Novel species interactions and environmental conditions reduce foraging competency at the temperate range edge of a range-extending coral reef fish

Poleward range extensions of coral reef species can reshuffle temperate communities by generating competitive interactions that did not exist previously. However, novel environmental conditions and locally adapted native temperate species may slow tropical invasions by reducing the ability of invaders to access local resources (e.g. food and shelter). We test this hypothesis on wild marine fish in a climate warming hotspot using a field experiment encompassing artificial prey release. We evaluated seven behaviours associated with foraging and aggressive interactions in a common range-extending coral reef fish (Abudefduf vaigiensis) and a co-shoaling temperate fish (Microcanthus strigatus) along a latitudinal temperature gradient (730 km) in SE Australia. We found that the coral reef fish had reduced foraging performance (i.e. slower prey perception, slower prey inspection, decreased prey intake, increased distance to prey) in their novel temperate range than in their subtropical range. Furthermore, higher abundance of temperate fishes was associated with increased retreat behaviour by coral reef fish (i.e. withdrawal from foraging on released prey), independent of latitude. Where their ranges overlapped, temperate fish showed higher foraging and aggression than coral reef fish. Our findings suggest that lower foraging performance of tropical fish at their leading range edge is driven by the combined effect of environmental factors (e.g. lower seawater temperature and/or unfamiliarity with novel conditions in their extended temperate ranges) and biological factors (e.g. increased abundance and larger body sizes of local temperate fishes). Whilst a future increase in ocean warming is expected to alleviate current foraging limitations in coral reef fishes at leading range edges, under current warming native temperate fishes at their trailing edges appear able to slow the range extension of coral reef fishes into temperate ecosystems by limiting their access to resources.

     

Interspecific variation in distributions and diets of coral reef butterflyfishes (Teleostei: Chaetodontidae)

This study examined within‐reef distributions for 19 species of butterflyfishes (Chaetodontidae) at Lizard Island, northern Great Barrier Reef, Australia, and compared spatial patterns of abundance among species with contrasting diets. Spatial variation in abundance of butterflyfishes was most prominent among physiognomic reef zones mainly due to significant zonation of eight species, including four obligate hard‐coral feeders (Chaetodon trifascialis, Chaetodon baronessa, Chaetodon plebeius and Chaetodon lunulatus) and four generalist species (Chaetodon auriga, Chaetodon citrinellus, Chaetodon kleinii and Chaetodon rafflesi). Distributions of obligate hard‐coral feeders were closely associated with spatial variation in percentage cover of scleractinian corals, but no more restricted compared with facultative hard‐coral feeders or non‐coral feeders. Species with highest dietary specialization (C. trifascialis and C. baronessa), however, exhibited the most pronounced zonation patterns and were restricted to habitats with greatest abundance of their preferred prey. While there are conspicuous links between dietary specialization v. spatial patterns in abundance of butterflyfishes, it remains unclear whether dietary specialization is the cause or consequence of more restricted distributions.     

Ecology shapes the evolutionary trade‐off between predator avoidance and defence in coral reef butterflyfishes

Antipredator defensive traits are thought to trade‐off evolutionarily with traits that facilitate predator avoidance. However, complexity and scale have precluded tests of this prediction in many groups, including fishes. Using a macroevolutionary approach, we test this prediction in butterflyfishes, an iconic group of coral reef inhabitants with diverse social behaviours, foraging strategies and antipredator adaptations. We find that several antipredator traits have evolved adaptively, dependent primarily on foraging strategy. We identify a previously unrecognised axis of diversity in butterflyfishes where species with robust morphological defences have riskier foraging strategies and lack sociality, while species with reduced morphological defences feed in familiar territories, have adaptations for quick escapes and benefit from the vigilance provided by sociality. Furthermore, we find evidence for the constrained evolution of fin spines among species that graze solely on corals, highlighting the importance of corals, as both prey and structural refuge, in shaping fish morphology.     

Within-colony feeding selectivity by a corallivorous reef fish: foraging to maximize reward?

