sDNA Metabarcoding: Opening the Doors to Understanding Carnivore Diets
Understanding carnivore diets, especially in Namibia where multiple large carnivores have overlapping niches, is important for conservation efforts and management. Analyzing a predator’s diet allows us to understand the roles they play in an ecosystem, how much they potentially compete with other predators, and a better management of prey species. However, many predators can be elusive or low in population numbers and visual monitoring of individuals to collect data on their diet can becomes laborious and difficult. As a result, scat analysis became a non-invasive and reliable method for assessing predator diet, and over the years we have seen a quick evolution of this methodology.
The life of a scat: From the field to the lab...
Historically, scat analyses included manual sorting and morphological identification of undigested remains in the scat samples. This method has been popular for many years and was the most common approach used to determine a carnivore’s diet. However, this method is time-consuming and requires prior knowledge and training for identifying components of all potential prey species (bone fragments, hairs, feathers, etc.). More recently, there has been an increase in the use of DNA sequencing and metabarcoding for dietary analysis, which allows for more accurate taxonomic identification of both predator (if the scat cannot be identified to species) and prey species.
How does sDNA (scat DNA) metabarcoding work?
After a scat sample is collected and adequately stored to prevent cross contamination or molding, DNA is extracted and amplified using universal PCR primers. The DNA is then sequenced and analyzed using a bioinformatics pipeline. Depending on previous studies that have been conducted on a particular species or in a specific area, DNA extractions may also be necessary as a first step to build a local prey DNA database that can be referenced during the analysis process (otherwise, how do you identify prey species without a DNA database for comparison?). Finally, the prey species are identified by comparing sequences from the scat samples to sequences in the reference library and finding matches that will allow for taxonomic identification.
Six main steps of DNA barcoding and metabarcoding (click on the image to enlarge).
In my current PhD project with ORC, I am using sDNA metabarcoding to determine lion, spotted hyena, black-backed jackal, leopard, and cheetah diets in the Greater Etosha Landscape. We collect scat samples opportunistically around waterholes and along the roads. We then ensure they are dry (simply by leaving them outside for a few days on brown paper bags) before processing them in the lab for longer-term storage before DNA analysis. I hope this project can provide insights into our top predators’ diets that will eventually contribute to management decisions and conservation efforts.