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On coral reefs, many small coral-associated fishes exhibit high levels of habitat specialisation, which can contribute to their susceptibility to habitat loss. However, high levels of habitat partitioning may buffer communities from the loss of particular habitat types. This study provides a quantitative evaluation of habitat specialisation, substratum selectivity and habitat overlap of 9 Eviota (Gobiidae) species in Kimbe Bay, Papua New Guinea. All but 1 locally common Eviota species were strongly associated with scleractinian coral substrata, and species ranged from habitat generalists to obligate coral specialists with some of the most extreme fine-scale patterns of habitat specialisation known for coral reef fishes. Patterns of substratum selectivity varied greatly within the genus, but many species showed distinct preferences for particular corals, most notably the scleractinian genera Acropora and Porites. Most species exhibited low habitat overlap and partitioned habitat on a fine spatial scale, but there were notable exceptions. Two Acropora coral specialists and some species with strong preference for massive Porites coral exhibited high overlap. Overall, the local abundance of Eviota species varied in relation to the degree of habitat specialisation, with the most generalised species more abundant than the habitat specialists. Habitat structure and species-specific differences in habitat specialisation, substratum selectivity and habitat overlap are likely to be key drivers explaining the distribution and abundance of Eviota species and the local community structure. Most importantly, many coral-dependent and less abundant species of Eviota may be vulnerable to habitat loss as a result of the ongoing degradation of coral reefs.

This study was supported by the start up fund of the University of Hong Kong (C.S.), the Fisheries Society of the British Isles (M.D.J.) and the ARC Centre of Excellence for Coral Reef Studies (P.L.M). This project was completed under approval of the James Cook University animal ethics committee (permit: A2210) and according to the University’s animal ethics guidelines. We thank the Marine and Aquaculture Research Facilities Unit (JCU) and the Integrative Systems Biology Laboratory (KAUST). Special thanks go to Damien Lightfoot for extracting RNA from . brains and Robert Lehmann for aiding with the genome mapping of . sequences. Am percula Am percula

[Extract:] In their study, Clark et al. suggest that previous studies on the effects of elevated levels of CO2 on the behaviour of coral reef fishes are not repeatable and that ocean acidification does not impair the behaviour of coral reef fishes, even though six significant behavioural effects were detected in their study, each of which was dismissed for a different reason. They then compare the means and variances of six previous ocean acidification studies in fish with a data distribution that is derived from a multi-species compilation of their own data to conclude that the results of previous studies are statistically improbable. However, Clark et al. did not closely repeat previous studies, as they did not replicate key species, used different life stages and ecological histories and changed methods in important ways that reduce the likelihood of detecting the effects of ocean acidification.

Most laboratory experiments examining the effect of ocean acidification on marine organisms use stable pH/pCO2 treatments based on average projections for the open ocean. However, pH/pCO2 levels vary spatially and temporally in marine environments, and this variation can affect organism responses to pH/pCO2. On coral reefs, diel pH/pCO2 variability at the individual reef scale has been reported in a few studies, but variation among microhabitats within a reef remains poorly understood. This study determined the pH/pCO2 variability of three different reefs, and three contrasting coral reef microhabitats (dominated by hard coral, soft coral, or open substrate) within each reef. Three SeaFET pH loggers were deployed simultaneously at the three microhabitats within a reef over a 9-day period. This was repeated at three different reefs around the Lizard Island lagoon. The loggers recorded pHT and temperature every 5 min. Water samples were collected from each microhabitat during four points of the tidal cycle (high, low, rising, and falling) and analysed for total alkalinity and dissolved inorganic carbon. The data show a clear diel pCO2 cycle, increasing overnight and decreasing during the day, in association with photosynthesis and respiration cycles. Diel pCO2 differed more between reefs than between microhabitats within reefs. Variation between reefs was most likely influenced by water flow, with the more protected (low flow) reefs experiencing a greater range in pCO2 (Δ 250 μatm) than the exposed (high flow) reefs (Δ 116 μatm). These results add to a growing body of the literature on the diel variation of pCO2 of shallow, nearshore environments and suggest that when projecting future pCO2 levels, it is important to consider reef metabolism as well as physical and hydrodynamic factors.

