Effect of landscape context on fish metacommunity structuring in stream networks

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Vertebrate metacommunity structure along an extensive elevational gradient in the tropics: a comparison of bats,rodents and birds

Aim We evaluated the structure of metacommunities for each of three vertebrate orders (Chiroptera, Rodentia and Passeriformes) along an extensive elevational gradient. Using elevation as a proxy for variation in abiotic characteristics and the known elevational distributions of habitat types, we assessed the extent to which variation in those factors may structure each metacommunity based on taxon‐specific characteristics. Location Manu Biosphere Reserve in the Peruvian Andes. Methods Metacommunity structure is an emergent property of a set of species distributions across geographic or environmental gradients. We analysed elements of metacommunity structure (coherence, range turnover and range boundary clumping) to determine the best‐fit structure for each metacommunity along an elevational gradient comprising 13 250‐m elevational intervals and 58 species of rodent, 92 species of bat or 586 species of passerine. Results For each taxon, the environmental gradient along which the metacommunity was structured was highly correlated with elevation. Clementsian structure (i.e. groups of species replacing other such groups along the gradient) characterized rodents, with a group of species that was characteristic of rain forests and a group of species that was characteristic of higher elevation habitats (i.e. above 1500 m). Distributions of bats were strongly nested, with more montane communities comprising subsets of species at lower elevations. The structure of the passerine metacommunity was complex and most consistent with a quasi‐Clementsian structure. Main conclusions Each metacommunity exhibited a different structure along the same elevational gradient, and each structure can be accounted for by taxon‐specific responses to local environmental factors that vary predictably with elevation. The structures of rodent and bird metacommunities suggest species sorting associated with habitat specializations, whereas structure of the bat metacommunity is probably moulded by a combination of species‐specific tolerances to increasingly cold, low‐productivity environs of higher elevations and the diversity and abundance of food resources associated with particular habitat types.     

A comparative analysis of metacommunity types in the freshwater realm

Most metacommunity studies have taken a direct mechanistic approach, aiming to model the effects of local and regional processes on local communities within a metacommunity. An alternative approach is to focus on emergent patterns at the metacommunity level through applying the elements of metacommunity structure (EMS; Oikos, 97, 2002, 237) analysis. The EMS approach has very rarely been applied in the context of a comparative analysis of metacommunity types of main microbial, plant, and animal groups. Furthermore, to our knowledge, no study has associated metacommunity types with their potential ecological correlates in the freshwater realm. We assembled data for 45 freshwater metacommunities, incorporating biologically highly disparate organismal groups (i.e., bacteria, algae, macrophytes, invertebrates, and fish). We first examined ecological correlates (e.g., matrix properties, beta diversity, and average characteristics of a metacommunity, including body size, trophic group, ecosystem type, life form, and dispersal mode) of the three elements of metacommunity structure (i.e., coherence, turnover, and boundary clumping). Second, based on those three elements, we determined which metacommunity types prevailed in freshwater systems and which ecological correlates best discriminated among the observed metacommunity types. We found that the three elements of metacommunity structure were not strongly related to the ecological correlates, except that turnover was positively related to beta diversity. We observed six metacommunity types. The most common were Clementsian and quasi‐nested metacommunity types, whereas Random, quasi‐Clementsian, Gleasonian, and quasi‐Gleasonian types were less common. These six metacommunity types were best discriminated by beta diversity and the first axis of metacommunity ecological traits, ranging from metacommunities of producer organisms occurring in streams to those of large predatory organisms occurring in lakes. Our results showed that focusing on the emergent properties of multiple metacommunities provides information additional to that obtained in studies examining variation in local community structure within a metacommunity.     

