Hidden in isolation: Two new crocodile species found in Mexico

The Caribbean holds secrets in its mangroves, lagoons, and coral-rimmed islands – some buried in sediment, others still alive. Off the coast of Mexico’s Yucatán Peninsula, researchers have made a discovery that rewrites part of crocodilian history. Two isolated island populations – one on Cozumel, the other on Banco Chinchorro – have been identified as distinct species of crocodiles.

For decades, these animals were assumed to be American crocodiles, part of the species Crocodylus acutus, which ranges from Baja California to Venezuela and across the Caribbean.

But new research reveals that these island populations are not merely remote relatives. They are genetically and physically distinct – products of isolation, adaptation, and evolutionary divergence.

This revelation comes from an international team led by McGill University, working alongside Mexican institutions. Their findings mark a turning point in crocodile biology and conservation.

Saving the new crocodile species

“Biodiversity is disappearing faster than we can discover what we’re losing,” said Professor Hans Larsson, who led the study. His team’s goal was to explore hidden patterns of crocodile diversity before development and climate change erased them.

Crocodiles are often seen as ancient, unchanging predators. Yet in the islands of the Yucatán, they tell a story of dynamic evolution and ecological specialization.

Island species often evolve rapidly, separated from their mainland ancestors by currents, storms, and time.

The two island populations – Cozumel and Banco Chinchorro – are part of the Mesoamerican Barrier Reef System, where prevailing ocean currents reduce genetic exchange with nearby coasts. These natural barriers, acting over thousands of years, allowed isolated populations to take new evolutionary paths.

Each island’s reptiles have stayed hidden in plain sight, their differences mistaken for regional quirks. But as the study shows, these are not minor variations. They are evidence of distinct evolutionary histories.

Island crocodiles are two separate species

To uncover the truth, Larsson’s team used Restriction-site Associated DNA Sequencing (RAD-seq), analyzing over 13,000 polymorphic genetic markers across crocodile populations from the Caribbean, Pacific Mexico, and Central America.

They found that the Cozumel and Banco Chinchorro crocodiles had exceptionally high numbers of unique alleles and genetic diversity, despite their small population sizes.

“These results were totally unexpected,” said José Avila-Cervantes, the study’s lead author and former student in Larsson’s lab.

Avila-Cervantes explained how they originally assumed all sampled animals were members of a single widespread species. But population structure analyses, genetic clustering algorithms, and phylogenetic reconstructions told a different story.

The team discovered that the two island populations form their own genetic clusters with no signs of admixture. Their genetic divergence from mainland Crocodylus acutus populations is greater than what separates some recognized crocodile species.

Species-level distinction confirmed

Genetics wasn’t the only signal of divergence. The researchers also analyzed skull shapes using geometric morphometrics. These analyses revealed dramatic differences in cranial morphology between island crocodiles and their mainland counterparts.

Cozumel crocodiles have notably long and narrow snouts – described as “longirostrine.” In contrast, Banco Chinchorro crocodiles have broader skulls adapted for durophagy, likely to help them crush hard-shelled prey.

Morphospace analysis placed each population in distinct zones, confirming that their physical differences mirrored their genetic splits.

Morphological distinctions extend to scale patterns as well. Banco Chinchorro individuals possess a greater number of post-occipital and nuchal scales, while Cozumel individuals have more irregular caudal scales. These features support species-level separation.

Crocodile species evolved in isolation

Genomic modeling suggests that the Cozumel and Banco Chinchorro populations have been genetically isolated for over 11,000 years. That’s long enough for new traits to evolve and for species to diverge.

Estimates suggest each island holds only 500 to 700 effective breeding individuals. While these numbers might seem modest, they are significantly larger than previously thought and are adequate to maintain genetic diversity, especially in isolated systems.

These findings highlight how isolation by environment – not just distance – can drive rapid evolutionary changes. Unlike other Crocodylus acutus populations, these two groups have adapted to harsh, specific conditions on their islands.

Adapting to extremes

Banco Chinchorro is a small atoll in the Caribbean Sea, distant from the mainland and sparsely inhabited by humans. Its crocodile population has developed exceptional traits to survive in this setting. Lagoon salinity on the atoll reaches levels as high as 65 ppt — more than twice the salinity of typical seawater.

Crocodiles here have adapted to tolerate these hypersaline conditions. Hatchlings survive in salt-saturated nursery sites, and adults exhibit slower growth rates, smaller clutch sizes, and reduced egg mass.

“The lower reproductive parameters for crocodiles in Banco Chinchorro are probably related to a smaller size of nesting females,” noted the researchers.

These ecological pressures are shaping the biology of the population. Females reach maturity at smaller sizes, and survival strategies now depend on both physiological tolerance and geographic seclusion.

Protecting crocodiles in Cozumel

Cozumel, in contrast, is a much larger island, closer to the Yucatán mainland and more affected by human activity. Urban development, tourism, and invasive species have introduced several stressors. Yet even here, the crocodile population shows signs of stable reproduction and unique genetic makeup.

Despite facing habitat fragmentation and limited protection compared to Banco Chinchorro, Cozumel’s crocodiles have preserved distinct traits and high genetic variation. The study calls for stronger protective measures to preserve their ecological niche.

Recognizing these reptiles as separate species could be the first step toward securing their future.

Naming the new crocodile species

The study suggests that the Cozumel and Banco Chinchorro populations should be officially described and named as new species. Doing so would have major conservation implications.

These crocodiles could become flagship species for preserving Caribbean mangrove ecosystems, which are under constant threat.

“Now that we recognize these crocodiles as distinct species, it’s crucial to protect their habitats. Limiting land development and implementing careful conservation strategies on Cozumel and Banco Chinchorro will be key to ensuring their survival,” said Larsson.

Because Banco Chinchorro is already designated as a Biosphere Reserve, it provides a model for effective conservation. Cozumel, however, has fragmented protections, and needs more attention from policymakers and environmental groups.

The evolution of new species

The discovery of these island crocodiles serves as a powerful reminder: evolution is not a closed chapter. It continues, quietly and sometimes dramatically, in the overlooked corners of the natural world.

The crocodiles of Cozumel and Banco Chinchorro are not just relics of the past. They are living examples of how isolation, environment, and time can create new life forms.

These new species may be rare, but they are real – and now, with science and will, perhaps they can be protected too.

The study is published in the journal Molecular Phylogenetics and Evolution.

Image Credit: McGill University.

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