Foraging theory predicts that individuals should choose a prey that maximizes energy rewards relative to the energy expended to access, capture, and consume the prey. However, the relative roles of differences in the nutritive value of foods and costs associated with differences in prey accessibility are not always clear. Coral‐feeding fishes are known to be highly selective feeders on particular coral genera or species and even different parts of individual coral colonies. The absence of strong correlations between the nutritional value of corals and prey preferences suggests other factors such as polyp accessibility may be important. Here, we investigated within‐colony feeding selectivity by the corallivorous filefish, Oxymonacanthus longirostris, and if prey accessibility determines foraging patterns. After confirming that this fish primarily feeds on coral polyps, we examined whether fish show a preference for different parts of a common branching coral, Acropora nobilis, both in the field and in the laboratory experiments with simulated corals. We then experimentally tested whether nonuniform patterns of feeding on preferred coral species reflect structural differences between polyps. We found that O. longirostris exhibits nonuniform patterns of foraging in the field, selectively feeding midway along branches. On simulated corals, fish replicated this pattern when food accessibility was equal along the branch. However, when food access varied, fish consistently modified their foraging behavior, preferring to feed where food was most accessible. When foraging patterns were compared with coral morphology, fish preferred larger polyps and less skeletal protection. Our results highlight that patterns of interspecific and intraspecific selectivity can reflect coral morphology, with fish preferring corals or parts of coral colonies with structural characteristics that increase prey accessibility.     

Corallivory in tubelip wrasses: diet,feeding and trophic importance

This paper describes a 2 month study of the patterns of abundance, feeding pressure, diet and feeding selectivity in corallivorous tubelip wrasses (Labridae), rarely studied, yet widespread and abundant group of corallivores on Indo‐Pacific coral reefs. The relative abundance and feeding pressure of corallivorous wrasses and butterflyfishes (Chaetodontidae) in Kimbe Bay, Papua New Guinea, were compared. Overall, tubelip wrasses were more than twice as abundant as corallivorous butterflyfishes and accounted for three times as many feeding bites on corals. The three most abundant tubelip wrasses (yellowtail tubelip Diproctacanthus xanthurus, Allen's tubelip Labropsis alleni and the tubelip wrasse Labrichthys unilineatus) were all obligate corallivores taking > 97% of bites from the surface of live corals. Labropsis alleni and D. xanthurus were highly selective, consuming preferred prey species in proportions significantly higher than expected given their availability. In contrast, L. unilineatus was fairly non‐selective and consumed most corals in direct accordance with their availability. As coral predators, tubelip wrasses are highly comparable to coral‐feeding butterflyfishes in the coral species consumed, range of dietary specialization and their reliance on live coral. Tubelip wrasses, however, may supersede butterflyfishes as the predominant corallivorous family in some Indo‐Pacific locations, and coral‐feeding tubelip wrasses are likely to be severely affected by coral decline.     

Seasonally fluctuating resources and temporal variability of interspecific competition

Summary The influence of seasonal availability of two critical resources (food and substrates from which food was harvested) on interspecific competition between striped surfperch (Embiotoca lateralis) and black surfperch (Embiotoca jacksoni) was examined. There was a strong depth-related gradient in density of prey and in cover of foliose algae; both declined with increasing bottom depth. Density of prey was reduced 5–10 fold during the winter season, but cover of substrates remained constant throughout the year. Although both fishes co-occurred throughout the same depth range, striped surfperch were more common in shallow habitats and black surfperch were more abundant deeper. Local abundance and distribution patterns of both surfperch species did not change seasonally. Stepwise regression analyses suggested that availability of favored substrates was a proximate influence on local patterns of surfperch distribution and abundance, and that interspecific competition depressed abundance of the two species to the same degree. Removal experiments conducted during the cold-water season revealed that interspecific competition influenced depth distribution of black surfperch but not striped surfperch. Seasonal change in density of prey was accompanied by marked changes in overlap in use of foraging substrates by the surfperches. The pattern of change in interspecific overlap suggested that surfperch competed for food only when prey were seasonally scarce. There was no difference in the agonistic tendencies of the two fishes, and the absolute and relative frequency of interspecific chases was independent of food level. These results have important implications regarding the impact of temporal variability of interspecific competition in natural communities. In the surfperch system, competition was characterized by constant and time-varying elements that had symmetrical and asymmetrical effects and involved both interference and exploitation mechanisms.     

Dietary shift in juvenile coral trout (<Emphasis Type="Italic">Plectropomus maculatus</Emphasis>) following coral reef degradation from a flood plume disturbance

Acute environmental disturbances impact on habitat quality and resource availability, which can reverberate through trophic levels and become apparent in species’ dietary composition. In this study, we observed a distinct dietary shift of newly settled and juvenile coral trout (Plectropomus maculatus) following severe coral reef habitat degradation after a river flood plume affected the Keppel Islands, Australia. Hard coral cover declined by ~28 % in the 2 yr following the 2010–2011 floods, as did the abundance of young coral trout. Gut contents analysis revealed that diets had shifted from largely crustacean-based to non-preferred prey fishes following the disturbances. These results suggest that newly settled and juvenile coral trout modify their diet and foraging strategy in response to coral habitat degradation. This bottom-up effect of habitat degradation on the diet of a top coral reef predator may incur a metabolic cost, with subsequent effects on growth and survival.     

