Ancient DNA Reveals New Spot in the Tree of Life for Extinct “Horned” Crocodile

Voay robustus Skull

A skull of the extinct horned crocodile from Madagascar (Voay robustus), which is part of the American Museum of Natural History’s paleontology collection. Credit: M. Ellison/©AMNH

New ancient DNA-based study on Madagascar crocodile suggests that modern crocodiles likely originated in Africa.

A study led by scientists at the American Museum of Natural History has resolved a long-standing controversy about an extinct “horned” crocodile that likely lived among humans in Madagascar. Based on ancient DNA, the research shows that the horned crocodile was closely related to “true” crocodiles, including the famous Nile crocodile, but on a separate branch of the crocodile family tree. The study, published today (April 27, 2021) in the journal Communications Biology, contradicts the most recent scientific thinking about the horned crocodile’s evolutionary relationships and also suggests that the ancestor of modern crocodiles likely originated in Africa.

“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 lead author Evon Hekkala, an assistant professor at Fordham University and a research associate at the American Museum of Natural History. “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.”

The arrival of modern humans in Madagascar between about 9,000 and 2,500 years ago preceded the extinction of many of the island’s large animals, including giant tortoises, elephant birds, dwarf hippos, and several lemur species. One lesser-known extinction that occurred during this period was that of an endemic “horned” crocodile, Voay robustus. 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. This suggests that both types persisted 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. Then, in the early part of the 20th century, it was thought that the specimens simply represented very old Nile crocodiles. And finally, in 2007, a study based on the 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 fully examine 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 have been at the Museum since the 1930s.

“This 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 paleogenomics 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.

Reference: “Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus” by E. Hekkala, J. Gatesy, A. Narechania, R. Meredith, M. Russello, M. L. Aardema, E. Jensen, S. Montanari, C. Brochu, M. Norell and G. Amato, 27 April 2021, Communications Biology.
DOI: 10.1038/s42003-021-02017-0

Other authors on the study include John Gatesy, Apurva Narechania, Shaena Montanari, and Mark Norell from the American Museum of Natural History; Robert Meredith and Matthew Aardema from the Museum and Montclair State University; Michael Russello from the University of British Columbia; Evelyn Jenson from the University of British Columbia and Newcastle University; and Christopher Brochu from the University of Iowa.

Funding was provided in part by the University of California, Riverside, Fordham University Faculty Fellowship, and the National Science Foundation grant no.s RAPID DEB-1931213, DEB-1556701, and DBI-1725932.

1 Comment on "Ancient DNA Reveals New Spot in the Tree of Life for Extinct “Horned” Crocodile"

  1. Modern crocodilian do have horn Nile crocodile some time have horn small horn Siamese crocodile Cuban crocodile have real horn the mesoeucrocodylia have horn like carntosaurus ceratosuchus but it look like voay pterosaur duckbill dinosaur but it has two horn more prove gator is a dinosaur .dwarf crocodile nose is fuse like dinosaur a primitive feature but it is advance modern crocodilian .modern crocodilian have no problem bringing back old feature it’ is very common the Nile crocodile nose is not fuse a advance feature most advance animal have this feature to get more oxygen the gator is fuse really is not close to Nile crocodile it is more advance most mesoeucrocodylia it is not fuse that why they know Nile crocodile is the most primitive modern crocodilian some gator type early mesoeucrocodylia the nose is fuse and there ancestor likely it is not fuse clearly spinosauridae it is fuse because it is fuse ankle primitive theropod.

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