyzing the relationships of fish using their genetic records going back 200 million years, Miller was able to identify a surprising evolutionary pattern: the speciation rates — that is, how quickly new species evolved — flip-flopped over time. There were periods lasting tens of millions of years when new species were evolving faster in the deep sea than in more shallow areas.

In some ways, this discovery raised more questions than it answered. What was causing fish to prefer one habitat over another? What made some fish able to move into the deep sea more easily than others? And how did these ancient shifts help create the diversity of species we have today?

When Miller mapped these flip-flopping speciation rates onto a timeline of Earth’s history, she was able to identify three major events that likely played a role.

“The first was the breakup of Pangea, which occurred between 200 and 150 million years ago,” said Miller. “That created new coastlines and new oceans, which meant there were more opportunities for fishes to move from shallow to deep water. There were suddenly a lot more access points.”

Next was the Cretaceous Hot Greenhouse period, which occurred approximately 100 million years ago and marked one of the warmest eras in Earth’s history. During this time, many continents were flooded due to sea-level rise, creating a large number of new, shallow areas across the earth.

“It was around this period that we really see shallow-water fishes take off and diversify,” said Miller. “We can trace a lot of the species diversity we see in the shallows today to this time.”

The third event was yet another major climatic change about 15 million years ago, known as the middle Miocene climatic transition. This was caused by further shifting of the continents, which caused major changes in ocean circulation and cooled the planet — all the way down to the deep sea.

“Around this time we see deep-sea speciation rates really speed up,” Miller said. “This was especially driven by cold-water fishes. A lot of the species you see today off the coasts of Washington and Alaska diversified during this time.”

But climate changes alone don’t explain how fish came to colonize the deep sea in the first place. Not every species has the right combination of traits to survive in deeper water and make use of the relatively limited resources beyond the reach of sunlight.

“To evolve into a new species in the deep sea, first you have to get there,” said Miller. “What we found was that not only were the speciation rates flip-flopping through time, but what the deep-sea fishes looked like was as well.”

The earliest fish that were able to transition into the deep sea tended to have large jaws. These likely gave them more opportunities to catch food, which can be scarce at depth. The researchers found that much later in history, fish that had longer, tapered tails tended to be most successful at making the transition to deep water. This allowed them to conserve energy by scooting along the seafloor instead of swimming in the water column.

“If you look at who lives in the deep sea today, some species have a tapered body and others have big, scary, toothy jaws,” Miller said. “Those two body plans represent ancestors that colonized the deep sea millions of years apart.”

While these events might seem like ancient history, they may be able to teach us about how today’s changing climate will affect life in our oceans. Miller hopes that future research can build on these findings and investigate how modern deep-sea fish will respond to climate change, and potentially inform conservation efforts.

“What we learned from this study is that deep-sea fishes tend to do well when oceans are colder, but with climate change, oceans are getting warmer,” she said. “We can expect that this is really going to impact fish in the deep-sea in the coming years.”

Co-authors are at the UW; at UC Irvine; at the NOAA Alaska Fisheries Science Center; at UC Davis; and at Clemson University.

This research was funded by the National Science Foundation.

For more information, contact Miller at ecmiller@ou.edu and Tornabene at ltorna1@uw.edu.

Press release written by Will Shenton, 91̽��College of the Environment.

Coral reefs typically evoke clear, turquoise waters and a staggering number of colorful fishes. But what supports such an abundance of life?

In a published May 23 in Science, a team of international researchers from Simon Fraser University, 91̽�� and other institutions reveals that the iconic abundance of fishes on reefs is fueled by an unlikely source: tiny, bottom-dwelling reef fishes.

The researchers show that these small vertebrates — no more than 2 to 3 centimeters in length — perform a critical function on coral reefs that permit large reef fishes to flourish.

“These fish are like candy,” said lead author , a Banting postdoctoral research fellow at Simon Fraser University in British Columbia. “They are tiny, colorful bundles of energy that get eaten almost immediately by any coral reef organism that can bite, grab or slurp them up.”

In fact, the vast majority of tiny fishes on reefs will be eaten within the first few weeks of their existence.

“We were all truly excited to see how entire reef communities were being fueled by some of the smallest vertebrates on earth — including some species that live for an average of just 65 days,” said co-author , an assistant professor at the 91̽��School of Aquatic and Fishery Sciences and curator of fishes at the Burke Museum of Natural History and Culture.

So how come these fishes aren’t disappearing from reefs? The researchers solved this mystery by examining the larvae of reef fishes, which normally undertake epic journeys across the open ocean to find a home. Few of them survive.

The tiny, bottom-dwelling fish, however, avoid this migration altogether. Most of the larvae appear to simply stay close to their parents’ reefs.

