Using Environmental DNA to Find Sharks

Sharks are often known as one of the fiercest predators in the ocean. Yet they are also one of the most threatened marine species—largely because they are hunted by humans for their highly valuable fins. How do we know they are being threatened?

Traditionally, researchers have estimated the population and diversity of sharks using two methods. One is by sending divers into the water to count the number of sharks and record which species they see. Another is to set up baited cameras in different locations to record the sharks that come near. When fewer species of sharks are examined using these methods, we conclude that there is a decrease in diversity and an increase in what’s called “dark diversity”.

Dark diversity is defined as the collection of local species that should be present in a certain region but cannot be detected. (The term is the biological equivalent to “dark matter” in physics, which describes matter that exists, but cannot be directly observed.) Accurate knowledge of dark diversity can help researchers devise conservation strategies for specific areas. Areas with high dark diversity would require restoration efforts to reduce environmental threats. On the other hand, areas with low dark diversity can be established as marine reserves and a potential source for recolonization.

Unfortunately, using traditional methods to estimate dark density are highly inaccurate. Have specific species of sharks truly vanished from the area? Or have the sharks just learned to avoid human detection? It’s hard to tell.

In a 2018 paper published in Science Advances, Boussarie et al. addressed this problem by testing a new non-invasive method to detect dark diversity of sharks. This new method is not based on visual observation. Instead, it detects DNA released from animals into the environment, known as environmental DNA (eDNA).

In this study, eDNA was extracted from water samples collected from various coral reefs located in the southwestern Pacific. The results showed that with only 22 samples, 13 shark species were detected using eDNA. In contrast, 2,758 samples from divers and 385 samples from baited cameras each detected only 9 species. This suggests that shark prevalence may be greater than previously thought.

The eDNA method has several advantages compared to traditional methods. Divers and bait cameras can only cover small areas due to limitations in visual range. They are also limited to short temporal periods—each dive usually lasts less than 2 hours, and a camera only works for a few hours at a time. Because eDNA can be detected days after being released and can be transported across distances through movement of water, the spatiotemporal scale of detection is much greater than traditional methods. This allows more species to be detected with significantly fewer samples.

There are, however, disadvantages to using eDNA. For example, eDNA cannot provide information on the size, health, age, sex or behavior of the sharks. Nevertheless, this study shows that eDNA is an accurate and efficient method to determine the dark diversity of sharks and other marine animals.

Reference: Environmental DNA illuminates the dark diversity of sharks.

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Johanna Lee
Johanna is a Science Writer at Promega. She earned her PhD in Biomedical Sciences at Baylor College of Medicine. She was a freelance writer and full-time mom for five years before joining Promega. Johanna is from Taiwan and she believes Taiwanese food is the best in the world. She loves doing yoga, traveling and spending time with her two kids.

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