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Living alligators expose why juvenile fossils can fool classification methods
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 incomplete, and subtle differences between certain species, along with major changes that can occur as an animal grows, complicate species identification. A paper published this month in Paleobiology lays the groundwork for a new approach to correctly identifying ancient animal fossils, with significant implications for vertebrate paleontology.
Authored by paleontologist James Napoli, a research instructor in the Department of Anatomical Sciences in the Renaissance School of Medicine (RSOM) at Stony Brook University, the study describes an experiment to determine whether the guidelines and statistical tests paleontologists often use to identify species could distinguish American alligators from Chinese alligators—living species that differ in size but are otherwise very similar.
The challenge of correctly identifying a vertebrate fossil is that, as all creatures grow, their skeletons change dramatically. Young and adult animals often look so different that it is difficult to tell whether they are the same species, an issue long recognized by paleontologists. Additionally, without being able to witness a species grow or sequence its DNA, proper identification becomes even more uncertain, making paleontologists extra cautious when identifying fossil vertebrates.
The two methods Napoli tested are known as geometric morphometrics and cladistic analysis of ontogeny, the developmental history of an organism from its earliest stages of life into adulthood. Geometric morphometrics quantifies the shape of bones using 3D landmark coordinates. Cladistic analysis of ontogeny uses computer algorithms that reconstruct evolutionary trees to build branching diagrams of a species' growth stages. Both methods are widely used by scientists attempting to classify fossils of juvenile animals.
When standard tests fell short
Napoli's research revealed that both methods failed to reproduce the correct classification for the living alligator specimens. They consistently failed to show that the specimens were different species or to associate baby alligator fossils with 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," he says.
Traits that persist through growth
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 change. These traits also distinguished the two alligator species, acting as anatomical "fingerprints" that can enable scientists to identify fossils even in very young animals.
Through this ontogenetic investigation, Napoli illustrates that traits related to the anatomy of blood vessels, nerves and 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," Napoli explains. "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."
A broader test for fossil debates
Because mammals and reptiles all develop according to the same principles—including ancient and extinct ones—this discovery and species-identification methodology are applicable to many different animal groups.
For example, Napoli suggests that if scientists had 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, details of 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," he writes in the paper.
Napoli believes that paleontologists should focus more on 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."
Publication details
James G. Napoli, Resolving the "ontogeny problem" in vertebrate paleontology, Paleobiology (2026). DOI: 10.1017/pab.2026.10105
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Citation: Living alligators expose why juvenile fossils can fool classification methods (2026, July 16) retrieved 16 July 2026 from https://phys.org/news/2026-07-alligators-expose-juvenile-fossils-classification.html
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