“Tiny fish larvae absolutely dominate the larval communities near reefs,” Brandl said. “Our data shows that these fish get a lot more bang for their buck with every egg they spawn, probably because they avoid the death trap of the open ocean.”

This, in turn, supplies adult tiny fish populations with a steady stream of babies that rapidly replace each adult that is eaten on the reef. In total, these fish represent almost 60 percent of all fish tissue consumed on reefs.

The researchers expect this pattern is occurring on coral reefs around the world. Additionally, because these small fish likely spend the entirety of their short lives on a specific reef, they are good indicators of how healthy a reef environment is, Tornabene explained. If the habitat starts to degrade, the fish populations will also take an almost immediate hit.

“In many ways, these miniature fishes are more than just a conveyer belt of nutrients,” Tornabene said. “If we keep a watchful eye on these tiny communities, they may serve as sentinels of the reef, warning us of big impending changes in the entire ecosystem.”

This study was funded by the BNP Paribas Foundation, the National Agency for Research (France), the Smithsonian Institution, the National Science and Engineering Research Council of Canada and the Australian Research Council.

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For more information, contact Tornabene at luke.tornabene@gmail.com or 206-685-4254 and Brandl at simonjbrandl@gmail.com or 604-348-6423.

This was adapted from a Simon Fraser University news release.

A $2.5 million National Science Foundation grant will daylight thousands of specimens from their museum shelves by CT scanning 20,000 vertebrates and making these data-rich, 3-D images available online to researchers, educators, students and the public.

The project oVert, short for openVertebrate, complements other NSF-sponsored museum digitization efforts, such as , by adding a crucial component that has been difficult to capture — the internal anatomy of specimens.

With virtual access to specimens, researchers could peel away the skin of a passenger pigeon to glimpse its circulatory system, a class of third graders could determine a copperhead’s last meal, undergraduate students could 3-D print and compare skulls across a range of frog species and a veterinarian could plan a surgery on a giraffe in a zoo.

“In a time when museums and schools are losing natural history collections and giving up due to costs, we are recognizing the information held in these specimens is only getting more valuable,” said project co-principal investigator , assistant professor of aquatic and fishery sciences at the 91̽�� and curator of fishes at the Burke Museum of Natural History and Culture.

“I think this project is going to help create a renaissance of the importance of natural history collections,” he said.

The 91̽��joins 15 other institutions in this new project, led by the Florida Museum of Natural History at the University of Florida. The grant will enable researchers over four years to transport specimens from museum collections to scanners, scan and upload images, and organize them on the public database for easy access.

More than one quarter of the world’s vertebrate species will be scanned and digitized through this project, and researchers will aim to include specimens from more than 80 percent of existing vertebrate genera. A selection of these will also be scanned with contrast-enhancing stains to characterize soft tissues. There are almost 70,000 vertebrate species described today, and more than half of those are fishes.

The 91̽��has already made a dent in many of the fish species included in this project through the effort, led by , a 91̽��professor of aquatic and fishery sciences and of biology. For the past two years, Summers and colleagues have used a small CT scanner at to produce scores of fish scans from specimens gathered around the world.

CT scanning is a non-destructive technology that bombards a specimen with X-rays from every angle, creating thousands of snapshots that a computer stitches together into a detailed 3-D visual replica that can be virtually dissected, layer by layer, to expose cross-sections and internal structures.

The scans allow scientists to view a specimen inside and out — its skeleton, muscles, internal organs, parasites, even its stomach contents — without touching a scalpel.

“Our goal is to provide data that offer a foothold into vertebrate anatomy across the Tree of Life,” said , oVert’s lead principal investigator and associate curator of amphibians and reptiles at the Florida Museum of Natural History. “This is a unique opportunity for museums to have a pretty big reach in terms of the audience that interacts with their collections. We believe oVert will be a transformative project for research and education related to vertebrate biology.”

In addition to the 91̽��and University of Florida, scanning will occur at the University of Michigan, Harvard University, Texas A&M University and the Field Museum at the University of Chicago. The team’s largest scanner can image specimens as large as a garbage can, so for large mammals, scientists will focus on scanning their skulls or other key anatomical features, Tornabene said.

In contrast, micro-CT scanners like the one at Friday Harbor Labs can pick up incredible detail of small vertebrates that are difficult to study at life size, he explained. 91̽��scientists have scanned some of the smallest fish in the world and can zoom in to the digital file to examine anatomy not visible with the naked eye. They can also 3-D print specimens larger than life.

“We are going to be exploring the capabilities of understanding vertebrate anatomy at the finest scales,” Tornabene said.

