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Pixels Preserve World’s Most Endangered Marine Mammal, the Vaquita

Full skeleton of a very rare female vaquita specimen collected in 1966.

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The vaquita (Phocoena sinus), an elusive porpoise found only in the shallow waters of Mexico’s northern Gulf of California, is one of the rarest and most endangered marine mammals on Earth. Measuring about 5 feet in length, it is the world’s smallest cetacean – a group that includes whales, dolphins and porpoises. Known for the distinctive dark rings around its eyes and mouth, the vaquita remained unknown to science until the latter half of the 20th century. Today, it has become a global symbol of the growing biodiversity crisis unfolding in the world’s oceans.

With only an estimated handful of individuals remaining, the vaquita is perilously close to extinction. Its dramatic decline has been driven almost entirely by accidental entanglement in gillnets, particularly those used to illegally catch totoaba, a large fish whose swim bladder is highly prized on international black markets. Although the totoaba fishery was banned decades ago, illegal fishing persists, fueled by organized wildlife trafficking networks and strong overseas demand.

Despite intensive conservation efforts, the vaquita’s future remains uncertain. Its survival now depends on urgent, coordinated international action to eliminate gillnet fishing in its habitat and protect one of the ocean’s most critically endangered species before it disappears forever.

Using advanced imaging technology, researchers from ����ʦapp, in collaboration with the San Diego Natural History Museum, SeaWorld California, and NOAA Fisheries, have digitally preserved the vaquita by scanning a complete skeleton of a female donated to the museum in 1966, creating a highly detailed digital record of the critically endangered porpoise.

In the study, published in , researchers combined medical CT scans, micro-CT imaging and digital photography to create one of the most comprehensive digital anatomical records of a vaquita ever assembled. The technology enabled the team to capture microscopic skeletal details and convert them into interactive 3D models. 

“By combining advanced imaging technologies with open-access data sharing, the effort not only safeguards a valuable record of one of the planet’s most endangered marine mammals, but also makes that information accessible to anyone,” said , first author, imaging lab assistant in the , and a Ph.D. candidate in the ����ʦapp Department of Biology within the Charles E. Schmidt College of Science. “The project will enable the production of scientifically accurate replicas for museums, classrooms and educational programs, helping to raise awareness and support conservation efforts for a species now teetering on the edge of extinction.”

Knaub worked closely with co-authors Brittany Aja Dolan, formerly with SeaWorld California, who spearheaded the project, Philip Unitt, curator of birds and mammals at the San Diego Natural History Museum, and Robert L. Brownell Jr., Ph.D., a biologist with Southwest Fisheries Science Center, Marine Mammal and Turtle Division, NOAA Fisheries, who collected the specimen in the 1960s as a graduate student.

To create a detailed digital archive, the researchers employed multiple imaging technologies that allowed them to document the skeleton at different scales. The specimen was first scanned using medical computed tomography (CT), a technology commonly used in hospitals that uses X-rays to create cross-sectional images of an object. The team then photographed individual bones and skeletal elements before conducting high-resolution micro-computed tomography, or micro-CT, scans. Unlike conventional CT scanners, micro-CT systems can reveal exceptionally fine anatomical details, capturing structures measured in microns – smaller than the width of a human hair.

“This project required an unusually intricate imaging workflow to capture the vaquita skeleton at multiple scales, from whole-bone structure down to microscopic internal detail,” said  , Ph.D., senior author and a professor, ����ʦapp Department of Biological Sciences. “By integrating medical CT, micro-CT and high-resolution photography, we were able to reconstruct both the external morphology and internal architecture of each bone in a way that preserves anatomical fidelity while remaining fully interactive in digital form. The result is not just a model, but a layered dataset that reflects the true complexity of the specimen.”

The scans produced thousands of cross-sectional images of the skeleton’s bones. Researchers then used specialized 3D imaging software to digitally isolate each bone and reconstruct them into highly detailed 3D models. These digital replicas can be rotated, enlarged and examined from any angle to study in a physical specimen without causing damage.

Because the original specimen is both fragile and exceptionally rare, direct handling and public access are extremely limited. To expand access, the resulting 3D models have been made freely available through the online repository MorphoSource.

“The success of this project was made possible by the advanced imaging capabilities available at the Berlin Family Bioimaging Lab,” said Tricia L. Meredith, Ph.D., co-author and director of research for ����ʦapp’s on-site lab schools, �����Ի���, and an assistant research professor in ����ʦapp’s College of Education. “Having access to high-resolution micro-CT systems, alongside the expertise to process and reconstruct large, complex datasets, was essential to transforming raw scan data into usable 3D models. This kind of integrated technological environment is what allows specimens like the vaquita to be preserved and shared at a level of detail that simply wasn’t possible until recently.”

The research was supported by ����ʦapp’s School of Environmental, Coastal, and Ocean Sustainability (ECOS), the Joshua M. Berlin Research Gift, ����ʦapp Laboratory Schools, and SeaWorld California.

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