Habitat specialization in tropical continental shelf demersal fish assemblages

The implications of shallow water impacts such as fishing and climate change on fish assemblages are generally considered in isolation from the distribution and abundance of these fish assemblages in adjacent deeper waters. We investigate the abundance and length of demersal fish assemblages across a section of tropical continental shelf at Ningaloo Reef, Western Australia, to identify fish and fish habitat relationships across steep gradients in depth and in different benthic habitat types. The assemblage composition of demersal fish were assessed from baited remote underwater stereo-video samples (n = 304) collected from 16 depth and habitat combinations. Samples were collected across a depth range poorly represented in the literature from the fringing reef lagoon (1-10 m depth), down the fore reef slope to the reef base (10-30 m depth) then across the adjacent continental shelf (30-110 m depth). Multivariate analyses showed that there were distinctive fish assemblages and different sized fish were associated with each habitat/depth category. Species richness, MaxN and diversity declined with depth, while average length and trophic level increased. The assemblage structure, diversity, size and trophic structure of demersal fishes changes from shallow inshore habitats to deeper water habitats. More habitat specialists (unique species per habitat/depth category) were associated with the reef slope and reef base than other habitats, but offshore sponge-dominated habitats and inshore coral-dominated reef also supported unique species. This suggests that marine protected areas in shallow coral-dominated reef habitats may not adequately protect those species whose depth distribution extends beyond shallow habitats, or other significant elements of demersal fish biodiversity. The ontogenetic habitat partitioning which is characteristic of many species, suggests that to maintain entire species life histories it is necessary to protect corridors of connected habitats through which fish can migrate.     

Metacommunity analysis of Mexican bats: environmentally mediated structure in an area of high geographic and environmental complexity

Aim We tested the hypothesis that distributions of Mexican bats are defined by shared responses to environmental gradients for the entire Mexican bat metacommunity and for each of four metaensembles (frugivores, nectarivores, gleaning insectivores, and aerial insectivores). Further, we identified the main environmental factors to which bats respond for multiple spatial extents. Location Mexico. Methods Using bat presence–absence data, as well as vegetation composition for each of 31 sites, we analysed metacommunity structure via a comprehensive, hierarchical approach that uses reciprocal averaging (RA) to detect latent environmental gradients corresponding to each metacommunity structure (e.g. Clementsian, Gleasonian, nested, random). Canonical correspondence analysis (CCA) was used to relate such gradients to variation in vegetation composition. Results For all bat species and for each ensemble, the primary gradient of ordination from RA, which is based on species data only, recovered an axis of humidity that matched that obtained for the first axis of the CCA ordination, which is based both on vegetation attributes and on species composition of sites. For the complete assemblage as well as for aerial and gleaning insectivores, analyses revealed Clementsian or quasi‐Clementsian structures with discrete compartments (distinctive groups of species along portions of an environmental gradient) coincident with the humidity gradient and with the Nearctic–Neotropical divide. Within‐compartment analysis further revealed Clementsian or quasi‐Clementsian structures corresponding to a gradient of elevational complexity that matched the second ordination axis in CCA. Frugivores had quasi‐nested structure, whereas nectarivores had Gleasonian structure. Main conclusions Our hierarchical approach to metacommunity analysis detected complex metacommunity structures associated with multiple environmental gradients at different spatial extents. More importantly, the resulting structures and their extent along environmental gradients are determined by ensemble‐specific characteristics and not by arbitrarily circumscribed study areas. This property renders compartment‐level analyses particularly useful for large‐scale ecological analyses in areas where more than one gradient may exist and species sorting may occur at multiple scales.     

