“Did they not teach you what the head looks like in college? Get under the head!” my boss screamed over the roaring electrofishing generator and the crashing of Lake Erie’s whitecaps against our ancient jon boat. Spitting out mayflies and slipping on fish slime, another intern and I tried to sandwich a 50” muskie between our 8” nets as I thought to myself, That’s not exactly the issue here, pal.
We were performing a fish survey along the coastline of Lake Erie, sweltering in our thick waders even though it was well past 2 am at night. On that particular trip, and on many since, I saw firsthand the problems inherent to traditional fisheries study methods.
I’ve spent hours trying to set a net perfectly where we think the fish will be, only to pull it up days later to find more holes and twists in the netting than fish. I’ve seen massive catfish drift right out of the electrofishing field and into waters too deep for our gear, because they’re impervious to that all but the lowest electrofishing frequencies. I’ve run creel surveys where anglers have sworn that the rock bass on their stringer was a smallmouth x bluegill hybrid.
Fisheries biologists anticipate and account for these mishaps while analyzing survey results, but the need for a highly accurate, noninvasive method of sampling stood unfilled until recently. Developed in the 1980s, environmental DNA testing pulls genetic material from an organism’s environment to test for that organism’s presence or absence.
The process can be broken into five stages:
- Marker Selection and Primer Design. Experts locate a species-specific genetic marker sequence, which is a DNA section that only members of that species have. Once they identify the marker, the scientists design a primer that can serve as a starting point for that marker sequence. This comes in handy later.
- Sample Collection. Water samples are taken from areas where DNA might accumulate, like eddies within a stream.
- Sample Preparation. The cooled water samples are filtered to isolate DNA.
- DNA Amplification: The isolated DNA is exposed to the primer, enzymes to cut up the DNA, and nucleotides to build it back together. Any DNA that has the marker sequence will be able to replicate itself with the primer and the available nucleotides.
- eDNA Screening and Detection. Scientists analyze the resulting DNA fragments and look for any of the appropriate marker sequence length. If there are any, the scientists can conclude that their target species is present in that environment.
Today the process is most commonly used in Asian carp studies. Fisheries biologists from state and federal governments as well as university researchers take advantage of eDNA testing to check waterways for the presence of these invasive fish.
Like any research method, eDNA testing has its pitfalls. It’s possible for a species to be present within a waterway without its DNA showing up in the assessment. Its DNA may have degraded due to light exposure, high or low temperatures, or extreme pH, or it may have been washed away entirely by fast flows. Even if a species’ presence is confirmed, eDNA can tell biologists nothing about the age structure of the population, how big its members are, or how many individuals there are.
Environmental DNA testing works best in combination with another method. The best data comes from a variety of surveying methods that are repeated many times, preferably over the course of many years. Luckily, with each passing year the data we have on hand improves. And personally, I am especially grateful for the fact that fisheries research continues to advance.
Originally published in Outdoor News.
Evans, Nathan T. and Lamberti, Gary A. 2018. “Freshwater fisheries assessment using environmental DNA: A primer on the method, its potential, and shortcomings as a conservation tool”. Fisheries Research (197): 60-66