Impacts of large and small barriers on fish assemblage composition assessed using environmental DNA metabarcoding

River fragmentation caused by instream barriers is a leading cause of biodiversity loss, particularly for freshwater migratory fish, the vertebrate group that has suffered the steepest decline. However, most studies have tended to focus on the impacts of large dams on only a few taxa. We estimated the cumulative impact of both large and small barriers on fish species richness and relative abundance along an altitudinal gradient in the main stem of the River Allier (France). Using eDNA metabarcoding, we identified 24 fish zero-radius operational taxonomic units (zOTUs), corresponding to 26 species distributed along the main stem of the river. Elevation explained the greatest amount of variation in fish distribution, together with average flow, barrier density and its interaction with cumulative barrier height. Based on eDNA, the largest discontinuity in species richness was not related to the location of Poutès, the largest dam in the system, but located downstream from it. Our results indicate that, in addition to the more obvious effects of large dams on migratory fish such as the Atlantic salmon, the cumulative effects of small barriers can have widespread impacts on fish species richness and relative abundance, which should not be overlooked. We suggest that, as for other fragmented rivers, acting on numerous small barriers might bring about greater benefits in fish species richness than focusing only on the largest dams