The UW’s three CT scanners will focus mainly on digitizing key species in the Burke Museum’s collection of 12 million fish specimens, as well as the museum’s large bat collection. In addition to Tornabene and Summers, Katherine Maslenikov, Burke Museum fish collections manager, and , curator of mammals at the museum and assistant professor of biology, will lead the effort at the UW.

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For more information, contact Tornabene at ltorna1@uw.edu or 206-685-4254 and Blackburn at dblackburn@flmnh.ufl.edu or 352-273-1943.

This release was adapted from a Florida Museum of Natural History .

The showy , a predator with venomous spines that has invaded Caribbean coral reefs, has found a new market to exploit: the “,” an area of ocean that lies below traditional SCUBA diving depths, where little is known about the reefs or the species that inhabit them.

Researchers from the 91̽�� and Smithsonian Institution have reported the first observed case of lionfish preying upon a fish species that had not yet been named. Their , published May 25 in PLOS ONE, may indicate an uncertain future for other fish found in the largely unexplored deep-ocean coral reefs.

“Lionfish aren’t going anywhere, and we are faced with the fact that they are permanent residents on Caribbean reefs,” said lead author , curator of fishes at the Burke Museum of Natural History and Culture in Seattle and an assistant professor at the UW’s School of Aquatic and Fishery Sciences.

“The hope is that the learning curve is quick and other fish realize lionfish are predators. Right now, studies have shown some prey species to be pretty naïve.”

The scientists discovered the new fish, which they named Palatogobius indendius (Ember goby), while on several submarine dives off the coasts of Curacao and Dominica. The new species described in the paper has a bright orange stripe down its spine and schools together in masses of about 100 fish — starkly different behavior from most gobies that hide as individuals in holes or cracks in the reef, making the new species an easy target for lionfish attacks.

From a submarine, they of a lionfish cornering, attacking and eating this new species. Lionfish employ hunting tactics that are unfamiliar to native reef-dwelling fish, such as using their long fins to slowly stalk and push prey into a corner. They also shoot jets of water out of their mouths to disorient their prey, and scientists have even recorded lionfish making a “roaring” sound to communicate and potentially ward off would-be predators.

The scientists are concerned that lionfish are now swimming to deeper reefs — down to nearly 250 meters (about 800 feet) below the surface off Curacao — and likely eating fish that live in those largely unexplored parts of the ocean.

“Once we discovered invasive lionfish — sometimes in huge numbers — inhabiting barely explored deep reefs, our concern was that these voracious predators might be gobbling up biodiversity before scientists even know it exists. This study suggests that they are doing just that,” said co-author , curator of fishes at the National Museum of Natural History.

The good news is the goby species being eaten by the lionfish appears to be abundant throughout the Caribbean. The researchers have observed it in large numbers on many submarine trips around the region. But almost a third of the fish species along deep reefs haven’t yet been named, and they could be at risk if lionfish continue to raid the area.

“The other species still undescribed on these reefs are very rare and occur in lower abundances than our new species. If they are getting eaten by lionfish, they may be in more trouble than the Ember goby,” Tornabene said.

“There are still many coral reef fish species that are waiting to be described — and some of them will inevitably end up in the guts of lionfish.”

As coral reef ecosystems around the world decline because of climate change, pollution, disease, coastal development and overfishing, the deep-water reefs hold a promise of refuge for species that are able to survive in deeper water. The presence of an invasive predator like the lionfish, which likely came to the Caribbean from an aquarium release off Florida in the early 1990s, could be devastating if they are eating native fish and exploiting the ecosystem with no known predators to keep them in check.

The researchers are one of only three teams of biologists in the world collecting specimens in the twilight zone parts of the ocean, and this team is the only one using a . They have taken about 150 dives to Caribbean reefs using a 6.5-ton submersible with two robot arms that stuns fish for capture by spraying water or anesthetic, then catches them using a vacuum hose.

“From inside a submarine, it’s really hard to catch a small fish that is swimming, and it requires incredibly skilled pilots and scientists and a lot of patience,” Tornabene said. “We’ve been able to do it with such success that we have come back from each trip with thousands of specimens.”

This summer, they will test a different submarine that can go to depths of more than 800 meters (about 2,700 feet) off the coast of Honduras.

The researchers plan to look inside the stomachs of lionfish captured in deep water to see what, in fact, they are eating. It’s possible they may find other new species, Tornabene said, and probably more of the new goby they recently discovered. They also are analyzing the genetics of this new fish from different parts of the Caribbean to see how connected different deep-reef systems are to one another.

The research was funded by a number of Smithsonian Institution grants and awards, and by the Prince Albert II of Monaco Foundation.

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For more information, contact Tornabene at ltorna1@uw.edu and Baldwin at baldwinc@si.edu.