Habitat characteristics play an important role in determining the structure of fish communities. The decline in fish diversity and abundance with the decline in coral diversity and cover may be explained by habitat specialisation and partitioning among reef fishes and/or preferences for particular corals that are susceptible to disturbance. These preferences may develop at different life history stages. Here, we investigated patterns of habitat specialisation and ontogenetic shifts in habitat preference among 14 co-existing damselfish species at Lizard Island lagoon on the Great Barrier Reef. Although live coral cover contributed only 26% of the substratum, 28% of adults and 57% of new settlers were mostly found on live coral, indicating a strong preference for live coral habitat by new settlers. Only a few species exhibited a high degree of habitat specialisation and low overlap in habitat use with other species. Specialisation differed among species and life stages. New settlers were more commonly associated with finely branched corymbose corals and using those habitats with higher frequency than expected based on habitat availability alone. Adults were more commonly linked to more open branching morphologies or non-coral substrata. Our results suggest that habitat loss may not uniformly impact on all life stages. While adult individuals may not be as reliant as juveniles on corals, detrimental effects of habitat loss on juvenile survival may have longer-term impacts on adult populations. As juveniles show preferential associations with particular coral species, such as corymbose corals, the loss of these growth forms is likely to have the most significant negative impacts on this critical life history stage.

Molecular responses of fishes to a heatwave are species specific and do not concur with measures of oxygen uptake in captivity., The marine heatwave of 2016 was one of the longest and hottest thermal anomalies recorded on the Great Barrier Reef, influencing multiple species of marine ectotherms, including coral reef fishes. There is a gap in our understanding of what the physiological consequences of heatwaves in wild fish populations are. Thus, in this study, we used liver transcriptomes to understand the molecular response of five species to the 2016 heatwave conditions. Gene expression was species specific, yet we detected overlap in functional responses associated with thermal stress previously reported in experimental setups. The molecular response was also influenced by the duration of exposure to elevated temperatures. This study highlights the importance of considering the effects of extreme warming events when evaluating the consequences of climate change on fish communities.

Global warming will have far-reaching consequences for marine species over coming decades, yet the magnitude of these effects may depend on the rate of warming across generations. Recent experiments show coral reef fishes can compensate the metabolic challenges of elevated temperature when warm conditions are maintained across generations. However, the effects of a gradual temperature increase across generations remain unknown. In the present study, we analysed metabolic and molecular traits in the damselfish Acanthochromis polyacanthus that were exposed to +1.5°C in the first generation and +3.0°C in the second (Step +3.0°C). This treatment of stepwise warming was compared to fish reared at current-day temperatures (Control), second-generation fish of control parents reared at +3.0°C (Developmental +3.0°C) and fish exposed to elevated temperatures for two generations (Transgenerational +1.5°C and Transgenerational +3.0°C). Hepatosomatic index, oxygen consumption and liver gene expression were compared in second-generation fish of the multiple treatments. Hepatosomatic index increased in fish that developed at +3.0°C, regardless of the parental temperature. Routine oxygen consumption of Step +3.0°C fish was significantly higher than Control; however, their aerobic scope recovered to the same level as Control fish. Step +3.0°C fish exhibited significant upregulation of genes related to mitochondrial activity and energy production, which could be associated with their increased metabolic rates. These results indicate that restoration of aerobic scope is possible when fish experience gradual thermal increase across multiple generations, but the metabolic and molecular responses are different from fish reared at the same elevated thermal conditions in successive generations.

Epigenetic inheritance is a potential mechanism by which the environment in one generation can influence the performance of future generations1. Rapid climate change threatens the survival of many organisms; however, recent studies show that some species can adjust to climate-related stress when both parents and their offspring experience the same environmental change2,3. Whether such transgenerational acclimation could have an epigenetic basis is unknown. Here, by sequencing the liver genome, methylomes and transcriptomes of the coral reef fish, Acanthochromis polyacanthus, exposed to current day (+0 °C) or future ocean temperatures (+3 °C) for one generation, two generations and incrementally across generations, we identified 2,467 differentially methylated regions (DMRs) and 1,870 associated genes that respond to higher temperatures within and between generations. Of these genes, 193 were significantly correlated to the transgenerationally acclimating phenotypic trait, aerobic scope, with functions in insulin response, energy homeostasis, mitochondrial activity, oxygen consumption and angiogenesis. These genes may therefore play a key role in restoring performance across generations in fish exposed to increased temperatures associated with climate change. Our study is the first to demonstrate a possible association between DNA methylation and transgenerational acclimation to climate change in a vertebrate. Transgenerational acclimation to warmer oceans has been seen for some marine species. This study shows that the coral reef fish has 193 genes correlated to such acclimation traits, suggesting an epigenetic basis of acclimation.

