After almost 150 years of controversy, scientists have finally solved the classification mystery surrounding the extinct horned crocodile and determined exactly where this cryptic croc belongs on the tree of life.

The extinct horned crocodiles (Voay robustus) were endemic to Madagascar as far back as 9,000 years ago and lived as recently as 1,300 to 1,400 years ago, according to fossil evidence. First discovered in 1872, the beasts are named for the distinctive horns on their skulls. Since their discovery, they have been classified in several different families, confused for other species and given several different names, with no clear evolutionary origin of their own.

In the new study, researchers from the American Museum of Natural History (AMNH) in New York City used DNA analysis to shed light on these ambiguous reptiles and determine whether they belong to their own unique group.

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"The DNA tells a different story," lead author Evon Hekkala, an AMNH associate at Fordham University in New York, told Live Science. "It tells us over and over again that appearances can be deceiving."

Complicated history

Madagascar is currently home to Nile crocodiles (Crocodylus niloticus), which are invasive to the island nation. The earliest evidence of Nile crocodiles in Madagascar is 300 years old, but Malagasy tales suggest that they may have migrated there much earlier and lived alongside horned crocodiles, Hekkala said.

Horned crocodiles were not particularly large crocs, but their heavyset skulls suggest they were likely a'robust,a' which led to their species name robustus, Hekkala said. "We don't have any complete skeletons, but they weren't spectacularly long," Hekkala said. "Based on the size of their skulls, they were likely similar in overall size to Nile crocodiles."

A number of other larger animals — including giant tortoises, elephant birds, dwarf hippos and several lemurs — also went extinct on the island around the same time as horned crocodiles did, but it is unclear what caused their demise, according to an AMNH statement.

It may have been due to the arrival of the invasive Nile crocodiles or more likely the arrival of the first humans on Madagascar as late as 2,500 years ago, according to the researchers. However, natural climate change also may have played a role.

"Some recent studies have indicated that parts of the island became drier," Hekkala said. "It could be that this benefited the newly arrived Nile crocodile and made the island more inhospitable to the endemic horned crocodile."

Classification nightmare

The limited fossil record and incomplete ecological history of Madagascar partly explain why it has taken almost 150 years to successfully place the horned crocodiles in their own evolutionary group. In addition, crocodile species are very similar physically, especially in their skulls, which scientists have historically used to classify them. But skull variations between individuals within the same species can be high, which can often make them appear to be from another species.

"Crocodile head shape varies dramatically with age, sex and even diet," Hekkala said. "So a large, old crocodile skull might look really distinct."

When the horned crocodiles were originally discovered, scientists classified them as true crocodiles — a subfamily containing Nile crocodiles and other modern-day crocodiles like the American crocodile (Crocodylus acutus) and saltwater crocodile (Crocodylus porosus) — and were given the name Crocodylus robustus.

This confusion was magnified in 1910 when a popular illustration of what a horned crocodile may have looked like was released in a scientific article, Hekkala said. Unfortunately, the image actually depicted a modern-day Nile crocodile, but it helped to solidify the theory that the horned crocodiles were true crocodiles. Some even argued that the horned crocodiles may just have been an ancestor of Nile crocodiles.

This remained the general consensus until 2007 when researchers analyzed the skulls of horned crocodile fossils to reveal significant physiological differences compared with those of Nile crocodiles. After this revelation, the horned crocodiles were put into a new subfamily called dwarf crocodiles — smaller crocodiles with short, stout skulls that diverged from the true crocodiles millions of years ago. The horned crocodiles were also given a new genus name, Voay, which means "crocodile" in the Malagasy language.

In the new study, AMNH researchers instead analyzed DNA evidence to determine which group the horned crocodiles really belonged to.

A new group

DNA analysis revealed that the horned crocodiles were not dwarf crocodiles like the 2007 study had suggested nor were they true crocodiles like earlier naturalists assumed. Instead, they belong to their own unique genus.

"What surprised us at that point was that it was not grouped within the true crocodiles, but adjacent to it," Hekkala said. "This makes it a bit like a long-lost lineage that was isolated on an island."

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The fact that this new group, which is closely related to true crocodiles, was endemic to Africa also suggests that this may be where crocodiles first evolved, which is the leading theory in the field. "Our data support the hypothesis that the modern crocodiles we see today originated in Africa," Hekkala said.

Getting to the bottom of the evolutionary mystery surrounding horned crocodiles is important because it helps scientists to build a better picture of how modern-day animals evolved and how they may be able to adapt to change, Hekkala said.

"Extinct species can act as bridges over knowledge gaps," Hekkala said. "They help us to time travel and to reconnect evolutionary histories to tell the story of life and extinction on Earth."

The study was published online April 27 in the journal Communications Biology.

Originally published on Live Science.