Seeing Without Eyes: Using eDNA to Track Amphibian Distributions
By Brandon K. Booker
Sitting by a pond on a calm evening in the heart of spring, the air thick with the sweet aromas of young burgeoning flowers, you watch dragonflies dance on the water’s surface as the mellifluous songs played by a symphony of frogs and toads fill your ears. You look down into the pond’s murky edge and think, “I wonder what creatures live in this watery home?” It’s in these moments you gain an appreciation for biodiversity and the natural world.
Over the past few decades natural aquatic habitats across Alberta have been disappearing. The probable causes are rooted in deforestation, residential development, and pollution from agricultural and industrial run-off. As a result we have observed changes in Alberta’s amphibian populations, yet still our current records may not accurately reflect the true distribution of amphibians across the province. Mapping geographic distribution is the first critical step to determine if a species is at risk. This has created a need for biodiversity monitoring techniques that are fast, effective, and can work across large geographic ranges.
Amphibians,due to their cryptic nature and transitory developmental stages, can be extremely difficult to detect. In fact, the manpower required for call monitoring and visual encounter surveys is far too great to obtain an understanding of the distribution of these species in a reasonable amount of time. This has resulted in the listing of certain species, such as the Canadian toad, as Data Deficient meaning there isn't sufficient information to determine its geographic distribution or if it is at risk. These limitations are the catalyst that facilitated the development of a novel approach to monitoring biodiversity in the form of “environmental DNA analysis.”
What is environmental DNA?
When amphibians visit aquatic habitats to lay eggs, and later as their young develop, DNA begins to accumulate in the water from sloughed skin, urine, feces, and mucus. After a short period of time the DNA concentration becomes sufficiently high for detection using molecular techniques. Taking proper water samples simply requires a collection tube, a highly concentrated salt solution, an ethanol solution, and about 20-30 minutes to visit the pond in question. The samples are brought to the lab where they are analyzed for species presence/absence.
The molecular analysis entails initially creating a library of known DNA sequences (libDNA) for the amphibians you are searching for, which is done using tissues from properly identified specimens. Then you obtain the sequences for the environmental DNA (eDNA) from the water samples collected at the pond. You compare the eDNA to the libDNA and every time there is a match you know what species have visited. It’s that simple. This technique has proven far more sensitive to amphibians than call monitoring and visual surveys, thus providing a greater likelihood of detection. This, in conjunction with a relatively low investment of time in the field, makes eDNA a powerful tool for understanding species distribution across a large geographic range.
How do we test the environmental DNA technique?
Working closely with Alberta Conservation Association we designed an approach that focuses on Canadian toad and wood frog distributions across central Alberta. As I mentioned earlier, the Canadian toad is considered a Data Deficient species by the Endangered Species Conservation Committee, most likely due to their cryptic nature and relatively low abundance at breeding sites. We chose to look for the wood frog as well because they are expected to be present in most of our sites at relatively high abundances and can serve as a “positive” control (i.e., we should be detecting their eDNA). We selected a number of sites that have been monitored for the presence of the Canadian toad and wood frog using visual encounter and call monitoring surveys. These surveys have shown that all of the sites had wood frogs visiting them; however, there were only a few sites that had Canadian toads. Water samples were collected from each pond and are currently being analyzed at the University of Alberta. The hope is that following eDNA analysis we find far more sites with Canadian toad present, indicating greater species abundance and distribution than we originally thought, although this may not be the case.
What can we do with eDNA?
Following the validation of the eDNA method this approach can be implemented over broad areas to detect amphibians. Over time this approach will enable the mapping of distributions of every amphibian species in Alberta, which shouldn’t be too hard because there are only 10 of them. It will require a great deal of collaboration with people who visit wetlands all over the province and are willing to collect water samples. As time rolls on we will begin to more accurately understand where our amphibians live. So maybe believing isn’t seeing; after all, you never know what lurks in that watery home until you take a deeper look…