Freshwater connectivity transforms spatially integrated signals of biodiversity

Aquatic ecosystems offer a continuum of water flow from headwater streams to inland lakes and coastal marine systems. This spatial connectivity influences the structure, function and dynamics of aquatic communities, which are among the most threatened and degraded on earth. Environmental DNA achieves biodiversity surveys in these habitats in a high-throughput, spatially integrated way. Here, we determine the spatial resolution of eDNA in dendritic freshwater networks that are typical of aquatic habitats. Our intensive sampling campaign comprised over 430 eDNA samples across 21 connected lakes, allowing us to analyse detections at a variety of scales, from different habitats within a lake to entire lake networks. We found strong signals of within-lake variation in eDNA distribution reflective of typical habitat use by both fish and zooplankton. Most importantly, we also found that connecting channels between lakes resulted in an accumulation of downstream eDNA detections in lakes with a higher number of inflows, and as networks increased in length. These findings have profound implications for the interpretation of eDNA detections in aquatic ecosystems in global-scale biodiversity monitoring observations.