Tracking the invisible invasive

India is using eDNA in the fight against invasive alien fish such as Gambusia and guppies, writes Nobinraja M

In the early 20th century, India was in the middle of a deadly malaria crisis. By the time the country gained independence, 75 million people were infected, and nearly 800,000 died each year due to this mosquito-borne disease. The scale of the problem was staggering.

The crisis prompted the Indian government to launch the National Malaria Control Programme in 1953, which eventually evolved into the National Malaria Eradication Programme (NEMP). The big weapon against malaria at the time? Spraying dichloro-diphenyl-trichloroethane (DDT) - a non-biodegradable pesticide used globally at that time for mosquito control.

But by the mid-1980s, a new idea began to spread. Instead of resorting to chemicals, why not use fish that naturally eat mosquito larvae?

The chosen species was Gambusia, a small North American fish known for being tough, fast-breeding, and voracious for mosquito larvae. 

In 1985, India officially added larvivorous fishes to its anti-malaria toolkit, but the first introduction of Gambusia in India dates back to the 1920s. Government health departments stocked Gambusia in village ponds, wells, tanks, and canals. Fisheries hatcheries bred them in bulk. All over India, these little fish were deployed as biological soldiers in the war against malaria.

But there was a catch.

Gambusia spread fast. Aggressive and competitive, it outcompeted native fish, amphibians, and aquatic insects, moving far beyond malaria-control sites through connected waterways and during floods. 

Ironically, later studies showed that mosquito larvae weren’t even their primary food source. Soon, guppies, colourful aquarium favourites, were added to the programme too. Unfortunately, guppies also exhibited a similar negative impact on the ecosystem.

Today, Gambusia and guppies are found across almost every state in India. Gambusia eat native fish eggs, tadpoles, and insects, breed rapidly, and bully other species. Both fish are tiny, bony, often thrive in dirty water and do not taste good. 

We know Gambusia can cause ecological harm from studies elsewhere and a few from India. A few studies show the extent and possible spread of their distribution, but we don’t know the scale of the invasion or its impact. Guppies are milder but can still be a threat.

Detecting and monitoring invasives

India’s freshwater systems are massive and complex. They host thousands of fish species, many of which are found nowhere else on Earth. But this richness makes it incredibly difficult to find invaders.

Traditional methods—netting, electrofishing, market surveys, and fisher interviews—are labour-intensive, expensive, and often miss rare, hidden, or hard-to-reach species. Most invasives are only noticed after they’ve exploded in numbers and started damaging fisheries or biodiversity. By then, control is nearly impossible.

And remember, India has millions of ponds, tens of thousands of reservoirs, and over 400 rivers. Covering them all with conventional surveys is unrealistic. Huge blind spots remain, and that’s precisely where invasions thrive.

Here’s where science takes a fascinating turn.

Back in the 1980s, researchers were experimenting with extracting DNA from old museum specimens, laying the groundwork for ancient DNA research. 

Every organism sheds DNA from skin cells, mucus, waste, or decay. These microscopic fragments float around in the environment. This is environmental DNA, or eDNA.

Over time, scientists discovered they could recover genetic traces not just from bones, but from soil, sediments, and even water. By the 2000s, they could detect species simply by collecting and analysing a few litres of water and analysing the DNA it contains.

With this, scientists can figure out which species are present without ever catching them. One eDNA survey can give a snapshot of an entire waterbody’s biodiversity: common species, rare ones, hidden ones, or even early-stage invasions.

Countries like Australia, Japan, and the United States already use eDNA as a key part of their invasive alien species surveillance, detecting threats early and enabling rapid response.

Gambusia is still being released into waterbodies in India. In a recent hearing, the National Green Tribunal ruled against the introduction of Gambusia and guppies into waterbodies to safeguard the country. But due to a lack of awareness and outdated scientific understanding within reputed government bodies, the tradition continues. 

Pioneering eDNA efforts in India

In India, eDNA is still new, but pioneering work has been ongoing in the last couple of years. One such new initiative is the eDNA-based invasive alien fish mapping project being done by Bengaluru-based ATREE, funded by the Department of Biotechnology, which is piloting large-scale monitoring of invasive alien fishes in selected Ramsar wetlands. This project will also focus on guppies and other invasive fish. 

The researchers’ team is also working to build a make-in-India, low-cost eDNA collection system that can revolutionise eDNA research in India. It can be carried to the field by anyone and is easy to use in citizen science applications. 

EDNA tests have already detected species that have never been caught in nets or reported by fishers. Using eDNA to detect invasive alien fish shows that if tools like eDNA had existed and been used decades ago, we might have caught their escape early, before they spread across the country.

Now, India has a chance to get ahead of invasions rather than react too late. By embedding eDNA into routine surveys, strengthening DNA libraries, and fostering interdisciplinary collaboration, India can build an early-warning system for aquatic invaders. 

(The author is a researcher focusing on the ecology and management of invasive alien fishes in India)