New Approach for Paleontologists When Identifying Vertebrae Fossils

Fossil finds are exciting moments that sometimes introduce the world to an ancient mammal or dinosaur that existed millions of years ago. But a longstanding problem in paleontology is that fossils are often not complete, and the subtlety of differences between certain species, and major changes that can occur while an animal grows, complicates identifying the species by the fossil.

A paper published this month in Paleobiology lays the groundwork for a new approach to correctly identifying an ancient animal fossil, the implications of which are significant for vertebrate paleontology.

Authored by paleontologist James Napoli, a research instructor in the Department of Anatomical Sciences in the Renaissance School of Medicine at Stony Brook University, the study describes an experiment to determine whether the guidelines and statistical tests paleontologists often use to identify species would work to identify American alligators apart from Chinese alligators — living species that differ in size but are otherwise very similar.

The issue regarding the correct identification of a vertebrate fossil is that as all creatures grow, the skeleton changes dramatically. Babies and adults of animals often look so different it is difficult to tell if they are the same species, an issue long recognized by paleontologists. Additionally, without being able to witness a species grow or sequence their DNA, proper identification becomes even more uncertain, which has made paleontologists extra cautious when identifying fossil vertebrates.

 The two methods Napoli tested are known as geometric morphometrics and cladistic analysis of ontogeny, which is the developmental history of an organism from its earliest stages of life well into adulthood. Geometric morphometrics quantifies the shape of bones using 3D landmark coordinates. Cladistic analysis of ontogeny uses computer algorithms used to reconstruct evolutionary trees to build branching diagrams of the growth stages of a species. Both methods are widely used by scientists attempting to classify fossils of juvenile animals.

Napoli’s research revealed that both methods failed to reproduce the correct classification for the living alligator specimens, consistently failing to show that they were different species, or failing to associate fossils of baby alligators to the correct species. Because of this result, Napoli says these methods are unreliable for classifying fossils.

“At that point in the research, I thought perhaps it was impossible to identify these fossils of baby animals,” Napoli said.

But as Napoli took a deeper look at the data, he found a light at the end of the tunnel. He realized that even though alligators change dramatically as they grow, specific kinds of traits never changed. These traits also distinguished the two species of alligator, acting as anatomical “fingerprints,” which can enable scientists to identify fossils even as very young animals.

Through this ontogenetic investigation, Napoli illustrates that traits relating to the anatomy of the blood vessels, nerves and the sinuses are very unlikely to vary during growth.

“I found that, overwhelmingly, the consistent traits that distinguish the two alligator species are the skeletal signals of soft-tissue anatomy like nerves or blood vessels, or represent fundamental architectural details of their skulls, such as different types of interlocking bone sutures,” explained Napoli. “Developmental biology explains that these traits are established during very early embryonic development, which is why they do not change later in an animal’s life.”

Because mammals and reptiles all develop according to the same principles — including ancient and extinct ones — this discovery and species identification methodology is applicable to many different animal groups.

For example, Napoli suggests that if scientists followed a similar path toward identifying Nanotyrannus, it could have ended the debate about whether this dinosaur was its own species without the discovery of the “Dueling Dinosaurs” specimen, news which he and colleagues published in 2025.

“I propose a general model for future taxonomic hypothesis tests in the fossil record, in which the hypothesis that two specimens are different ontogeny stages of a single species can be falsified by the discovery of character differences that cannot be attributed plausibly to ontogenetic variation,” Napoli wrote.

Napoli believes that paleontologists should focus more on the anatomical traits not affected by ontogeny when analyzing fossils to correctly identify species. He argues that “our understanding of the fossil record will change significantly as these new guidelines are accepted and used by paleontologists.”