Ancient DNA of "Horned" Crocodile Sheds Light on Croc Family Tree

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Close up of the teeth on the jaw of an extinct horned crocodile (Voay robustus) specimen. Specimens from the Museum’s scientific collections, including this skull of an extinct crocodile, provided the research team with ancient DNA for their study.
© E. Hekkala

New research based on two skulls that have been in the Museum’s collection since the early 1930s resolves a long-standing controversy about an extinct “horned” crocodile that lived in Madagascar.

The research team found that the horned crocodile, Voay robustus, known for the two bony knobs at the top of its head, was closely related to “true crocodiles,” but on a separate branch of the crocodile family tree. 

Extinct horned crocodile skull retains an upper row of pointy teeth.
This skull of the extinct horned crocodile from Madagascar (Voay robustus) has been part of the American Museum of Natural History’s scientific collections since the early 1930s.
M. Ellison/© AMNH

“This crocodile was hiding out on the island of Madagascar during the time when people were building the pyramids and was probably still there when pirates were getting stranded on the island,” said Evon Hekkala, an associate professor at Fordham University and a research associate at the Museum who is the lead author of the study, which is published today in the journal Communications Biology. “They blinked out just before we had the modern genomic tools available to make sense of the relationships of living things. And yet, they were the key to understanding the story of all the crocodiles alive today.”

Early explorers to Madagascar noted that Malagasy peoples consistently referred to two types of crocodiles on the island: a large robust crocodile and a more gracile form with a preference for rivers, suggesting that both types existed until very recently. But only the gracile form, now recognized as an isolated population of the Nile crocodile, Crocodylus niloticus, is currently is found on the island.

Despite nearly 150 years of investigation, the position of the horned crocodile in the tree of life has remained controversial. In the 1870s, it was first described as a new species within the “true crocodile” group, which includes the Nile, Asian, and American crocodiles.

In the early part of the 20th century, it was thought that the specimens simply represented very old Nile crocodiles. Then, in 2007, a study based on physical characteristics of the fossil specimens concluded that the horned crocodile was actually not a true crocodile, but in the group that includes dwarf crocodiles.

“Teasing apart the relationships of modern crocodiles is really difficult because of the physical similarities,” Hekkala said. “Many people don’t even realize that there are multiple species of crocodiles, and they see them as this animal that’s unchanging through time. But we’ve been trying to get to the bottom of the great diversity that exists among them.”

To investigate the horned crocodile’s place in the evolutionary tree, Hekkala and her collaborators at the Museum made a number of attempts to sequence DNA from fossil specimens, including two well-preserved skulls that were collected during the Museum’s Mission Franco-Anglo-American expedition from 1927–1930.

“This is a project we’ve tried to do on and off for many years, but the technology just hadn’t advanced enough, so it always failed,” said study co-author George Amato, emeritus director of the Museum’s Institute for Comparative Genomics. “But in time, we had both the computational setup and the paleogenomic protocols that could actually fish out this DNA from the fossil and finally find a home for this species.”

The results place the horned crocodile right next to the true crocodile branch of the evolutionary tree, making it the closest species to the common ancestor of the crocodiles alive today.

“This finding was surprising and also very informative to how we think about the origin of the true crocodiles found around the tropics today,” Amato said. “The placement of this individual suggests that true crocodiles originated in Africa and from there, some went to Asia and some went to the Caribbean and the New World. We really needed the DNA to get the correct answer to this question.”