Coral mortality versus structural collapse as drivers of corallivorous butterflyfish decline

As climate change increasingly threatens biodiversity, identifying specific drivers of species loss as well as the attributes of species most vulnerable to climatic disturbances is a key challenge to ecologists and conservationists. Here we assess the effects of coral loss versus declines in structural complexity on obligate and facultative coral feeding butterflyfishes on coral reefs in the central and western Indian Ocean. In the inner Seychelles, the abundance of the obligate coral feeding group declined markedly in response to live coral mortality (r ² = 0.48), but showed no further decline with respect to erosion of the physical matrix of the reef. Conversely, the facultative feeding group showed no decline in response to live coral loss, reflecting their feeding versatility; however they did decline in response to structural erosion of the reef framework (r ² = 0.26). There were no significant changes in either obligate or facultative corallivore abundances at a reference location (Chagos archipelago), highlighting that butterflyfish populations are stable in the absence of habitat disturbance. While specialised coral dependant fishes are highly vulnerable to coral loss caused by climate-induced coral bleaching, the structural collapse of dead coral colonies may have significant, but more variable, impacts across a wide range of fishes. If conservation and mitigation planning are to be effective, there is a clear need to better understand the mechanisms of reef structural collapse and the dynamics of system recovery following large-scale disturbance.     

Implications of feeding specialization on the recruitment processes and community structure of butterflyfishes

Synopsis When settling on coral reefs, fish larvae generally change from zooplanktivory to diverse forms of benthic feeding. Whereas food has not been reported to directly influence settlement, it is hypothesized that food resource might play a major role in the recruitment processes of butterflyfishes. Benthic feeding was found to occur immediatly after settlement, and was related to the degree of specialization of adult diets. Among obligate coral feeders scleractinian polyps were the exclusive diet of new recruits. In non-obligate corallivorous chaetodontids tentacles of sedentarian polychaetes were the preferred prey of juveniles for all the species studied, and represented on average 36.2% of their prey by weight. They formed a transitional food resource for these species which mainly fed on scleratinian polyps when adults (51.6% by weight). Among the chaetodontids studies, some recruited within adult home sites, whereas others exhibited size-specific distributions. The different patterns observed were not closely related to food specialization of the adults. The importance of food resources to the community structure of butterflyfishes on coral reefs is discussed.     

Habitat associations of juvenile versus adult butterflyfishes

Many coral reef fishes exhibit distinct ontogenetic shifts in habitat use while some species settle directly in adult habitats, but there is not any general explanation to account for these differences in settlement strategies among coral reef fishes. This study compared distribution patterns and habitat associations of juvenile (young of the year) butterflyfishes to those of adult conspecifics. Three species, Chaetodon auriga, Chaetodon melannotus, and Chaetodon vagabundus, all of which have limited reliance on coral for food, exhibited marked differences in habitat association of juvenile versus adult individuals. Juveniles of these species were consistently found in shallow-water habitats, whereas adult conspecifics were widely distributed throughout a range of habitats. Juveniles of seven other species (Chaetodon aureofasciatus, Chaetodon baronessa, Chaetodon citrinellus, Chaetodon lunulatus, Chaetodon plebeius, Chaetodon rainfordi, and Chaetodon trifascialis), all of which feed predominantly on live corals, settled directly into habitat occupied by adult conspecifics. Butterflyfishes with strong reliance on corals appear to be constrained to settle in habitats that provide access to essential prey resources, precluding their use of distinct juvenile habitats. More generalist butterflyfishes, however, appear to utilize distinct juvenile habitats and exhibit marked differences in the distribution of juveniles versus adults.     

