Ancient DNA Sheds Light on Evolutionary History of Extinct ‘Horned’ Crocodile

Wednesday, April 28, 2021

A skull of Voay robustus collected at Ampoza during the joint Mission Franco-Anglo-American expedition from 1927-1930. Image credit: Hekkala et al., doi: 10.1038/s42003-021-02017-0.

An international team of scientists has recovered and analyzed partial mitochondrial genomes from 1,300-1,400-year-old specimens of Voay robustus, a recently extinct species of ‘horned’ crocodile that lived in Madagascar. Their results indicate that this endemic represented the sister lineage to true crocodiles (Crocodylus) and that the ancestor of modern crocodiles likely originated in Africa.

The arrival of modern humans in Madagascar between 9,000 and 2,500 years ago preceded the extinction of much of the island’s vertebrate megafauna including giant tortoises, elephant birds that ranged to enormous size, dwarf hippos, and several lemur species.

One lesser-known extinction that occurred during this period was the demise of Voay robustus.

Early explorers to the island noted that Malagasy peoples consistently referred to two types of living 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 found on the island.

Voay robustus 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 Dr. Evon Hekkala, a researcher at Fordham University and 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.”

Despite nearly 150 years of investigation, the position of Voay robustus in the tree of life has remained controversial.

In 1872, French naturalists Alfred Grandidier and Léon Vaillant described it as a new species and placed it 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 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,” Dr. 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 place of Voay robustus in the evolutionary tree, Dr. Hekkala and her colleagues made a number of attempts to sequence mitochondrial DNA from fossil specimens.

“This 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 Dr. George Amato, emeritus director of the Institute for Comparative Genomics at the American Museum of Natural History.

“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 Voay robustus 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,” Dr. 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.”

The results appear in the journal Communications Biology.


E. Hekkala et al. 2021. Paleogenomics illuminates the evolutionary history of the extinct Holocene ‘horned’ crocodile of Madagascar, Voay robustusCommun Biol 4, 505; doi: 10.1038/s42003-021-02017-0