Plant metacommunity structure remains unchanged during biodiversity loss in English woodlands

The metacommunity concept provides important insights into large‐scale patterns and dynamics of distributions of interacting species. However, temporal change of metacommunity structure is little studied and has not been previously analysed in the context of biodiversity change. As metacommunity structure is determined by multiple species distributions, it is expected to change as a result of biodiversity loss. To examine this process, we analysed structural change of a southern English woodland metacommunity at two points in time, seven decades apart. During this interval, the metacommunity lost β‐diversity through taxonomic homogenization. We performed an ‘elements of metacommunity structure’ (EMS) analysis to examine metacommunity structure, based upon three structural elements: coherence (i.e. gaps in species range along a structuring gradient), spatial turnover (replacements), and species range boundary clumping. We predicted that metacommunity structure would decrease in spatial turnover and thus become more nested over time. We tested for change in individual structural elements with z‐scores and examined the role of spatial and environmental variables as potential structuring mechanisms through correlation with EMS ordination axes. Our results demonstrated that the metacommunity had a Clementsian structure that was maintained over time. Despite no change in broad structure, coherence and species range boundary clumping increased. Spatial turnover increased along the first structuring gradient but decreased on the second gradient. We hypothesise that this difference between gradients may reflect the presence of competing processes affecting spatial turnover. The mechanisms of biological structuring involved both environmental and spatial factors at the scale of the individual woodland. Therefore, our results suggest that broad metacommunity structure would not be a good landscape‐scale indicator for conservation status. Conversely, knowledge that metacommunity structure does not change over time could assist in long‐term conservation strategy because fundamental metacommunity structural processes are resistant to environmental change.     

A heat wave and dispersal cause dominance shift and decrease biomass in experimental metacommunities

In experimental metacommunities with marine benthic microalgae, we tested whether heat stress changes effects of connectivity and habitat heterogeneity on metacommunity structure and functioning, by manipulating a simulated heat wave, dispersal frequency and a light intensity gradient. We found that all measures of mean local and regional diversity and community biomass significantly declined after the heat wave and showed no sign of recovery. Additionally, dispersal decreased diversity and increased dominance in both the heat stressed and control communities. Together the heat wave and high dispersal frequency induced a dominance shift by spreading a temperature tolerant but low yielding species from its source patches with low light intensity across the metacommunity, an effect that increased with time. Although different species became dominant at high dispersal frequency with and without the heat wave, the shift towards a temperature tolerant species was not sufficient to maintain total community biomass. Thus, short‐term disturbance may cause longer‐term loss of ecosystem function due to dominance shifts in the composition of communities. This study illustrates the importance of employing multispecies approaches when attempting to predict responses of communities to environmental changes.     

A Complex Metacommunity Structure for Gastropods Along an Elevational Gradient

The metacommunity framework integrates species‐specific responses to environmental gradients to detect emergent patterns of mesoscale organization. Abiotic characteristics (temperature, precipitation) and associated vegetation types change with elevation in a predictable fashion, providing opportunities to decouple effects of environmental gradients per se from those of biogeographical or historical origin. Moreover, expected structure is different if a metacommunity along an elevational gradient is molded by idiosyncratic responses to abiotic variables (expectation=Gleasonian structure) than if such a metacommunity is molded by strong habitat preferences or specializations (expectation=Clementsian structure). We evaluated metacommunity structure for 13 species of gastropod from 15 sites along an elevational transect in the Luquillo Experimental Forest of Puerto Rico. Analyses were conducted separately for the primary axis and for the secondary axis of correspondence extracted via reciprocal averaging. The metacommunity exhibited quasi‐Clementsian structure along the primary axis, which represented a gradient of gastropod species specialization that was unassociated with elevation. The secondary axis represented environmental variation associated with elevation. Along this axis, the metacommunity exhibited Clementsian structure, with specialists characterizing each of three suites of sites that corresponded to three distinct forest types. These forest types are associated with low (tabonuco forest), mid‐ (palo colorado forest), or high (elfin forest) elevations. Thus, variation among sites in species composition reflected two independent processes: the first decoupled from elevational variation and its environmental correlates, and the second highly associated with environmental variation correlated with elevation. Abstract in Spanish is available at http://www.blackwell‐synergy.com/loi/btp .     