Spatiotemporal distribution of nocturnal coral reef fish juveniles in Moorea Island,French Polynesia

This study aimed to investigate the spatial structure of nocturnal fish communities at settlement on coral reefs in Moorea Island lagoon, French Polynesia; and the temporal consistency of habitat selection between winter (April to June 2001) and summer (November 2001). The Moorea lagoon was divided into 12 habitat zones (i.e., coral reef zones), which were distinct in terms of depth, wave exposure, and substratum composition. Nocturnal visual censuses among the 12 habitats found that the recently settled juveniles of 25 species recorded were dispatched among three communities spatially distributed according to the distance from the reef crest (reef crest, barrier reef, and fringing reef communities). This spatial communities structure of nocturnal juveniles was consistent in both winter and summer and would be explained primarily by a current gradient in Moorea lagoon (current speed was high near the reef crest and decreased towards the beach) and by the topographic characteristics of reef zones. Among the 25 species, 13 were recorded in both winter and summer. A comparison of the spatial distribution between summer and winter for 13 species that occurred during both seasons found that only 4 differed between the two seasons. For these species, habitat selection would be organized primarily by some stochastic processes such as inter- and intraspecific competition, predation, and food availability. Overall, the present study allowed us to highlight that most nocturnal coral reef fish juveniles at Moorea Island exhibited striking patterns in their distribution and current and topographic characteristics of reef zones might exert considerable influence on the distribution of fishes.     

Geographic variation in resource use by specialist versus generalist butterflyfishes

Localised patterns of resource use can be constrained by multiple factors. Comparison of resource use at multiple locations with differing resource availability can allow fundamental specialists to be distinguished from species that simply feed predominantly on prey types that are locally abundant. This study investigates geographic variation in the feeding ecology of coral‐feeding butterflyfishes to examine whether patterns of resource use and levels of dietary specialisation vary among distinct locations, corresponding with changes in resource availability. Our specific aims were to investigate whether the dietary niche breadth of four butterflyfishes varies among five geographically separated locations and assess whether each species utilises similar resources in each location. Resource availability and dietary composition of four butterflyfishes were quantified at three sites across each of five geographic locations throughout the Pacific. Niche breadth, niche overlap, and resource selection functions were calculated for each species at each site and compared among locations. Availability of dietary resources varied significantly among locations and sites. Chaetodon vagabundus, C. citrinellus and C. lunulatus had low levels of dietary specialisation and used different resources in each location. Chaetodon trifascialis had high levels of dietary specialisation and used the same few resources in each location. Our results indicate that relative levels of dietary specialisation among different butterflyfishes do hold at larger spatial scales, however, geographical variation in the dietary composition of all butterflyfishes indicates that prey availability has a fundamental influence on dietary composition. Highly specialised species such as C. trifascialis will be highly vulnerable to coral loss as they appear to be largely inflexible in their dietary composition. However, the increased feeding plasticity observed here for C. trifascialis suggests this species may have a greater capacity to respond to coral loss than previously assumed.     

Prey selection by coral-feeding butterflyfishes: strategies to maximize the profit

Synopsis Factors that structure preferences among food corals were examined for the obligate coral-feeding butterflyfishChaetodon multicinctus. In the field, fish show a simple repetitious pattern of foraging composed of (1) pre-encounter search for coral colonies, and (2) post-encounter inspection/orientation, bite, and consumption of polyps. Rose coral,Pocillopora meandrina, and the massive coral,Porites lobata, were taken in higher proportions than their percentage substrate cover, while finger coral,Porites compressa, was taken in lower proportion. Paired presentations of coral colonies in the lab gave similar results:Poc. meandrina was preferred overPor. lobata which was preferred overPor. compressa. Poc. meandrina tissue had the highest energy content, lowest handling time, and highest profitability. Energy content did not differ amongPorites tissues, but handling time was greater and more inspective eye movements were made while foraging on the branched finger coral,Por. compressa. Experimental manipulation of coral colony morphology indicate preferences amongPorites are most likely structured by handling costs. Predictions of a simple prey-choice foraging model are supported in theC. multicinctus system if abundance of the branched coralPor. compressa is estimated as that available to fishes rather than percentage substrate cover. The relative size and abundance of stinging nematocysts are also consistent with observed foraging patterns in the field, but await immunological confirmation. Coral-feeding butterflyfishes offer unique opportunities to test models of foraging ecology in reef fishes, and the direction of future studies is suggested.     

