Recognition of the complex spatial and temporal variability of abundance and diversity found in many populations has led to a greater focus on the roles of heterogeneity, stochasticity, and disturbance in the structure and persistence of communities. This focus is directly relevant to coral reef communities that are characterized by very high species diversity in a spatially heterogeneous environment, display stochastic variability in community structure at small spatial and temporal scales, and are subject to major disturbances. We monitored coral and fish assemblages over 14 years on fixed sites spread over 80 km of the southern Great Barrier Reef (GBR), Australia, and found evidence of large‐scale resilience and predictable recovery of these assemblages. Sometime between November 1987 and October 1989, live coral cover on the shallow northeast flanks of some reefs in the southern GBR decreased from >80% to <10%, probably as a result of storm damage. We compared the fish and benthic communities present in these areas prior to the disturbance (1983–1984) with those present in 1992 and the subsequent changes through to 1998. Hard coral cover increased slowly from 1992 to 1994, then accelerated to be indistinguishable from pre‐impact levels by 1998. The response of the coral assemblages was largely due to the predominance of tabulate Acropora species and their characteristics of rapid growth and competitive dominance. Patterns of species richness of the fish families Acanthuridae, Chaetodontidae, Scaridae, and Pomacentridae mirrored that of hard coral, except the Pomacentridae had not recovered to pre‐impact levels by 1998. Of the 26 fish species analyzed for changes in abundance, 88% decreased after the disturbance, then subsequently increased, with all but two recovering to pre‐impact levels by 1998. Although processes such as settlement and immigration are ultimately responsible for replenishment of local populations, our data suggested that habitat plays a strong role in modifying fish assemblages. Thus, both coral and fish assemblages demonstrated resilience to large‐scale natural disturbance and predictability in the structure of the assemblages, with most taxa approaching the asymptote of abundance and species richness that existed prior to the disturbance.

With marine biodiversity declining globally at accelerating rates, maximising the effectiveness of conservation has become a key goal for local, national and international regulators. Marine protected areas (MPAs) have been widely advocated for conserving and managing marine biodiversity yet, despite extensive research, their benefits for conserving non-target species and wider ecosystem functions remain unclear. Here, we demonstrate that MPAs can increase the resilience of coral reef communities to natural disturbances, including coral bleaching, coral diseases, Acanthaster planci outbreaks and storms. Using a 20-year time series from Australia's Great Barrier Reef, we show that within MPAs, (1) reef community composition was 21-38% more stable; (2) the magnitude of disturbance impacts was 30% lower and (3) subsequent recovery was 20% faster that in adjacent unprotected habitats. Our results demonstrate that MPAs can increase the resilience of marine communities to natural disturbance possibly through herbivory, trophic cascades and portfolio effects.

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Summary 1.The impact of environmental disturbance and habitat loss on associated species is expected to be dependent on a species' level of specialization. We examined habitat use and specialization of coral reef fish from the diverse and ecologically important family Pomacentridae, and determined which species are susceptible to declines in coral cover due to disturbance induced by crown-of-thorns seastar (COTS, Acanthaster planci L.). 2.A high proportion of pomacentrid species live in association with live coral as adults (40%) or juveniles (53%). Adults of many species had strong affiliations with branching corals, while juveniles favoured plating growth forms, reflecting the sizes of refuge provided by coral types. 3. Juveniles of species that associated with coral had narrower niche breadths than adult conspecifics, due to associations with specific coral types. The especially high coral association and narrower niche breadth of juveniles suggest that the presence of live coral is crucial for many species during early life history, and that disturbance-induced coral loss may have serious flow-on effects on adult abundance. 4. Microhabitat availability was a poor predictor of fish species abundance. Significant correlations between coverage of coral types and abundance of five adults and two juvenile species were detected; however, these relationships explained <35% and <10% of the variation in abundance of adult and juvenile species, respectively. 5. Niche breadth explained 74% of the variation in species' mean response to coral decline and it is clear that disturbance has a greater impact on resource specialists, suggesting that increasing frequency and intensity of coral loss will cause reef fish communities to become dominated by habitat generalists at the expense of coral-dwelling specialists.

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