Contrasting metacommunity structure and beta diversity in an aquatic‐floodplain system

Habitat connectivity and dispersal interact to structure metacommunities, but few studies have examined these patterns jointly for organisms across the aquatic–terrestrial ecotone. We assessed metacommunity structure and beta diversity patterns of instream benthic invertebrates, riparian carabid beetles (Order: Coleoptera; Family: Carabidae) and riparian spiders (Order: Araneae) at fifteen sites in a river‐floodplain system. Sampling took place over a three‐year period (2010–2012) in the Rhine‐Main‐Observatory LTER site on the Kinzig River, central Germany. This allowed disentangling the combined influence, and temporal variability, of habitat connectivity (i.e. between aquatic and terrestrial) and dispersal ability (i.e. between spiders and beetles, and aerial and aquatic dispersing invertebrates) on the dominant paradigms structuring these metacommunities. We found mostly consistent differences in the manner that metacommunities were structured between groups, with lower levels of variability explained for beetles compared to the other groups. Beetles were consistently structured more by turnover than nestedness components, with greater beta diversity than expected by chance and a minor spatial compared to environmental signal emerging with variance partitioning. Conversely, spiders and benthic invertebrates had lower beta diversity and greater nestedness than null expectation, and a clearer spatial signal controlling metacommunity structure. Our results suggest varying levels of mass effects and species sorting shape river‐floodplain metacommunities, depending on habitat connectivity and dispersal ability. That is, greater connectivity and lower fragmentation along the river compared to the terrestrial zone promoted mass effects, and differences in overall dispersal ability and mode (i.e. active and passive) for instream and riparian communities shifted paradigms between mass effects and species sorting.     

A comprehensive framework for the evaluation of metacommunity structure

The metacommunity framework is a powerful platform for evaluating patterns of species distribution in geographic or environmental space. Idealized patterns (checkerboard, Clementsian, evenly spaced, Gleasonian and nested distributions) give the framework shape. Each pattern represents an area in a multidimensional continuum of metacommunity structures; however, the current approach to analysis of spatial structure of metacommunities is incomplete. To address this, we describe additional non‐random structures and illustrate how they may be discerned via objective criteria. First, we distinguish three distinct forms of species loss in nested structures, which should improve identification of structuring mechanisms for nested patterns. Second, we define six quasi‐structures that are consistent with the conceptual underpinnings of Clementsian, Gleasonian, evenly spaced and nested distributions. Finally, we demonstrate how combinations of structures at smaller spatial extents may aggregate to form Clementsian structure at larger extents. These refinements should facilitate the identification of best‐fit patterns, associated structuring mechanisms, and informative scales of analysis and interpretation. This conceptual and analytical framework may be applied to network properties within communities (i.e. structure of interspecific interactions) and has broad application in ecology and biogeography.     

Seasonal and interannual effects of hypoxia on fish habitat quality in central Lake Erie

1. Hypoxia occurs seasonally in many stratified coastal marine and freshwater ecosystems when bottom dissolved oxygen (DO) concentrations are depleted below 2–3 mg O₂ L^?1. 2. We evaluated the effects of hypoxia on fish habitat quality in the central basin of Lake Erie from 1987 to 2005, using bioenergetic growth rate potential (GRP) as a proxy for habitat quality. We compared the effect of hypoxia on habitat quality of (i) rainbow smelt, Osmerus mordax mordax Mitchill (young‐of‐year, YOY, and adult), a cold‐water planktivore, (ii) emerald shiner, Notropis atherinoides Rafinesque (adult), a warm‐water planktivore, (iii) yellow perch, Perca flavescens Mitchill (YOY and adult), a cool‐water benthopelagic omnivore and (iv) round goby Neogobius melanostomus Pallas (adult) a eurythermal benthivore. Annual thermal and DO profiles were generated from 1D thermal and DO hydrodynamics models developed for Lake Erie’s central basin. 3. Hypoxia occurred annually, typically from mid‐July to mid‐October, which spatially and temporally overlaps with otherwise high benthic habitat quality. Hypoxia reduced the habitat quality across fish species and life stages, but the magnitude of the reduction varied both among and within species because of the differences in tolerance to low DO levels and warm‐water temperatures. 4. Across years, trends in habitat quality mirrored trends in phosphorus concentration and water column oxygen demand in central Lake Erie. The per cent reduction in habitat quality owing to hypoxia was greatest for adult rainbow smelt and round goby (mean: ?35%), followed by adult emerald shiner (mean: ?12%), YOY rainbow smelt (mean: ?10%) and YOY and adult yellow perch (mean: ?8.5%). 5. Our results highlight the importance of differential spatiotemporally interactive effects of DO and temperature on relative fish habitat quality and quantity. These effects have the potential to influence the performance of individual fish species as well as population dynamics, trophic interactions and fish community structure.     