Abundance,diversity, and feeding behavior of coral reef butterflyfishes at Lord Howe Island

Endemic species are assumed to have a high risk of extinction because their restricted geographic range is often associated with low abundance and high ecological specialization. This study examines the abundance of Chaetodon butterflyfishes at Lord Howe Island in the south‐west Pacific, and compares interspecific differences in local abundance to the feeding behavior and geographic range of these species. Contrary to expected correlations between abundance and geographic range, the single most abundant species of butterflyfish was Chaetodon tricinctus, which is endemic to Lord Howe Island and adjacent reefs; densities of C. tricinctus (14.1 ± 2.1 SE fish per 200m²) were >3 times higher than the next most abundant butterflyfish (Chaetodon melannotus), and even more abundant than many other geographically widespread species. Dietary breadth for the five dominant butterflyfishes at Lord Howe Island was weakly and generally negative correlated with abundance. The endemic C. tricinctus was a distinct outlier in this relationship, though our extensive feeding observations suggest some issues with the measurements of dietary breadth for this species. Field observations revealed that all bites taken on benthic substrates by C. tricinctus were from scleractinian corals, but adults rarely, if ever, took bites from the benthos, suggesting that they may be feeding nocturnally and/or using mid‐water prey, such as plankton. Alternatively, the energetic demands of C. tricinctus may be fundamentally different to other coral‐feeding butterflyfishes. Neither dietary specialization nor geographic range accounts for interspecific variation in abundance of coral reef butterflyfishes at Lord Howe Island, while much more work on the foraging behavior and population dynamics of C. tricinctus will be required to understand its’ abundance at this location.     

Orientation behavior of butterflyfishes (family Chaetodontidae) on coral reefs: spatial learning of route specific landmarks and cognitive maps

Synopsis Foraging butterflyfishes follow predictable paths as they swim from one food patch to another within their territories and home ranges. The pattern is repeated throughout the day. The behavior is described in species belonging to the coral feeding guild. Habit formation and spatial learning are implicated. Foraging paths are based on learned locations of route specific landmarks. When a coral head is removed the fish look for it in its former location. If pairs of foraging fish are deflected from the path, they resume their routine pattern at the first landmark they encounter. Periodically, fish make excursions of 30 m or more to distant parts of the reef. Usually they follow different paths on the outbound and homeward legs of these excursions. The critical question is: Are the paths novel? If they are, it is evidence for the use of cognitive maps. Certainly fishes living in the highly structured coral reef environment are prime candidates to use cognitive maps in their orientation behavior.     

Specialist corallivores dominate butterflyfish assemblages in coral‐dominated reef habitats

This study examined the dietary habits and functional composition of butterflyfishes in the Chagos Archipelago, central Indian Ocean. Eighteen species of butterflyfishes were recorded in Chagos, including six obligate corallivores (Chaetodon bennetti, Chaetodon guttatissimus, Chaetodon meyeri, Chaetodon trifascialis, Chaetodon trifasciatus and Chaetodon zanzibarensis), five facultative corallivores (Chaetodon auriga, Chaetodon falcula, Chaetodon interruptus, Chaetodon kleinii and Chaetodon madagaskariensis), two non‐corallivores (Chaetodon lunula and Chaetodon xanthocephalus) and a further five species (Chaetodon citrinellus, Chaetodon lineolatus, Heimitaurichthys zoster, Heniochus monoceros and Forcipiger flavissimus), for which local dietary habits were not studied. There were marked differences in the abundance of butterflyfishes among sites and between reef zones, mostly associated with variation in abundance of scleractinian corals. Obligate coral‐feeding species (mostly C. trifascialis) dominated across all sites. This study suggests that coral feeding and high levels of dietary specialization contribute to high population‐level fitness among coral reef butterflyfishes. Despite being more vulnerable to habitat disturbances and coral loss, it appears likely that specialist coral‐feeding butterflyfishes are also much more resilient to occasional disturbances, and therefore dominate in a wide range of coral reef habitats.     

Habitat associations of juvenile fish at Ningaloo Reef, Western Australia: the importance of coral and algae

Habitat specificity plays a pivotal role in forming community patterns in coral reef fishes, yet considerable uncertainty remains as to the extent of this selectivity, particularly among newly settled recruits. Here we quantified habitat specificity of juvenile coral reef fish at three ecological levels; algal meadows vs. coral reefs, live vs. dead coral and among different coral morphologies. In total, 6979 individuals from 11 families and 56 species were censused along Ningaloo Reef, Western Australia. Juvenile fishes exhibited divergence in habitat use and specialization among species and at all study scales. Despite the close proximity of coral reef and algal meadows (10's of metres) 25 species were unique to coral reef habitats, and seven to algal meadows. Of the seven unique to algal meadows, several species are known to occupy coral reef habitat as adults, suggesting possible ontogenetic shifts in habitat use. Selectivity between live and dead coral was found to be species-specific. In particular, juvenile scarids were found predominantly on the skeletons of dead coral whereas many damsel and butterfly fishes were closely associated with live coral habitat. Among the coral dependent species, coral morphology played a key role in juvenile distribution. Corymbose corals supported a disproportionate number of coral species and individuals relative to their availability, whereas less complex shapes (i.e. massive & encrusting) were rarely used by juvenile fish. Habitat specialisation by juvenile species of ecological and fisheries importance, for a variety of habitat types, argues strongly for the careful conservation and management of multiple habitat types within marine parks, and indicates that the current emphasis on planning conservation using representative habitat areas is warranted. Furthermore, the close association of many juvenile fish with corals susceptible to climate change related disturbances suggests that identifying and protecting reefs resilient to this should be a conservation priority.     

