Sampling design for landscape level environmental DNA monitoring programs

During traditional monitoring programs researchers often use occupancy models to quantity the probability a species occupies an area while accounting for imperfect detection. This approach uses as two-level model. Traditionally, presence or absence data are collected for species, however, recently scientists have started to use environmental DNA (eDNA) in monitoring programs. Examples of eDNA include skin cells, mucus, eggs, urine, or feces that organisms deposit into their surroundings. Sampling for eDNA can be a more efficient and less expensive way of detecting rare or elusive species compared to current standard methods (such as visual species counts, acoustic surveys). After a sample is collected, scientists use molecular techniques such as quantitative polymerase chain reaction (qPCR), which amplifies a targeted species’ s DNA in the sample and allows researchers to determine if eDNA is present or absent. Due to this sampling design, a third level added to the traditional 2-level occupancy model to account for sampling. USGS scientists uses these models to help agencies such as U.S. Fish and Wildlife Service plan monitoring programs for species such as invasive carp.