The frequency of metapopulations, metacommunities and nestedness in a fragmented landscape

Metapopulation and metacommunity theory may be extremely useful for understanding community composition and species distributions in fragmented landscapes. However, how well particular spatial ecological models represent natural systems is not known and so the general importance of those models is unclear. In three naturally fragmented landscapes in Tasmania, Australia, I sampled beetles from 67 sites, including continuous forest, small forest patches in a sedgeland matrix, streamside forest, and the matrix. Of forty commonly captured beetle species, at least 37% do not form metapopulations of any kind because they do not disperse far enough, disperse too far, or occur in the matrix. Only 7.5% of the species showed distributions consistent with a mainland‐island metapopulation, which was surprising given the mainland‐island structure of the landscape. These patterns were also consistent with a classic metapopulation. Deterministic metapopulations were probably common, involving at least 32% of species. Most predicted metacommunity patterns were not observed because only subsets of the fauna followed a particular metacommunity model. Seven, mostly flying, species were influenced only by habitat quality, supporting the Species‐sorting or Mass‐effects models, and the strong distinction between the beetle fauna of Eucalyptus patches and the matrix suggested an over‐riding influence of a Species‐sorting process. Seven, mostly flightless, species showed a negative relationship with increasing patch isolation, while another six, mostly flying, species showed the opposite pattern, with higher frequency of occurrence in more isolated patches. Both groups were strongly nested. The flying species were probably excluded from less isolated sites through interactions with poor dispersers , providing a novel mechanism leading to a nested distribution. The Patch‐dynamics and Species‐sorting processes were equally consistent with the pattern, emphasizing that these models are relatively simplistic when confronted with real community data. Additional complexity needs to be built into the models to accommodate the diverse patterns observed in natural communities.     

Future ocean climate homogenizes communities across habitats through diversity loss and rise of generalist species

Predictions of the effects of global change on ecological communities are largely based on single habitats. Yet in nature, habitats are interconnected through the exchange of energy and organisms, and the responses of local communities may not extend to emerging community networks (i.e., metacommunities). Using large mesocosms and meiofauna communities as a model system, we investigated the interactive effects of ocean warming and acidification on the structure of marine metacommunities from three shallow‐water habitats: sandy soft‐bottoms, marine vegetation, and rocky reef substrates. Primary producers and detritus—key food sources for meiofauna—increased in biomass under the combined effect of temperature and acidification. The enhanced bottom‐up forcing boosted nematode densities but impoverished the functional and trophic diversity of nematode metacommunities. The combined climate stressors further homogenized meiofauna communities across habitats. Under present‐day conditions metacommunities were structured by habitat type, but under future conditions they showed an unstructured random pattern with fast‐growing generalist species dominating the communities of all habitats. Homogenization was likely driven by local species extinctions, reducing interspecific competition that otherwise could have prevented single species from dominating multiple niches. Our findings reveal that climate change may simplify metacommunity structure and prompt biodiversity loss, which may affect the biological organization and resilience of marine communities.     

