Environmental DNA reveals anadromous river herring habitat use and recolonization after restoration of aquatic connectivity

Abstract

AbstractRestoring and sustaining anadromous fish populations is a grand challenge in the conservation of freshwater ecosystems. Alewife Alosa pseudoharengus and Blueback Herring Alosa aestivalis are two closely related anadromous fish for which responses to fish passage restoration are poorly known. We used a targeted environmental DNA method to sample 17 major tributaries of the Chesapeake Bay, USA, to determine the spatial extent of habitat use during the spawning season and the associations of habitat use with watershed characteristics. To help understand responses to restoration of fish passage, the study included portions of eight watersheds where dam removals, fish ladders, or dam failures provided access to habitats that were previously inaccessible to anadromous fish. Overall, 27.5% of samples showed positive detections for river herring, including at least one sample in 16 of 17 tributaries sampled. The presence of both species combined was negatively associated with elevation (relative influence [RI] = 29.8%) and positively associated with a watershed area (RI = 14.5%) and percent cropland (13.6%) of the watershed. In species‐specific analyses, both Alewife (RI = 24.8%) and Blueback Herring (26.2%) presence was negatively associated with elevation, Alewife were more common in watersheds with high percentages of cropland (RI = 19.1%), whereas Blueback Herring were more common in streams with large watersheds (23.2%). The use of formerly blocked spawning habitats was generally greater upstream of sites where dams were removed (2%–100% of habitat used) compared with sites where fish ladders were installed (0%–66.8% of habitat used). The broad‐scale sampling enabled by eDNA methods made it possible to identify habitat use patterns that can be applied to prioritize future restoration efforts and predict species‐specific responses.