Finding fish using their DNA

SOURCE: Thomsen P.; Møller P.; Sigsgaard E.; Knudsen S.; Jørgensen O.; Willerslev E. (2016) Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes. PLoS ONE 11(11): e0165252. doi:10.1371/journal.pone.0165252

 

NETS AREN’T CUTTING IT

Monitoring populations of fish is important for commercial and non-commercial species. Commercial species consumed by humans, such as halibut and cod (Figure 1), are well studied and their population size is used to set catch limits each year. Non-commercial species are not as well studied due to a lack of economic interest. Yet, monitoring of many non-commercial species can give us important information about how the marine world is functioning. Understanding how different fish species will migrate in response to climate change is an important focus for scientists, but not enough is known about where fish currently live to make proper predictions. Understanding where species will live in the future will help managers determine locations of management areas.

Figure 1. Atlantic Cod (Gadus morhua). Image Credit: Hans-Petter Fjeld, Wikipedia Commons.

One common method for monitoring fish populations makes use of a trawl (Figure 2). Trawling uses a towed net, pulled through the water behind a boat. After towing for a set distance, the net is brought on board where the fish are identified and counted. Unfortunately, this method is time consuming and can be harmful to the fish as well as the ecosystem on the seafloor. One alternative method to trawling for fish surveys is using eDNA.

Figure 2. Drawing of trawl. Image credit: NOAA, Wikimedia Commons.

WHAT IS eDNA?

As fish move through the ocean they shed DNA in a similar way to you shedding skin cells which contain your DNA. The DNA left behind by fish or other living organisms is called environmental DNA, or eDNA. Scientists can collect a water sample, extract the free-floating DNA, sequence it and use the unique codes found within the floating pieces to determine which fish were in the water. It is easier, quicker, and cheaper than performing trawls. In addition, eDNA is a non-invasive process that reduces accidental mortality and can detect species that are less likely to get stuck in trawls due to their size or swimming speeds. The use of eDNA to determine fish stocks is not well studied in the ocean but has been used in addition to traditional survey techniques in several freshwater systems. In this study the researchers compare the results of trawl surveys to eDNA surveys in the ocean.

 

TESTING the eDNA METHOD IN GREENLAND

Philip Thomsen and his colleagues conducted their study in the Davis Strait off Greenland. The scientists visited several locations, collected a water sample and then performed a bottom trawl. They counted the number and type of fish as well as their weight from each trawl. Back in the lab the researchers extracted DNA from the water sample and sequenced it. They then compared the sequences (unique codes) to databases of known sequences to determine which fish were present in the samples.

 

COMPARING TRAWL AND eDNA DATA

It turns out that both methods, trawling and eDNA, produced similar results (Figure 3). A total of twenty-six families were found using both the trawling and eDNA methods. While there was a lot of overlap between the two, 3 families were only found with eDNA and 2 families were only found with the trawl. Some of the families found in the eDNA samples but not the trawls tend to hang out in the upper portions of the water column, explaining why they were not caught in the trawls which were conducted at the ocean floor.

 

In general, the fish density determined by the trawl and the number of eDNA sequences corresponded to one another. For example, the green halibut was the most abundant species according to both the trawl and eDNA data. However, for some families, there was a difference in the number of times the family was detected between the two methods. For example, the Greenland shark was detected in several eDNA samples but was only caught in one trawl. This is likely because the Greenland shark can easily avoid trawls. This means that the Greenland shark population is likely much higher than calculated from trawling data. This is one example of how eDNA data may help us to better understand fish populations than trawling.

 

One drawback of the eDNA method is that researchers are not always able to determine the identity of the sequence all the way to the species level. Rather, like this study, they often get less specific classification like genus or family level. This is because the DNA captured from the water is often just a snapshot of the all the DNA belonging to the fish. For example, in this study, the scientists were be able to determine a particular sequence was from a Cod, but couldn’t determine if it was an Atlantic cod or a Polar cod.


Figure 3. Overview of the results from trawling and eDNA. Families on the left were only detected by trawling. Families on the right were only detected by eDNA. Families in the middle were detected using both methods. Image credit: Thomsen P. et al. (2016) Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes. PLoS ONE 11(11): e0165252. doi:10.1371/journal.pone.0165252

WHAT’S NEXT?

Phillip Thomsen and his colleges determined that sampling eDNA can be a useful supplement to deep-water trawling. The data provided by eDNA could help researchers better estimate the distribution and stocks of commercial and non-commercial fishes. The data can help managers better determine fish quotas and monitor movement of fish with climate change.

 

While eDNA is helpful in determining which fish are present, additional research is needed to see how well eDNA can determine the number of each type of fish. While it is easy to detect presence or absence of a species, knowing how many of that species you have is tricky. The amount of DNA you find doesn’t necessarily correspond to the amount of that fish in the water. Many factors can impact the amount of DNA in water including the fact that some fish lose more DNA than others or some circumstances can remove DNA from the water. Understanding these factors and others is a high priority for future studies.

Share this:

Elizabeth Brannon

I recently graduated with a Ph.D. in Biology and Environmental Science from the University of Rhode Island where I studied greenhouse gas emissions from wastewater treatment. I am committed to developing a better understanding of the impacts we have as humans on the planet. I'm a hard core New England sports fan and when I'm not cheering on the Patriots you can find me outside on an adventure!

Leave a Reply