Alpha and beta diversity and species co‐occurrence patterns in headwaters supporting rare intermittent‐stream specialists

Abstract Intermittent rivers are the focus of a burgeoning subdiscipline of freshwater science, driven by mounting recognition of their ubiquity, biodiversity, and climate sensitivity. However, our understanding of their ecology is hampered by a reliance on unstandardised diversity measures, an underrepresentation of certain stream types in metacommunity research and a reticence to acknowledge biotic interactions as a potentially fundamental driver of catchment‐scale patterns in assemblage composition. This study analysed both local‐ and catchment‐scale responses of invertebrates to flow intermittence and hydrological isolation in an understudied ecosystem type (low‐gradient, groundwater‐fed headwaters). We compared responses of conventional (taxonomic richness, Shannon diversity) and more robust (coverage‐adjusted Hill–Shannon) α‐diversity metrics to drying, and analysed changes in β‐diversity components as a function of hydrological and spatial distances between samples. We also inferred the influence of biotic interactions on metacommunity structure, using hierarchical species distribution modelling to capture species‐to‐species associations after accounting for hydrological variability and dispersal traits. The conventional and robust α‐diversity metrics exhibited broadly similar shifts, although richness overestimated the decline in α‐diversity with intermittence and the Shannon index failed to detect a significant interaction between flow duration and hydrological isolation. Decomposition of β‐diversity revealed a dominance of species turnover over nestedness along the flow gradient, a finding contrary to prevailing conceptual wisdom in intermittent river ecology and one we attribute to the climatic and geological context of our study. Even after accounting for differences in hydrological niche occupation, we discovered a significant propensity for species to co‐occur with others of similar conservation status, implying that competition/colonisation trade‐offs involving rare specialists and widespread generalists could underpin metacommunity assembly in some drying headwater networks. Our results suggest that enhancing aquatic habitat connectivity in headwaters harbouring intermittent‐stream specialists could be counterproductive, and conservation plans should instead look to safeguard isolated habitats serving as biotic refuges for rare species.