New eDNA technique can improve accuracy of tracking fish populations

A technique developed by researchers at Shanghai Ocean University could allow scientists to detect all species present in a body of water and their related populations, just by taking a mere water sample.

The team has developed a new approach to the use of environmental DNA, or eDNA, to estimate species abundance with less bias and variability, offering a more reliable tool for ecological monitoring and biodiversity protection.

Led by Li Chenhong, a professor at the university's College of Fisheries and Life Science, the research was published in the journal Molecular Ecology Resources on Feb 6.

"Wherever living things exist, they leave their traces. In the same way, a fish that swims through will leave a DNA 'trace' in the water, too," Li said.

He explained that eDNA refers to DNA fragments released by organisms into the environment, including water, soil and air. These fragments come from sources such as shed skin cells, scales and DNA released during respiration, excretion and reproduction.

The eDNA technique has become a popular method for monitoring species in ecological studies due to its cost-effectiveness, efficiency and noninvasive nature. It has potential applications in biodiversity assessment, endangered species protection and invasive species monitoring.

The technique is particularly relevant in China, where large-scale ecological protection initiatives, such as the 10-year fishing ban in the Yangtze River, have been implemented. With the limitations of traditional fishery survey methods, eDNA provides a valuable alternative for studying biological resources and the environment.

While using eDNA for species detection and abundance estimation is not new, most studies have relied on eDNA concentration to quantify species abundance. However, this method can be unreliable due to variations in physiological activity and environmental factors.

"For example, if one individual fish is more active in feeding or production, it will shed more eDNA samples, and its quantity may be overestimated," Li said.

He emphasized that these factors pose challenges to the eDNA concentration approach, making it necessary to develop a method that is less sensitive to individual variations in eDNA release.

"We are taking the approach of genetic sequence variation — using the number of segregating sites — to explore the relationship between eDNA and species abundance," he said. "The inherent redundancy nature of segregating sites ensures that each individual organism is counted only once regardless of the number of copies of DNA detected in the samples."

He likened the segregating sites in genetic sequences to fingerprints, noting that each organism, even within the same species, has unique variations.

By focusing on genetic variation, the new method minimizes the impact of factors such as life stage, weight, feeding, season, temperature and microbial communities, resulting in more stable, precise and efficient estimates of species populations, he said.

Li said he began the research about four years ago, driven by the demand for eDNA applications from fishery management, biological conservation authorities and ecological research institutions.

The technique can be applied in aquatic, soil and air environments, providing support for quantitative species analysis, biodiversity monitoring, scientific research and ecological conservation measures.

"We have made a breakthrough with this new approach, and we will continue our research to tackle the challenges for large-scale practical application in the wild to better monitor and protect species and the ecology," he said.