A moose is lounging in a marsh. A sturgeon swims at the bottom of a lake. A salamander wriggles along the edge of a stream. For the biologist, unless he is in the right place at the right time, it is difficult to know in detail the presence — or absence — of animals on the territory. Especially if it is rare species.
Recent advances in the field of “environmental DNA”, however, make it possible to see this more clearly. A Canada-wide project, launched a year ago, promises to facilitate the census of 150 species of vertebrates – fish, amphibians, birds, reptiles and mammals – throughout the territory.
“Environmental DNA is an extremely powerful tool,” argues Valérie Langlois, professor at the National Institute for Scientific Research (INRS) and co-director of the iTrackDNA project, which spans a four-year period. His work will be presented at the COP15 on biodiversity which opens on Wednesday in Montreal.
The principle of environmental DNA (eDNA) is as follows: a sample of water, typically a liter or two, is taken and finely filtered. The material collected is then analyzed in the laboratory. The genetic material found there is compared to a database. If the signature of an animal is detected, it means that it was present near the place of collection.
These methods are still very recent: they only date back to 2008, recalls Louis Bernatchez, professor of biology at Laval University, specialist in genomics and fish. “Since that time, the field has grown exponentially,” says the man who is also part of the iTrackDNA management team.
Incredible discoveries have thus been made thanks to the excrement, hair, scales, mucus, saliva or urine that animals leave behind. The majority of eDNA analyzes relate to aquatic environments. We learn about the fish that live there, but also about the land animals that frequent them.
To go further, members of iTrackDNA, whose other co-director is from the University of Victoria, are developing tests that work on soil samples. A pinch of soil taken from a trail can determine which small mammals pass by. Elsewhere in the world, teams have even filtered the air floating in a zoo, then detected the genetic trace of dozens of species present…
A monk’s work
iTrackDNA’s goal is to develop test kits for some of the most important species in Canada. Partners in the field — such as organizations, industry players and Indigenous communities — can then collect samples, send them to the lab, and learn about the wildlife issues that affect them.
To know what you find, however, you have to know what you are looking for. It is therefore necessary to have a reliable and complete file of the genetic profile of the targeted species. The Canadian team is focusing on mitochondrial DNA, which is found in hundreds of replicates in every cell. It is easier to detect in the environment than DNA from the cell nucleus.
To have a solid base on which to work, Valérie Langlois and her colleagues set themselves the goal of sequencing the mitochondrial DNA of 12 individuals from each of the 150 species. In some cases, data already exists, but it is fragmented. The team is now aiming for extreme reliability. “We take one step back to take two forward,” explains the researcher engaged in the work of a monk.
Few eDNA projects around the world are based on such a systematic and rigorous approach, says Ms.me Langlois. “Each laboratory develops its own methods. We have to find a consensus to standardize our ways of doing things,” she says.
The Canadian group is also collaborating on the development of the first international standard governing eDNA. If researchers in this field succeed in adopting standardized analysis methods and centralizing their data, they will be able to contribute even more effectively to the characterization and protection of biodiversity.
In search of the wolverine
Currently, the iTrackDNA team has designed around 30 tests, in particular for lake sturgeon and American eel. All iTrackDNA results are published online in open databases.
Of course, the 150 species targeted are only a small slice of Canada’s wildlife diversity. However, some animals sometimes give a good idea of the overall health of the natural environment in which they live. These species then act as canaries in the mine.
In general, one of the strengths of eDNA is its ability to detect invasive species. Mr. Bernatchez’s team has also collaborated with the Quebec Ministry of Forests, Wildlife and Parks to establish the presence of Asian carp in the St. Lawrence River. In the future, eDNA could be used routinely to check whether the ballast water of large ships contains invasive species.
The method also makes it possible to follow the progression of parasites on the territory. Mme Langlois gives an example: white-tailed deer live easily with a nematode, the brainworm, which is however dangerous for moose. With climate change, deer are moving further and further north, where their larger cousins live. eDNA techniques make it possible to “map” the progression of the parasite and its host.
The iTrackDNA project also makes it possible to better characterize the populations of rare species, which move over very large territories, such as the wolverine. “The wolverine is a mythical species for Aboriginal people,” says Ms.me Langlois. We haven’t seen any for a long time. Are there any left? The Saint-Félicien zoo will help researchers obtain hair and mucus samples to build the sheet for Gulo Gulo in their genetic library.
The iTrackDNA team will be present at COP15. She will be holding a booth with her partner, Genome Canada. Mme Langlois will also give presentations in the delegates’ room and to the general public.