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Fish Detection by eDNA

Fish Detection by eDNA
Illustration - Ron Finger

Emerging Science—If you have heard of eDNA (environmental DNA), I am betting it was in conjunction with detecting Asian carps entering the Great Lakes. If you have not heard of eDNA, it is a procedure for detecting the presence of an organism from a water, soil, or air sample. DNA (deoxyribonucleic acid) is the genetic material present in all living organisms. Within the DNA strands are sequences of nucleic acid (genes or DNA fragments), some of which are unique to that species. The eDNA in the environment may come from scales, mucus, feces, gametes, or decomposition of the dead organism. Detection of a DNA fragment unique to a species is proof that the organism is somewhere in the system. Although technically complex, the process is largely automated allowing the rapid and economical assessment of many samples.

While good for surveillance, especially for unwanted invaders like Asian carp or zebra mussels, could eDNA be useful for assessing the abundance of fish populations? Collaborative studies by Arizona Game and Fish Department, U.S. Fish and Wildlife Service, U.S. Geological Survey, and University of Arizona fishery scientists attempted to answer whether eDNA measures were related to fish abundance, at what level of fish abundance were they detected by eDNA, and other important questions.

In 21,000-acre Roosevelt Lake, abundance of gizzard shad and largemouth bass estimated by gill net and electrofishing catch rates of gizzard shad and largemouth bass were little related to eDNA results.* eDNA was more effective at estimating shad than bass, possibly because the water samples for eDNA analysis were taken near the surface of open water where the shad live.

Studies in three streams in Arizona and New Mexico compared the detection of two rare bluehead sucker species by snorkel surveys and eDNA sampling.** The suckers were detected by snorkelers in all three streams but only in two streams by eDNA. The results suggest that there may be a threshold effect—a certain density of fish is needed to have a high likelihood of detecting the fish’s presence by eDNA.


eDNA will not make skilled fishery biologists tending gill nets and operating electrofishers obsolete, and it is hard to get fish population size structure and growth rate from a DNA sample. But eDNA will be a very valuable tool as aquatic resource managers become increasingly concerned about loss of biodiversity and accrual of unwanted invaders.


*Perez, C. R., and 8 co-authors. 2017. Comparison of American Fisheries Society (AFS) standard fish sampling techniques and environmental DNA for characterizing fish communities in a large reservoir. N. Am. J. Fish. Mgmt. 37:1010-1027.

**Ulibarri, R. M., and 5 co-authors. 2017. Comparing efficiency of American Fisheries Society standard snorkeling techniques to environmental DNA sampling techniques. N. Am. J. Fish. Mgmt. 37:644-651.

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