Processes driving individual variation in environmental DNA deposition rates in Daphnia magna

Abstract

The abundance of environmental DNA (eDNA) in water samples has been proposed as a sensitive, cost‐efficient, and non‐invasive alternative to infer population abundance and biomass, regardless of the acknowledgment that a number of biotic and abiotic factors can lead to substantially varying rates of eDNA deposition among organisms in a population. We tested how metabolic, nutritional, and life history processes shape intraspecific eDNA deposition rates in the freshwater invertebrate Daphnia magna. We extracted water samples from individual D. magna raised in glass vials under a 2 × 2 longitudinal factorial manipulation of temperature and food levels over their entire lifespan, and quantified eDNA daily deposition rates using digital droplet PCR (ddPCR). Analyzed using a hypothesis‐driven nested mixed‐effect modeling framework, we showed that per individual D. magna eDNA deposition rate varied by an order of magnitude over the course of each individual's lifespan due to multiple causes. We identified that large and pregnant D. magna had the highest eDNA deposition rates, particularly under warmer conditions with higher food levels, and thus, should be considered a prime target for field detections. We found that recently deceased individuals could potentially bias eDNA monitoring efforts by releasing a relatively higher amount of eDNA through decomposition. Our work supplies a more nuanced understanding of myriad factors that shape eDNA deposition, suggesting new and more useful ways to interpret eDNA monitoring data. We recommend that future work using eDNA to estimate population abundance or biomass should account for both energetic conditions and the reproductive cycle facing their target organism and prioritize sampling effort toward metabolically active individuals, especially when working with size‐structured populations that exhibit wide variation in body mass.