1. Refugia are critical to the persistence of individuals, populations and communities in disturbed environments, yet few studies have considered how the position of refugia within the landscape interacts with the behavioural responses of component species to determine the influence of disturbance events on mobile animals.2. An 18-month quantitative electrofishing survey was undertaken on the Selwyn River, a stream that is intermittent in its middle reaches, to determine how the direction and distance to refugia affect the response of fish populations to drying, and how landscape context interacts with flow permanence to produce spatial patterns in communities. 3. Overall, the propensity of fish to take refuge in perennial reaches during drying episodes, and the rate and extent of recolonization from these refugia upon rewetting, depended upon the direction and distance to refugia and the behaviour of component species. 4. In the upper river, Canterbury galaxias (Galaxias vulgaris), upland bullies (Gobiomorphus breviceps) and brown trout (Salmo trutta) migrated upstream to permanent water as the stream dried from the bottom up, but frequent drying and slow recolonization by most species combined to produce a fish community in intermittent reaches that was quantitatively and qualitatively different to that in neighbouring perennial reaches. 5. In the lower river, fish did not appear to migrate downstream to permanent water as the stream dried from the top down, but a lower frequency of drying episodes and faster recolonization by upland bullies and eels (Anguilla spp.) from downstream refugia allowed the fish community in intermittent reaches to converge with that in neighbouring perennial reaches during prolonged wetted periods. 6. Longitudinal patterns of increasing fish density and species richness with flow permanence are interpreted as the product of species-specific responses to drying events and the spatial position of refugia within the riverscape.

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Generalized additive models (GAMs) offer an alternative approach to developing habitat suitability functions; these models may resolve some of the criticisms that have been made of conventional habitat suitability criteria and the associated composite suitability index (CSI). The potential advantages of GAMs include the ability to (1) account for correlation among habitat variables, (2) include interactions among variables, (3) make quantitative predictions of abundance or probability of occurrence at given flows, and (4) identify sharp thresholds in habitat selection. We developed CSIs and GAMs for two data sets—abundance of benthic invertebrates (mayflies Deleatidium spp. and caddisflies Aoteapsyche spp.) and habitat selection of large brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss—and applied them in an instream habitat analysis. The GAMs performed only slightly better than CSIs. The GAMs for two of the four taxa examined (Deleatidium and brown trout) had strong negative velocity–depth interaction terms, although their inclusion improved the model fit only marginally. The main effect of negative velocity–depth interaction terms was to constrain model predictions in deep, fast‐flowing water, and these GAMs gave more realistic results when applied to conditions beyond those from which they were developed (i.e., larger rivers or higher flows). The GAMs hold a number of potential advantages over conventional CSIs and offer an opportunity to develop more defensible habitat suitability models; ultimately, however, the performance of any model will be limited by the quality of the calibration data.

Most of the world's alluvial plain rivers have undergone hydrological and geomorphical modifications due to water abstraction, dam and levee construction, gravel mining and other human activities. Some of these rivers function as benchmark systems for identifying and quantifying the ecological responses to hydrological and geomorphological changes. Benchmark systems are critical for understanding these responses, for predicting the effects of future changes, and for trialling restoration and mitigation measures. The Selwyn River of New Zealand is a benchmark system for undammed alluvial rivers that are under intense pressure for water abstraction, and are subject to large flow fluctuations.The Selwyn is a remarkably complex river, and increased understanding of this system will provide insight for understanding and managing other rivers in its class. Hydrological properties that characterize the Selwyn include strong surface watergroundwater interactions, contiguous ephemeral, intermittent, perennial-losing and perennial-gaining reaches and an expanding and contracting dry segment that persists for most of the year. The dry segment, in combination with broad spatial variation in aquifer structure and rainfall, cause the upstream (runoff-fed) and downstream (groundwater-fed) river sections to function very differently. These sections are also dissimilar in channel morphology; the upstream section has a braided planform, with mobile bars, and abundant islands and remnant channels, and the downstream section has a single, meandering channel, stable bars and no islands. As in many alluvial plain rivers, large floods drive reach-scale channel evolution. This paper introduces a long-term research program that is underway at the Selwyn River, and explores the hydrological and morphological dynamics that characterize the river. We focus on groundwater-surface water interactions, flow-permanence patterns and flood-dependent geomorphology. Hydrological and meteorological data are summarized in a conceptual model of relationships between prevailing weather systems, runoff, aquifer recharge and river flow. The physical template described in this paper governs ecological processes such as dispersal, succession and nutrient cycling. A conceptual model is proposed to organize predictions about dispersal in response to changes in hydrological connectivity.

An electrofishing survey of daytime shelter microhabitat use of bullhead Cottus gobio in a southern English chalk stream revealed positive selection for moderate water velocity, vegetation cover and coarse substrata. Water depth, other forms of cover, shade and substratum embeddedness had no significant influence on the distribution of fish. Microhabitat use was size-dependent, with patches occupied by adult fish containing coarser substrata and less blanket weed (Cladophora algae) than those occupied by smaller juvenile conspecifics. Differences in substratum use between size-classes were less pronounced in parts of the stream shaded by the tree canopy. In laboratory tanks stocked at low fish density, both juveniles and adults favoured use of cobbles over pebbles. The response of fish to increased conspecific density was size-dependent; juveniles reduced use of the coarse substratum whereas adults maintained their predominance in this habitat. An apparently greater shift by juveniles when in the presence of adults was significant at a ¼ 0Á10 only, as was an apparent reduction in interactions between size-classes under low light intensity. The displacement of small juvenile fish from the preferred cobble substratum is consistent with the hypothesis that intraspecific competition contributes to the size-related microhabitat shift observed in the field. Although there was a tendency for the strength of competition to be reduced at low light levels, the mechanism by which tree canopy cover affects microhabitat use remains uncertain. # 2005 The Fisheries Society of the British Isles