Environmental DNA quantification in a spatial and temporal context: a case study examining the removal of brook trout from a high alpine basin

Analysis of aquatic environmental DNA (eDNA) is a promising tool to determine species distribution, abundance, and biomass. Understanding how the amount of eDNA collected is affected by spatial and temporal processes needs to become better understood before eDNA quantification can be used in species management. In this study, we analyzed how the amount of eDNA changed across space and time in a high mountain basin where nonnative fish were being removed. We sampled from restoration (sites with fish removal activities; n?=?6) and control sites (sites with no fish removal activities where fish were present; n?=?3) and found the number and biomass of fish removed were related to the quantities of DNA collected and not related to site position within the drainage. Our results indicate that the amount of eDNA collected in an open system can provide an index of population size despite inherent complications of analyzing a spatially connected and temporally dynamic watershed. However, there are complications when applying these methods in species management: (1) small increases in eDNA density corresponded to large increases in trout density; (2) eDNA and traditional field techniques disproportionately target certain life stages, complicating comparisons between techniques; and (3) eDNA index values may need to be calibrated when sampling different species, life stages, environments, and habitats. We call for further research before this process can be used in a management context.