New Haven, Conn. — In most narratives, the story of evolution is the story of organisms emerging from the ocean and eventually populating the land.

But for some species that evolution also involved a return trip. Dozens of major mammal and reptile groups ultimately made their way back to the beach and into the water. A new Yale study has undertaken the task of explaining when and how this happened — and which species fully re-committed to the life aquatic.

The study appears 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 earned his doctorate as a student in 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.”

For the study, the researchers analyzed hundreds of specimens in the collection of the Yale Peabody Museum and dozens of other institutions around the world, taking new measurements (more than 11,000), photographs, and CT scans. The team also made use of classic paleontology methods, phylogenetic machine-learning algorithms, and even World War II-era naval statistics — all to reconstruct one of the most significant evolutionary transitions in natural history.

“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, associate professor of Earth and planetary sciences in Yale’s Faculty of Arts and Sciences (FAS), associate curator of vertebrate paleontology and vertebrate zoology at the Peabody Museum, and senior author of the new study.

“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.”

The lack of a robust, comprehensive explanation for when various animal groups fully returned to the water has divided the scientific community for years. Researchers had to rely upon their own interpretations of fragmentary fossil samples that had uncertain relationships to one another — with some features suggesting the animals lived on land and other features suggesting they lived in the water.

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

To help solve this challenge, he developed a method that used simple but powerful machine-learning models, trained on modern species, to predict the aquatic habits and associated soft-tissue adaptations of ancient extinct species with historically contentious ecologies.

For example, the researchers were able to weigh in on the controversy surrounding Spinosaurus, the ancient and ambiguously aquatic dinosaur that has been the subject of intense debate among paleontologists. Spinosaurus lived from roughly 113 to 94 million years ago in what is now northern Africa.

One body of evidence suggests that Spinosaurus frequently dived and hunted for prey underwater, like a seal or penguin; another body of evidence suggests that Spinosaurus walked and foraged for food near the water’s edge, like a modern-day heron.

“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.”

Conversely, the researchers did not see highly or fully aquatic habits for mesosaurs — a group of small marine reptiles that lived 290 to 274 million years ago in what is now South Africa and eastern South America. Although mesosaurs gave birth to live young, which has suggested to some scientists that they lived a fully aquatic lifestyle, Gordon said their limb proportions point to a semi-terrestrial lifestyle.

“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 research team was able to establish that all Paleozoic marine reptiles (all marine reptiles around before the dinosaurs appeared) regularly returned to land and lived, at most, an amphibious lifestyle. The team also was able to predict with more than 90% accuracy whether an animal had soft-tissue flippers and highly or fully aquatic habits, based on forelimb proportions.

The researchers also adapted a technique from the 1940s for their new method.

“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.”

The new method could be applied to other evolutionary transitions as well, such as the ability to walk on two legs in human ancestors and the ability to fly in the dinosaurian ancestors of birds, the researchers say.

“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.”

Additional co-authors of the study are Lisa Freisem, a Yale doctoral student in the GSAS, and Christopher Griffin, an assistant professor of geosciences at Princeton and former postdoctoral fellow at Yale.

Funding for the study came from the Yale Institute for Biospheric Studies, the International Union for Conservation of Nature’s Crocodile Specialist Group, and the National Science Foundation.