Dozens of major groups of mammals and reptiles made this remarkable evolutionary reversal. Now, a new study from Yale University is shedding light on when and how these transitions occurred, as well as which ancient animals became fully aquatic and which continued to depend on land.

The findings were published in the journal Current Biology.

"These secondarily aquatic groups adapted in strikingly similar ways to their new aquatic home -- evolving flippers and a suite of other features that made them better swimmers," said lead author Caleb Gordon, who completed his doctorate at Yale's Graduate School of Arts and Sciences (GSAS) earlier this year and is now a postdoctoral researcher at the Florida Museum of Natural History. "As a result, they've become textbook examples of convergent evolution, which can tell us a lot about the processes driving and constraining adaptive change in response to similar environmental cues."

Using Ancient Fossils and AI to Reconstruct Evolution

To investigate these evolutionary changes, the researchers examined hundreds of fossil and modern specimens housed at the Yale Peabody Museum and dozens of other institutions worldwide. They collected extensive new data, including measurements (more than 11,000), photographs, and CT scans.

The team combined traditional paleontological techniques with machine learning models that account for evolutionary relationships. They also incorporated a statistical approach originally used by naval forces during World War II. Together, these methods offered a new way to investigate one of the most remarkable transitions in vertebrate evolution.

"Reconstructing the lives of extinct life forms in a scientifically rigorous way, as opposed to just telling stories, is a precise and delicate undertaking," said Bhart-Anjan Bhullar, senior author of the study. Bhullar is an associate professor of Earth and planetary sciences in Yale's Faculty of Arts and Sciences (FAS) and an associate curator of vertebrate paleontology and vertebrate zoology at the Peabody Museum.

"It requires a careful interweaving of data from modern organisms, of which our understanding is necessarily far deeper, and knowledge of these living organisms' genealogy relative to fossil forms," he said. "Caleb's work accomplishes all of this and more, and on a massive evolutionary scale."

For decades, scientists have disagreed about when particular groups of prehistoric animals became fully adapted to life underwater. The fossil record often provides incomplete or conflicting clues, making it difficult to determine whether an extinct species primarily lived on land, in water, or in both environments.

Some skeletal features may indicate an aquatic lifestyle, while others suggest that the same animal remained capable of moving and feeding on land. These contradictions have led researchers to different conclusions about how ancient species behaved.

"In these cases, paleontologists are often stuck, as different lines of evidence disagree about what the ancient animal was like," Gordon said.

To address this uncertainty, Gordon developed a method using relatively simple but effective machine learning models trained on living animals. By identifying relationships between skeletal proportions and known lifestyles, the models can estimate how extinct species used aquatic environments. They can also predict soft tissue adaptations, including swimming structures that rarely survive in fossils.

Spinosaurus May Have Spent Most of Its Life Underwater

One of the most striking findings concerns Spinosaurus, a giant prehistoric dinosaur whose relationship with water has generated considerable controversy.

Spinosaurus lived approximately 113 million to 94 million years ago in what is now northern Africa. Although scientists generally agree that it was associated with aquatic environments, exactly how it moved, hunted, and spent its time remains a subject of debate.

Some evidence points to an animal that frequently submerged itself and pursued prey underwater, much like seals or penguins. Other findings suggest a lifestyle closer to that of a modern heron, with Spinosaurus walking and searching for food along shorelines and in shallow water.

The Yale team's analysis provides new support for the more aquatic interpretation.

"Our results shed new light on how much time Spinosaurus spent submerged, which could support the underwater hunting view," Gordon said. "We confidently recovered highly aquatic habits for Spinosaurus, indicating that it spent the vast majority of its time submerged in the water."

Although the findings do not settle every question about how Spinosaurus hunted, they strengthen the case that this enormous predator spent much more of its life underwater than on land.

Ancient Marine Reptiles That Never Fully Left Land

The researchers reached a different conclusion about mesosaurs, small marine reptiles that lived between 290 million and 274 million years ago in regions now forming parts of South Africa and eastern South America.

Mesosaurs have long interested paleontologists because they gave birth to live young, a characteristic some researchers have interpreted as evidence of a fully aquatic existence. However, the new analysis suggests that their limbs were not adapted for a life spent entirely in water.

Instead, their skeletal proportions indicate that mesosaurs regularly moved between aquatic and terrestrial environments.

"They spent a lot of time on land, like a modern-day alligator or platypus does," Gordon said. "Mesosaurs didn't completely leave the land behind."

The findings also suggest a broader pattern among the earliest marine reptiles. According to the researchers, all Paleozoic marine reptiles (all marine reptiles around before the dinosaurs appeared) continued to return to land regularly. None appeared to have evolved a completely aquatic lifestyle, with even the most water adapted species remaining amphibious.

The researchers found that forelimb proportions were particularly useful for distinguishing these lifestyles. Using this information, their models could predict with more than 90% accuracy whether an animal possessed soft tissue flippers and whether it had highly or fully aquatic habits.

A World War II Technique Helps Solve an Evolutionary Mystery

An especially unusual part of the research involved adapting a statistical method developed during the 1940s.

"Caleb resurrected a statistical technique from a bygone era," said co-author Jacques Gauthier, a professor of Earth and planetary sciences at Yale and curator-in-charge for vertebrate paleontology at the Peabody Museum. "It was developed during WWII to estimate the probability that an approaching blip on the radar screen was an enemy plane. Caleb cleverly used it to get at whether or not an extinct animal had limbs modified for swimming."

By repurposing this approach, the researchers could assess the likelihood that an extinct species possessed specialized swimming adaptations, even when direct evidence of those features was missing.

The method could eventually help scientists investigate other major changes in evolutionary history. Potential applications include studying when human ancestors developed the ability to walk on two legs and how the dinosaur ancestors of birds evolved the ability to fly.

A New Way to Understand Extinct Animals

Because most prehistoric vertebrates are known primarily through their fossilized skeletons, reconstructing their behavior is one of paleontology's greatest challenges. Bones preserve valuable information, but they rarely provide a complete picture of how an animal lived.

Traditionally, scientists have interpreted particular skeletal features to make arguments about the lifestyles of extinct species. Those interpretations can differ significantly, especially when fossils are incomplete or several anatomical characteristics point toward different conclusions.

The new approach offers a more systematic way to evaluate that evidence, using patterns observed in living species to make testable predictions about animals that disappeared millions of years ago.

"Bones are all that is left to us of the vast majority of vertebrate animals that have lived on Earth," Bhullar said. "We want to know so very much about these creatures and the succession of lost worlds they inhabited, but we have so little on which to base our conclusions. From skeletal remains, people have tried to discern life habits, generally making an argument on the basis of one preferred set of features or another. Caleb's method removes the subjectivity from this process and allows the data to speak for themselves."

The study's additional co-authors are Lisa Freisem, a doctoral student at Yale's Graduate School of Arts and Sciences, and Christopher Griffin, an assistant professor of geosciences at Princeton University who previously worked as a postdoctoral fellow at Yale.

Research support was provided by the Yale Institute for Biospheric Studies, the International Union for Conservation of Nature's Crocodile Specialist Group, and the National Science Foundation.