Species-specific habitat distribution of coral reef fish assemblages in relation to habitat characteristics in an Okinawan coral reef

We determined the species-specific habitat associations of coral reef fishes and environmental characteristics in an Okinawan coral reef in Japan. We focused on three families (Pomacentridae, Gobiidae and Labridae) and attempted to determine differences in habitat utilization. We selected six sites along the coast of Amitori Bay, from the entrance to the innermost part, in order to cover a wide range of habitat characteristics (exposed habitat, semi-exposed habitat and sheltered habitat). The species diversity of coral assemblages was greater at the exposed and semi-exposed habitats, whereas branching coral mostly covered the sheltered habitat. The environmental factors that determine the species-specific spatial association in fishes differed among families. Both biological characteristics (coral morphology and coral species diversity) and physical characteristics (water depth and wave exposure) affected the spatial association of pomacentrids and gobiids. In contrast, physical characteristics such as substrate complexity and water depth affected the species-specific spatial association of labrid species. Further study is needed to determine the ecological factors that regulate the species-specific habitat preference in Okinawan coral reefs.     

Wave energy and swimming performance shape coral reef fish assemblages

Physical factors often have an overriding influence on the distribution patterns of organisms, and can ultimately shape the long-term structure of communities. Although distribution patterns in sessile marine organisms have frequently been attributed to functional characteristics interacting with wave-induced water motion, similar evidence for mobile organisms is lacking. Links between fin morphology and swimming performance were examined in three diverse coral reef fish families from two major evolutionary lineages. Among-habitat variation in morphology and performance was directly compared with quantitative values of wave-induced water motion from seven coral reef habitats of different depth and wave exposure on the Great Barrier Reef. Fin morphology was strongly correlated with both field and experimental swimming speeds in all three families. The range of observed swimming speeds coincided closely with the magnitude of water velocities commonly found on coral reefs. Distribution patterns in all three families displayed highly congruent relationships between fin morphology and wave-induced water motion. Our findings indicate a general functional relationship between fin morphology and swimming performance in labriform-swimming fishes, and provide quantitative evidence that wave energy may directly influence the assemblage structure of coral reef fishes through interactions with morphology and swimming performance.     

Coral reef mesopredators switch prey,shortening food chains,in response to habitat degradation

Diet specificity is likely to be the key predictor of a predator's vulnerability to changing habitat and prey conditions. Understanding the degree to which predatory coral reef fishes adjust or maintain prey choice, in response to declines in coral cover and changes in prey availability, is critical for predicting how they may respond to reef habitat degradation. Here, we use stable isotope analyses to characterize the trophic structure of predator–prey interactions on coral reefs of the Keppel Island Group on the southern Great Barrier Reef, Australia. These reefs, previously typified by exceptionally high coral cover, have recently lost much of their coral cover due to coral bleaching and frequent inundation by sediment‐laden, freshwater flood plumes associated with increased rainfall patterns. Long‐term monitoring of these reefs demonstrates that, as coral cover declined, there has been a decrease in prey biomass, and a shift in dominant prey species from pelagic plankton‐feeding damselfishes to territorial benthic algal‐feeding damselfishes, resulting in differences in the principal carbon pathways in the food web. Using isotopes, we tested whether this changing prey availability could be detected in the diet of a mesopredator (coral grouper, Plectropomus maculatus). The δ¹³C signature in grouper tissue in the Keppel Islands shifted from a more pelagic to a more benthic signal, demonstrating a change in carbon sources aligning with the change in prey availability due to habitat degradation. Grouper with a more benthic carbon signature were also feeding at a lower trophic level, indicating a shortening in food chains. Further, we found a decline in the coral grouper population accompanying a decrease in total available prey biomass. Thus, while the ability to adapt diets could ameliorate the short‐term impacts of habitat degradation on mesopredators, long‐term effects may negatively impact mesopredator populations and alter the trophic structure of coral reef food webs.