Size structure of the metazoan community in a Piedmont stream

We characterized the size structure of virtually the entire metazoan community in a fourth order, sandybottomed Piedmont stream during late summer. Our study, the first to sample across all habitat types and sizes of metazoans in an aquatic ecosystem, indicates that at the community level, stream size spectra may be bimodal for the benthos or trimodal when fish are included. Animals spanning 10 orders of magnitude in dry mass (from gastrotrichs to fish) were quantitatively collected from nine habitat types. The bimodal benthic size spectrum was characterized by a meiofaunal component (mostly oligochaetes and micro-crustacea) and a macrobenthic component (mostly the introduced asiatic clam, Corbicula fluminea). Insects contributed little to overall standing crop. Size-specific contribution to whole-community metabolism was assessed using allometric equations for respiration, and we found a distinctly bimodal distribution across the entire metazoan size range, with peaks in the meiofaunal and benthic macrofaunal size ranges. Our bimodal benthic size spectrum is similar to that observed for marine benthos but not to other freshwater benthic systems, possibly because the entire range of habitat types and/or animal sizes were not sampled in the latter. Numerous factors may influence size spectra in stream ecosystems, including local geomorphic (habitat) conditions, water level fluctuations, species introductions, and predation processes.     

Elements of metacommunity structure of Paraguayan bats: multiple gradients require analysis of multiple ordination axes

Techniques to evaluate elements of metacommunity structure (EMS; coherence, species turnover and range boundary clumping) have been available for several years. Such approaches are capable of determining which idealized pattern of species distribution best describes distributions in a metacommunity. Nonetheless, this approach rarely is employed and such aspects of metacommunity structure remain poorly understood. We expanded an extant method to better investigate metacommunity structure for systems that respond to multiple environmental gradients. We used data obtained from 26 sites throughout Paraguay as a model system to demonstrate application of this methodology. Using presence–absence data for bats, we evaluated coherence, species turnover and boundary clumping to distinguish among six idealized patterns of species distribution. Analyses were conducted for all bats as well as for each of three feeding ensembles (aerial insectivores, frugivores and molossid insectivores). For each group of bats, analyses were conducted separately for primary and secondary axes of ordination as defined by reciprocal averaging. The Paraguayan bat metacommunity evinced Clementsian distributions for primary and secondary ordination axes. Patterns of species distribution for aerial insectivores were dependent on ordination axis, showing Gleasonian distributions when ordinated according to the primary axis and Clementsian distributions when ordinated according to the secondary axis. Distribution patterns for frugivores and molossid insectivores were best described as random. Analysis of metacommunities using multiple ordination axes can provide a more complete picture of environmental variables that mold patterns of species distribution. Moreover, analysis of EMS along defined gradients (e.g., latitude, elevation and depth) or based on alternative ordination techniques may complement insights based on reciprocal averaging because the fundamental questions addressed in analyses are contingent on the ordination technique that is employed.     

Elements of metacommunity structure of river and riparian assemblages: Communities,taxonomic groups and deconstructed trait groups

The elements of metacommunity structure (EMS) framework gives rise to important ecological insights through the distinction of metacommunities into several different idealised structures. We examined the EMS in assemblages occupying a low-mountain river system in central Germany, sampled over three consecutive years. We compared the idealised distributions of assemblages in both the riparian floodplain zone (carabid beetles and spiders) and the benthic instream environment (benthic invertebrates). We further deconstructed instream organisms into taxonomic and trait groups to examine whether greater signal emerges in more similar species groups. We found little evidence of strong competition, even for trait-modality groups, and nestedness was almost non-existent. In addition to random distributions, Gleasonian distributions (indicating clear, but individualistic turnover between sites) were the most commonly identified structure. Clear differences were apparent between different trait groups, particularly between within-trait modalities. These were most evident for different dispersal modes and life cycle durations, with strong dispersers showing possible signs of mass effects. While random distributions may have partly reflected small sample sizes, clearly coherent patterns were evident for many groups, indicating a sufficient gradient in environmental conditions. The prevalence of random distributions suggests many species are responding to a variety of environmental filters in these river-floodplain metacommunities in an anthropogenically-dominated landscape, whereas Gleasonian distributions indicate species are responding idiosyncratically to a primary environmental gradient. Our findings further emphasise the prevalence of context dependency (spatio-temporal variability) in metacommunity studies, thus we stress the need to further disentangle the causes of such variation.     

