Abstract
Major disturbance events can profoundly influence biodiversity patterns, although the extent to which such shifts are predictable remains poorly understood. We used environmental DNA (eDNA) to compare forested versus recently deforested stream insect communities across disjunct regions of New Zealand, to test for parallel shifts in response to widescale disturbance. Although eDNA analyses revealed highly distinct species pools across regions, they detected concordant functional diversity shifts linked to recent deforestation, including parallel decreases in the diversity of grazing taxa. The finding that taxonomically distinct freshwater biotas have experienced broadly concordant functional shifts in the wake of deforestation indicates that disturbance can drive deterministic ecological change. By contrast, the finding that some closely related species within functional groups show discordant responses to deforestation suggests that ecological differentiation among cryptic taxa may contribute to idiosyncratic shifts. These findings highlight the potential of eDNA for resolving subtle species‐level differences among anthropogenically impacted ecological assemblages.