Science

Is a Bottleneck Effect Endangering Chinese Alligators?

The effect is what happens when the population of a species shrinks so much that the surviving individuals are not just fewer in number but also contain fewer genetic variations.

The sleek Chinese alligators living inconspicuously in the murky wetlands of the Yangtze river are being pushed to the edge of extinction again. Less than 120 individuals survive in the wild. The trouble is that the captive population, present in sufficient numbers in two natural reserves in China, might be suffering from a population bottleneck, according to a recent study from Zhejiang University, Hangzhou.

Such a bottleneck happens when the population of a species shrinks so much that the surviving individuals are not just fewer in number but also contain fewer genetic variations.

If we were to compare the long strands of DNA between two individuals of the same species, we would find some subtle differences. These differences help the population adapt to changing environmental conditions, withstand the outbreak of new diseases, etc. The larger the number of individuals in a naturally healthy population, the larger the number of variations that confer adaptability – and more resilient will the population be to changes in its environment.

However, this is not the case when the population shrinks. Fewer individuals means fewer differences. For example, certain genetic variations present in some members of the population might help in fighting off a disease. If the population shrinks to the extent that these variations are no longer present, all the afflicted animals might succumb.

Once a population shrinks, the bottleneck effect persists when it expands again because it’s hard to reacquire the variations once lost. Even as the few remaining individuals multiply and their population increases, the variations they manage to pass on are only the ones that have survived.

The variations that researchers from Zhejiang University looked at in the captive alligator populations all belonged to the major histocompatibility complex (MHC) genes. These genes are central to the surveillance mechanisms in our body, which recognise the presence of harmful foreign organisms or infectious agents (bacteria, viruses, etc.) and help destroy them. They control the production of MHC proteins in each cell, which identify and display molecules derived from the invading threats. In doing so, the infected cells are flagged for destruction. These flags are recognised by our defence system, which fights and eliminates the infection.


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The study analysed variations in three different MHC genes in the captive alligator population. Surprisingly, they found that all three genes had only two variants in the entire population.

The variations can be lost for many reasons. When a population grows, breeding between closely related individuals becomes inevitable. And because the DNA of closely related individuals is similar, the progeny’s DNA has very little variation. “This is expected. The test samples in the study comprise reproductively active ~15-year-old individuals from a captive population that had been initiated only 30 years back,” Ramesh Aggarwal, who has carried out similar genetic studies on the Indian mugger at the Centre for Cellular and Molecular Biology, Hyderabad, explained to The Wire. “Most of the tested samples will be siblings or closely related individuals with a narrow genetic base.”

Another factor could be the isolated environment in which the alligators are bred. While the alligators may have been brought in a protected environment, the same protection also prevents the animals from being exposed to pathogens found in the wild. With fewer pathogens to fight against, the gene variants involved in building immunity fade away.

Aggarwal, however, disagrees with the conclusions that have been drawn from the study: “Even though this study has [addressed the effect], which is a matter of great concern throughout the world, the study in itself is deficient in design and data generated to infer that the captive population is indeed suffering” the consequences of a genetic bottleneck.

Closer home, the mugger, a.k.a. the marsh crocodile – the most common species of crocodile in India – is doing fine even in captivity. Nikhil Whitaker, curator of the Madras Crocodile Bank Trust and Centre for Herpetology, told The Wire, “[Crocodilians bred in captivity] have been doing fine in this situation for decades, and we know that for a fact. Unlike mammals, where you might see manifestations in behaviour, abnormalities in embryo, growth rates and so on, in captivity people have bred crocodiles up to the seventh generation with no visible changes.”

When Aggarwal and his research group analysed the DNA of captive populations from the Madras Crocodile bank, they could find significant variations in the genes. “Even though healthy variation can be seen in the mugger crocodiles, the same can’t be said for the gharial. According to the ongoing studies conducted by a team led by Jeffrey Lang, the gharial population is suffering from a severe bottleneck,” Aggarwal said.


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Gharials, unlike muggers, have been classified as ‘critically endangered’ by the International Union for the Conservation of Nature. The steady decline in their numbers, attributed to overhunting, construction of dams, sand-mining, etc., could be a possible reason for this bottleneck. But we don’t know anything for sure yet.

The populations of many other animals have faced similar loss in genetic variation. For example, the Tasmanian devil is being threatened by a form of infectious cancer. The disease is able to inflict their population like wildfire because of their low genetic diversity, which doesn’t give them enough resilience to fight back.

This study highlights the importance of saving a species by saving its home. While captive breeding is necessary to save the species, it is no substitute for their natural habitats. In some cases, the loss of genetic diversity might be the first step on a species’s path towards extinction. “Genetic studies hold great promise for conservation,” Aggarwal said. “However, they must be conducted with utmost care and seriousness to avoid wrong interpretations.”

These critically endangered  alligators, one of the only two species present in the world, are endemic to China. They belong to the ancient Crocodilian order – an order that survived the meteorite strike that wiped off the dinosaurs. However, in the face of the damage inflicted by humankind, the future of this species might be as murky as the waters they inhabit.

The paper was published in the journal Scientific Reports on July 17, 2017.

Neelakshi Varma is a masters student in molecular biology at the Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru.

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