By Ladd Knotek
Region 2 Fisheries Biologist 

What in the World are eDNA and Genetic Assignment? ... And Why Should Anglers Care?


September 14, 2017

Photo provided

Bull trout caught and released in Seeley Lake. Fish like this can be traced back to their tributary of origin (likely Morrell Creek) using genetic assignment to complement ongoing population monitoring efforts.

The number of new genetic analysis techniques is rapidly expanding and many provide biologists the opportunity to uncover new information about Montana's fisheries and invasive species that threaten them. Among these new techniques are genetic assignment and analysis of environmental DNA (eDNA); both of which have been applied in Clearwater Basin lakes and streams.

Environmental DNA (eDNA) simply refers to fragments of genetic material from different plants and animals that occur naturally in the environment. In the case of fish and other aquatic critters, DNA is contained in cells that are continually shed into the water; thus becoming "e"DNA. This eDNA persists in standing and flowing water for some time, is unique for each type of organism or species, and can be detected in very small quantities by scientists with the equipment to look for it (see photo).

As techniques for eDNA sampling have been developed and refined, they have provided biologists with an important new tool for the fisheries toolbox. For instance, we can now collect a water sample from a river or stream and quickly confirm if a certain species is present upstream by filtering the water and using a laboratory analysis to look for its unique DNA. This is not to say that eDNA sampling will replace traditional field sampling techniques and fisheries surveys; it's simply an additional method that allows us to be more efficient and answer some basic questions about geographic distribution. For instance, if biologists are wondering which tributaries within a larger stream system contain native cutthroat trout, they can collect water (eDNA) samples at the mouth of each tributary and get a good idea where these fish are found. By narrowing the search, they can then efficiently follow up with traditional field sampling to collect fish and obtain information on the relative number of different fish species, size structure and genetic purity for cutthroat trout populations.

Another important application for eDNA sampling is monitoring various waters for new species introductions. For example, the same basic methods described above can be used to periodically test lake outlets for invasive plants and animals (e.g., Eurasian milfoil or mussels) or unauthorized fish introductions. In these cases, eDNA can provide a cost-effective method to detect new species introductions early, before the populations explode and become unmanageable. In partnership with Clearwater Resource Council (CRC) and other groups, lake and stream monitoring for aquatic invasive species (AIS) introductions using eDNA is becoming standard practice.

Genetic assignment is a different technique where an individual fish can be traced back to its tributary of origin or source population. With this method, "assignments" are based on comparisons of genetic markers from an individual fish with the presence and frequency of these markers in the tributary populations where the fish may have originated. If the genetic make-up of tributary source populations is distinct, there is a high probability that an individual from one of the populations can be accurately matched or assigned to the population where it originated.

In one recent application, we collected genetic samples from juvenile bull trout in all Clearwater Basin tributary streams where viable migratory populations had been identified: Morrell Creek, Deer Creek, Marshall Creek, East Fork Clearwater River and West Fork Clearwater River. Downstream of these suitable tributaries (where all spawning and rearing occurs), adult and sub-adult bull trout are common in the interconnected main stem lakes. Our goal was to determine the tributary of origin for each fish captured in the lakes to evaluate habitat use and the spatial scale of bull trout movements, as well as monitor the relative levels of recruitment from tributary populations over time.

Photo provided

Sampling gear for the 21st century fisheries biologist; equipment used to collect environmental DNA (eDNA) includes a water pump, micro-filters, and sterile bags for transport to the lab.

After the genetic composition of juvenile fish from tributaries was analyzed in the lab, distinctive genetic "baselines" were established for each tributary population. We then collected samples from bull trout captured in lakes throughout the system. The origin of these fish was unknown until the genetic make-up of each fish was compared with the distinctive characteristics of baseline populations in the tributaries. When these comparisons were made, fish from the lakes could be "assigned" back to their tributary of origin with high certainty. The accuracy of the process was verified using numerous test samples of fish with known tributary origin.

Sampling eDNA and determining source populations for wild trout using genetic assignment are certainly exciting new techniques with high cost-effectiveness and application for many situations and species. However, like any scientific technique or sampling method, they have their advantages and limitations. Biologists around Montana and fisheries researchers at our universities are in the process of refining new genetic tools and defining where they can be most useful in facilitating sound management of aquatic resources.

If you have questions about these techniques or other fisheries/aquatic topics in the Seeley Lake area, contact Ladd at 542-5506.


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