How to design optimal eDNA sampling strategies for biomonitoring in river networks

Abstract

The current biodiversity crisis calls for appropriate and timely methods to assess state and change of bio-diversity. In this respect, environmental DNA (eDNA) is a highly promising tool, especially for aquatic ecosystems. While initial eDNA studies assessed biodiversity at a few sites, technology now allows analyses of samples from many points at a time. However, the selection of these sites has been mostly motivated on an ad-hoc basis, and it is unclear where to position sampling sites in a river network to most effectively sample biodiversity. To this end, hydrology-based models might offer a unique guidance on where to sample eDNA to reconstruct the spatial patterns of taxon density based on eDNA data collected across a watershed. Here, we performed computer simulations to identify best-practice criteria for the choice of positioning of eDNA sampling sites in river networks. To do so, we combined a hydrology-based eDNA transport model with a virtual river network reproducing the scaling features of real rivers. In particular, we conducted simulations investigating scenarios of different number and location of eDNA sampling sites in a riverine network, different spatial taxon distributions, and different eDNA measurement errors. We identified best practices for sampling site selection for taxa that have a scattered versus an even distribution across the network. We observed that, due to hydrological controls, non-uniform patterns of eDNA concentration arise even if the taxon distribution is uniform and decay is neglected. We also found that uncertainties in eDNA concentration estimates do not necessarily hamper model predictions. Knowledge of eDNA decay rates improves model predictions, highlighting the need for empirical estimates of these rates under relevant environmental conditions. Our simulations help define strategies for the design of eDNA sampling campaigns in river networks, and can guide the sampling effort of field ecologists and environmental authorities.