Environmental DNA: Using Ecosystems as Crime Labs
The World Today
In a world that is changing quickly under the strain of climate change, expansion, and loss of habitat—all of which threaten biodiversity—it is vital to have tools that help us understand how those changes occur, what is changing, and what remains the same. That information allows scientists to explain the danger to organisms of all sizes, point out the presence of invasive species, and help control how humans interact with the world around them. One such tool is environmental DNA or eDNA.
“The smallest of clues help solve the most complex of mysteries in a crime scene by unraveling the chain of events. With eDNA, you are using the clues available within the environment to discover who is there, who is not, new changes, and regular activities.” – Dr. Robert Adamski, Associate Professor of Captive Wildlife Care
An excellent example of this is using soil samples to identify a list of species present in a specific area. Some organisms are never seen. Yet, their presence is documented through the use of DNA.
Another example of understanding a landscape occurs when we look deep into amber. We can piece together a world that no longer exists simply by identifying the organisms, pieces of organisms, pollen, and other clues that are trapped in the amber. Because that world is no longer available to study in person, we look at the clues and build scientific data libraries to answer more significant questions. We can even determine the annual rainfall from a million years ago by examining the gasses trapped within the ice in glacial sheets.
What Is Environmental DNA (eDNA)?
At its simplest, eDNA is the physical evidence that organisms leave behind as they encounter a biome. What that means is that a scientist can collect evidence about the environment and the organisms that live there by collecting samples of feces or scat and biological debris, such as urine stains, bones, and hair.
The list of what you can collect is extensive, but it is not just collecting these critical items that matter. A good example would be collecting scat from a transect—a measured plot of land—and then determining a list of organisms in that area. The scat would tell you the organism that left the clue as well as the organisms that creature consumed.
A coyote’s scat might include several invertebrate pieces, bones from small mammals, plant parts, such as berries and seeds. From that one sample, you could determine that many different organisms live in that area, and that information is valuable. More specifically, we are talking about DNA. So, in the coyote scat is the DNA of the coyote, the DNA of creatures it consumes, and the DNA from plants that it ate. You can also find DNA in other sources, such as water, within the soil, fecal samples, etc.
How does it work?
Environmental DNA is complicated. It appears in the forms of nuclear, mitochondrial, or chloroplast DNA. As each organism utilizes its environment, it leaves behind samples of DNA. By using science to isolate and then identify segments of eDNA, we can begin to map out the organisms that live in that environment.
Because some organisms are “never seen,” we cannot say for sure that they are present in an environment. Traditionally, we would look for physical clues—scat, tracks, monitor trail cams, etc.—to identify organisms that live in an environment. The problem with that type of collection is that it takes a long time to amass that level of data and it is limited to what we see and find.
With eDNA, the DNA’s presence tells us who is there and what they are doing. An excellent example of this occurs by monitoring species’ existence in a wetland. By taking random samples of water, we can look for DNA for a specific organism or a family of organisms. We can extract data that tells us if the organism is present, where the organism is in the wetland, the population of that organism, the wetland’s diversity, and other essential details for the marsh’s management.
Many organisms are environmentally fragile or at risk for extinction. It is challenging to find a rare organism in its environment. But we can do just that by gathering environmental samples and then looking for DNA. DNA is not stable in all settings. While it can exist for a million years in permafrost, it may only last a few days in freshwater.
DNA can also tell us a great deal about time, place, creature, and habits. We currently look at Y chromosomes’ mutations to track the heredity of humans. We can look at a person’s DNA and tell you their ancestry based on DNA mutations. Scientists are tracking the migration of humanity out of Africa before the last ice ages, a beautiful example of how DNA helps us unravel the past. We can prove that an organism is still alive—available in its ecosystem—by looking at water samples, isolating DNA fragments, and then pairing them to the organism.
How DNA Is Transforming Conservation Biology
One way that eDNA is transforming conservation biology is that it speeds up amassing quality data. It takes much longer to sample an environment using traditional scientific methods. With eDNA, we can make better decisions about how to manage ecosystems.
Another meaningful way that eDNA impacts conservation biology is to enable scientists to spot invasive species much more quickly. That means we can identify invasive organisms and act faster to remove them from the environment. That process and time-saving benefits mean restoration is much less expensive, and there is less damage to the environment. The method also allows scientists to understand the population of the invasive species and the population of the species displaced by the invader.
An example of how this works is seen in the Florida Everglades’ restoration process, where Burmese Pythons are not expanding their population and displacing many native species.
Challenges and Opportunities with DNA Testing
Beyond the fragile nature of eDNA in an environment is determining if multiple samples belong to the same individual. Because most mitochondrial DNA is transferred by the mother. It is currently impossible to tell if a segment of eDNA is from one species, a genetically similar species, or even if they come from one or more individuals within that species. That makes it nearly impossible to tell critical data such as population size, the sex of the organism, and other important data sets.
The Future Of DNA
There are few instances where advancements in biology create a renaissance within the science community. That is what eDNA is doing. It makes possible the collection of critical data that helps us better understand an environment, its challenges, and opportunities. The future of eDNA will only get brighter as we improve the technique across chemistry, sample preservation, and technology. It is safe to say that eDNA is the future of conservation biology.
Working to Change the World
Environmental DNA is already changing the way we do research. As we improve the technology around DNA and sequencing and study DNA, eDNA will only become more powerful. It is a game-changer that will expand outside of conservation biology and become a tool of many branches of science, such as molecular ecology. The presence of eDNA is improving research methodology and making it possible to scale current scientific standards and opening doors on the scale of Darwin’s discoveries.
At Unity College, as “America’s Environmental College,” we’re focused on helping the next generation of environmentally conscious professionals gain tools, like eDNA, to positively impact the world around them. It’s why we offer innovations in Hybrid Learning, providing a blend of online and in-the-classroom learning to help them, and you, get up to speed and on how to protect the planet.
Three of our programs—Wildlife and Fisheries Biology, Environmental Science, and Captive Wildlife Care—take you front and center for some of the most spectacular careers in science. In them, we explore eDNA. It’s an opportunity that allows you to walk in the footsteps of Darwin, but with a little twist. You remain in the modern world but work with science that breaks barriers.