Seasonal influence on detection probabilities for multiple aquatic invasive species using environmental DNA

Aquatic invasive species (AIS) are a threat to freshwater ecosystems. Documenting AIS prevalence is critical to effective management and early detection. However, conventional monitoring for AIS is time and resource intensive and is rarely applied at the resolution and scale required for effective management. Monitoring using environmental DNA (eDNA) of AIS has the potential to enable surveillance at a fraction of the cost of conventional methods, but key questions remain related to how eDNA detection probability varies among environments, seasons, and multiple species with different life histories. To quantify spatiotemporal variation in the detection probability of AIS using eDNA sampling, we surveyed 20 lakes with known populations of four aquatic invasive species: Common Carp (Cyprinus carpio), Rusty Crayfish (Faxonius rusticus), Spiny Waterflea (Bythotrephes longimanus), and Zebra Mussels (Dreissena polymorpha). We collected water samples at 10 locations per lake, five times throughout the open water season. Quantitative PCR was used with species-specific assays to determine the presence of species DNA in water samples. Using Bayesian occupancy models, we quantified the effects of lake and site characteristics and sampling season on eDNA detection probability. The probability of detection varied seasonally, and the seasonal variation was species-specific and related to species life histories. Zebra Mussels were the most detectable of our species, and detection probability peaked in midsummer when only five water samples were required to achieve a 95% probability of detection. Spiny Water flea detection also peaked in mid to late summer, but were overall the most difficult to detect. Common Carp were most detectable in the spring and Rusty Crayfish were most detectable in early fall, corresponding to key life history events. Our results provide critical information for decision makers interested in using eDNA as a multispecies monitoring tool and highlight the importance of sampling when species are in DNA releasing life history stages.