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Upper Midwest Environmental Sciences Center

Relationship between fish presence and abundance in Arizona standing waters measured through standard techniques and environmental DNA

Principal Investigators: Jon Amberg

Impact of UMESC Science

Results from this study will advance our understanding of environmental DNA (eDNA) and how its detection relates to fish presence and abundance and traditional sampling techniques. A shift from traditional, labor intensive sampling methods to more modern molecular techniques can provide resource managers information needed to promote sport fisheries and healthy ecosystems in a cheaper, safer, and faster way.


Sport fisheries are important economic assets to state, federal, and private entities; as well as a cherished pastime for many. If sport fisheries are to be sustained or enhanced, effective fisheries management is crucial. Potential issues that currently effect aquatic communities include invasive species introductions; balance between predators and prey; and relationship between fishes and their habitat. Accurate and precise measurements of fish presence and abundance are necessary to provide needed information to biologists managing these communities.

Further developments of convenient and suitable sampling approaches to diagnose potential issues in aquatic communities are critical due to limited budgets and increasing environmental concerns. Current methods to sample fish communities can be biased and expensive, necessitating further refinement of current standard methods and development of new ones. Sampling fish is expensive and this expense increases with water body size. 

Recently, methods involving examination of deoxyribose nucleic acids in water samples (environmental DNA or eDNA) have shown promise for characterizing fish species present in water bodies. Measurements of eDNA shed by aquatic species can be sensitive and effective for species detection, especially for early detection of invasive species.With the assumption aquatic vertebrates release eDNA into the water (from feces, secretions, or tissues) in proportion to their biomass, eDNA may also be effective for estimating species biomass through measurement of the number of eDNA copies in a water sample, or the proportion of positive “hits” for a species in a collection of eDNA samples.

Although eDNA has been used successfully to characterize species presence and relative abundance in a limited number of tests, further evaluation of the procedure is necessary to identify its utility in standard fish monitoring surveys. Furthermore, ability to relate eDNA presence and abundance with fish samples collected by traditional methods, such as net sets or transects either within or across water bodies remains unclear.  We will investigate how characterization of fish species presence and relative abundance by eDNA in Arizona impoundments compares to data from traditional methods such as electrofishing and netting.

Arizona impoundments range widely in size from the largest in the United States (i.e., Lake Mead) to small ponds or “tanks” usually used to water livestock. Fish species of interest to managers monitoring these sites include many valuable non-native sport fishes. Valuable sport species in Arizona include largemouth bass Micropterus salmoides, bluegill sunfish Lepomis macrochirus; crappie Poxomis spp.; trouts and chars salmonidae; and channel catfish Ictalurus punctatus. Over $800 million dollars a year is spent on sportfishing-related activities in Arizona. Monitoring abundance and health of popular sport fishes in a system is critical to managing a lake for sportfishing. Measuring balance among common piscivore and insectivore fishes in sport fish communities is also important. Environmental DNA may provide an effective tool for incorporation into standard monitoring protocols of sportfish communities in the future. 

Sport fisheries can be compromised due to presence of undesirable species. For example, gizzard shad Dorosoma cepedianum can be a valuable forage fish in northern lakes where the species cannot overwinter, and populations can be carefully controlled; however, in southern waters, the species can overpopulate and compete with more desirable sport fishes. For example, in Arizona’s Lake Roosevelt, gizzard shad are rapidly expanding in distribution and abundance, becoming a concern for fisheries managers. The use of eDNA may prove important to evaluate the possible extent of imbalance in fish communities related to undesirable species such as gizzard shad. Furthermore, development of eDNA may provide an early-warning tool for identifying presence and abundance of non-desirable fishes (e.g., gizzard shad in other lakes in the Salt River chain), or other species, such as golden algae Prymnesium parvum and quagga mussels Dreissena rostriformis bugensis at early stages of invasion.

Rapid evaluation of species presence and abundance by eDNA, if successful, would allow fisheries managers to diagnose potential problems in fish communities at early stages (such as the invasion of Gizzard Shad) and apply management actions that would have a better likelihood of success to control populations. It would allow them to monitor many lakes and ponds at lower cost than traditional sampling techniques, especially water bodies that are isolated, privately-owned, where boats cannot be launched, or are currently lower priority in management plans but still important. Utilization of eDNA would be especially beneficial where numerous small water bodies dot the landscape in a management area with few biologists.

Methods are selective and each has its own limitation therefore it is especially crucial to have at least some knowledge of the natural history of fish in the water body to be sampled. To account for variation in catachability, standardization of sampling methods and sampling times is critical in developing adequate relationships between catch per unit effort (CPUE) and fish density. Our goal is to identify any relationship between amount of eDNA in a water sample/underlying sediment and CPUE of a particular fish species captured in a nearby electrofishing transect or net set (gill nets). Many studies have shown that CPUE is related to fish density and we will use CPUE as a surrogate measure of fish abundance.

Our goal is to test whether eDNA can characterize fish species presence and relative abundance in Arizona impoundments in a manner similar to traditional standard methods such as electrofishing and netting.  Water body size is an important factor to consider when determining proper management strategies such as the use of eDNA; therefore, our main efforts will be focused in two types of Arizona water bodies: a large reservoir and small lakes (e.g. those < 200 ha in surface area). We will concentrate on species of greatest concern, especially  gizzard shad and largemouth bass. If time and expense permits, analysis of other species’ eDNA to detect presence and abundance will be included. These species may include one or more of the following: black crappie Pomoxis nigromaculatus; smallmouth bass Micropterus dolomieu; bluegill sunfish Lepomis macrochirus; redear sunfish Lepomis microlophus; channel catfish Ictalurus punctatus; flathead catfish Pylodictis olivaris; and common carp Cyprinus carpio. Water samples will also be analyzed for presence and abundance of golden algae, an invasive species of major concern for Arizona lakes and ponds.


  • Determine if the percent of water samples containing the DNA of gizzard shad and largemouth bass and other selected species can be related to catch per effort of these species in adjacent boat electrofishing and netting samples in a large reservoir (within-impoundment comparison).
  • Determine if the number of eDNA copies in individual water samples can be related to catch per effort of these species in adjacent boat electrofishing and netting samples in a large reservoir (within-impoundment comparison).
  • Determine if the number of eDNA copies in individual water samples can be related to boat electrofishing catch per unit effort of select species across standing waters less than 200-ha (among-impoundment comparison).

 UMESC Scientist prepares eDNA sample.

UMESC Scientist prepares eDNA sample.



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