Environmental DNA: A New Approach to Monitoring Fish in Yellowstone National Park

from: Yellowstone Science 25(1)

by Colleen R. Detjens & Kellie J. Carim

Environmental DNA (eDNA) is genetic material obtained from an environmental sample such as soil, sediment, water, or ice without directly handling the organism from which it originated (Thomsen and Willerslev 2015). This DNA is shed from the organism into the environment in a variety of forms, including skin cells, mucus, feces, or tissue. Biologists are able to collect this DNA and analyze it to determine the presence of specific species. In fact, this technique is so sensitive that even a single copy of DNA from an animal may be detected in an environmental sample. In recent years, eDNA-based sampling methods have become an increasingly common tool for wildlife managers. Within Yellowstone National Park (YNP), fisheries biologists have begun using eDNA from water samples to understand the distribution of various fish species. In collaboration with researchers at the National Genomics Center for Wildlife and Fish Conservation, located at the Forest Service Rocky Mountain Research Station in Missoula, Montana, we hope to contribute to the growing body of knowledge on the effectiveness and limitations of eDNA sampling as a monitoring tool.

Applications and Analysis

There are many potential benefits to collecting eDNA samples in conjunction with native fish restoration projects in YNP. Because eDNA sampling does not require fish be observed, biologists can survey waters without having to electrofish, handle, or stress fragile populations. The sensitivity of this tool may also allow biologists to detect invasive species while numbers are still low, which could prove invaluable to containing the spread of an invasion (Goldberg et al. 2013). The use of eDNA may also be helpful in determining the effectiveness of rotenone treatments to remove non-native fish from watersheds where native fish are being restored. Finally, biologists can use the amount of DNA in a sample to understand the relative abundance of a species at the landscape level (Takahara et al. 2012, Pilliod et al. 2013). In essence, eDNA samples provide a powerful snapshot in time for biologists to catalog information not on just one species, but potentially an entire biological community.

Following water sample collection, eDNA samples are taken to a laboratory and analyzed using a meticulously designed test that can detect any DNA from the fish species of interest, as well as DNA from other non-target species. Therefore, samples can be reanalyzed multiple times to detect DNA from any additional species that may have been present at the time of sample collection but not part of the original research study. The samples can be preserved in a freezer and analyzed months or even years later for fish or wildlife species that may not have been the initial target of investigation.
Because of YNP’s immense size and rugged landscape, access to study sites is often gained on foot. Hiking in and out of remote locations and sampling via electrofishing or netting take a lot of time, effort, and personnel; this is when the eDNA method becomes a valuable tool. Due to its high sensitivity and the efficiency of its use, eDNA sampling may be the most effective way to determine whether or not a species is present in remote areas.

Limitations

Despite the many benefits of using eDNA-based monitoring methods, there are still some limitations that can affect the accuracy of detecting a species. DNA that is free-floating in the environment will eventually degrade; factors such as temperature and exposure to ultraviolet light will speed the degradation process (Strickler et al. 2015). As a result, the further you are from a fish in the stream, the less likely you are to collect its DNA in a sample. Additionally, the rate at which fish shed DNA may not always be consistent and could be affected by conditions such as diet, temperature, and spawning activities (Klymus et al. 2015). Consequently, the ability of eDNA sampling to replace traditional methods of estimating species presence or abundance is not completely understood and, therefore, warrants further study.

Because eDNA-based methods can detect a single copy of DNA, preventing cross-contamination of samples must be carefully considered. Samples must be handled with caution to avoid contamination during both field collection and laboratory processing. For example, biologists must take care to avoid the transfer of DNA from their waders, which are exposed to DNA when working in bodies of water. Also, it is possible to detect fish DNA in a water sample after movement through, or defecation by, fish predators (Merkes et al. 2014). However, many of these limitations can be accounted for by carefully choosing sample locations, avoiding contamination during the sampling process, and implementing rigorous lab protocols. Researchers at the National Genomics Center for Wildlife and Fish Conservation have been at the forefront of the efforts to understand these limitations and help wildlife managers, like those in Yellowstone, collect samples with the highest possible quality.

eDNA in Yellowstone National Park

Within YNP, eDNA sampling was used to estimate the geographic extent of non-native
brook trout within Soda Butte Creek, which helped direct eradication efforts and allowed biologists to confidently exclude portions of the drainage where the use of rotenone was not needed. Environmental DNA sampling has also been used in follow-up sampling to verify the success of rotenone treatments, including the treatment of Elk Creek to remove non-native brook trout (see “Preservation of Native Cutthroat Trout in Northern Yellowstone,” this issue). The use of eDNA may also prove to be a valuable tool for assessing the recovery of Yellowstone cutthroat trout in Yellowstone Lake and may be able to confirm the presence of spawning fish in tributaries where other visual survey methods in recent years have not detected them. Cutthroat trout eDNA in Yellowstone Lake spawning streams may also be useful for estimating the relative abundance of spawning fish throughout the spawning period. In addition, environmental samples aimed at detecting terrestrial organisms, such as bears and river otters, could provide additional insight on the use of cutthroat trout as a prey source for these animals, especially in the remote tributaries of Yellowstone Lake. All of this information will be extremely valuable to managers as native cutthroat trout continue to recover within the Yellowstone Lake ecosystem.

Literature Cited

Goldberg, C.S., A. Sepulveda, A. Ray, J. Baumgardt, and L.P. Waits. 2013. Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshwater Science 32:792-800.