Metacommunities of spiders in grassland habitat fragments of an agricultural landscape

Arthropod communities in fragmented agricultural landscapes depend on local processes and the interactions between communities in the habitat islands. We aimed to study metacommunity structure of spiders, a group that is known for high dispersal power, local niche partitioning and for engaging in species interactions. While living in fragmented habitats could lead to nestedness, other ecological traits of spiders might equally lead to patterns dominated either by species interactions or habitat filtering. We asked, which community pattern will prevail in a typical agricultural landscape with isolated patches of semi-natural habitats. Such a situation was studied by sampling spiders in 28 grassland locations in a Hungarian agricultural landscape. We used the elements of metacommunity structure (EMS) framework to distinguish between alternative patterns that reveal community organization. The EMS analysis indicated coherent species ranges, high turnover and boundary clumping, suggesting Clementsian community organization. The greatest variation in species composition was explained by local habitat characteristics, indicating habitat filtering. The influence of dispersal could be detected by the significant effect of landscape composition, which was strongest at 500 m. We conclude that dispersal allows spiders to respond coherently to the environment, creating similar communities in similar habitats. Consistent habitat differences, such as species rich versus species poor vegetation, lead to recognisably different, recurrent communities. These characteristics make spiders a predictable and diverse source of natural enemies in agricultural landscapes. Sensitivity to habitat composition at medium distances warns us that landscape homogenization may alter these metacommunity processes.     

Do metacommunity theories explain spatial variation in fish assemblage structure in a pristine tropical river?

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Marine reserves indirectly affect fine‐scale habitat associations,but not overall densities,of small benthic fishes

Many large, fishery‐targeted predatory species have attained very high relative densities as a direct result of protection by no‐take marine reserves. Indirect effects, via interactions with targeted species, may also occur for species that are not themselves targeted by fishing. In some temperate rocky reef ecosystems, indirect effects have caused profound changes in community structure, notably the restoration of predator–urchin–macroalgae trophic cascades. Yet, indirect effects on small benthic reef fishes remain poorly understood, perhaps because of behavioral associations with complex, refuge‐providing habitats. Few, if any, studies have evaluated any potential effects of marine reserves on habitat associations in small benthic fishes. We surveyed densities of small benthic fishes, including some endemic species of triplefin (Tripterygiidae), along with fine‐scale habitat features in kelp forests on rocky reefs in and around multiple marine reserves in northern New Zealand over 3 years. Bayesian generalized linear mixed models were used to evaluate evidence for (1) main effects of marine reserve protection, (2) associations with habitat gradients, including complexity, and (3) differences in habitat associations inside versus outside reserves. No evidence of overall main effects of marine reserves on species richness or densities of fishes was found. Both richness and densities showed strong associations with gradients in habitat features, particularly habitat complexity. In addition, some species exhibited reserve‐by‐habitat interactions, having different associations with habitat gradients inside versus outside marine reserves. Two species (Ruanoho whero and Forsterygion flavonigrum) showed stronger positive associations with habitat complexity inside reserves. These results are consistent with the presence of a behavioral risk effect, whereby prey fishes are more strongly attracted to habitats that provide refuge from predation in areas where predators are more abundant. This work highlights the importance of habitat structure and the potential for fishing to affect behavioral interactions and the interspecific dynamic attributes of community structure beyond simple predator–prey consumption and archetypal trophic cascades.