The impacts of ocean acidification will depend on the ability of marine organisms to tolerate, acclimate and eventually adapt to changes in ocean chemistry. Here, we use a unique transgenerational experiment to determine the molecular response of a coral reef fish to short-term, developmental and transgenerational exposure to elevated CO2, and to test how these responses are influenced by variations in tolerance to elevated CO2 exhibited by the parents. Within-generation responses in gene expression to end-of-century predicted CO2 levels indicate that a self-amplifying cycle in GABAergic neurotransmission is triggered, explaining previously reported neurological and behavioural impairments. Furthermore, epigenetic regulator genes exhibited a within-generation specific response, but with some divergence due to parental phenotype. Importantly, we find that altered gene expression for the majority of within-generation responses returns to baseline levels following parental exposure to elevated CO2 conditions. Our results show that both parental variation in tolerance and cross-generation exposure to elevated CO2 are crucial factors in determining the response of reef fish to changing ocean chemistry.

The distribution of coral reef fishes is often closely linked to the availability of preferred habitats. However, even in specialized gobies associated with a single coral species, their distribution does not always match that of the coral host. The coral goby Paragobiodon xanthosoma is primarily restricted to shallow water ( 30 m. Here, we use observational and experimental approaches to test whether depth-associated changes in morphology and partial mortality of the coral decrease habitat quality. Quantitative surveys from the surface to 30 m found pronounced changes in colony morphology over depth. S. hystrix colonies most likely to be occupied by P. xanthosoma were those with shallow-water characteristics, especially lower partial mortality and a more complex branching structure. In a binary choice experiment, P. xanthosoma individuals preferentially selected colonies from shallow water (5 m) over deep water (30 m) and with high complexity over low complexity when colonies were collected from a standardized depth (15 m). Finally, a transplant experiment examined the effect of depth-associated changes in the coral habitat on patterns of growth of P. xanthosoma. When the depth of placement was standardized, the growth of P. xantho soma was 8-fold lower on colonies collected from deep water (30 m) compared to colonies from shallower water (5 and 15 m). Together, these patterns suggest that depth-related changes in the morphology of the coral host are responsible for driving patterns of distribution over depth in their associated reef fish.

Elevated CO2 levels associated with ocean acidification (OA) have been shown to alter behavioural responses in coral reef fishes. However, all studies to date have used stable pCO2 treatments, not considering the substantial diel pCO2 variation that occurs in shallow reef habitats. Here, we reared juvenile damselfish, Acanthochromis polyacanthus, and clownfish, Amphiprion percula, at stable and diel cycling pCO2 treatments in two experiments. As expected, absolute lateralization of A. polyacanthus and response to predator cue of Am. percula were negatively affected in fish reared at stable, elevated pCO2 in both experiments. However, diel pCO2 fluctuations reduced the negative effects of OA on behaviour. Importantly, in experiment two, behavioural abnormalities that were present in fish reared at stable 750 µatm CO2 were largely absent in fish reared at 750 ± 300 µatm CO2. Overall, we show that diel pCO2 cycles can substantially reduce the severity of behavioural abnormalities caused by elevated CO2. Thus, past studies may have over-estimated the impacts of OA on the behavioural performance of coral reef fishes. Furthermore, our results suggest that diel pCO2 cycles will delay the onset of behavioural abnormalities in natural populations.

Marine heatwaves, which are increasing in frequency, duration and intensity owing to climate change, are an imminent threat to marine ecosystems. On coral reefs, heatwave conditions often coincide with periods of peak recruitment of juvenile fishes and exposure to elevated temperature may affect their development. However, whether differences in the duration of high temperature exposure have effects on individual performance is unknown. We exposed juvenile spiny damselfish, Acanthochromis polyacanthus, to increasing lengths of time (3, 7, 30 and 108 days post-hatching) of elevated temperature (+2°C). After 108 days, we measured escape performance at present-day control and elevated temperatures, standard length, mass and critical thermal maximum. Using a Bayesian approach, we show that 30 days or more exposure to +2°C leads to improved escape performance, irrespective of performance temperature, possibly owing to developmental effects of high temperature on muscle development and/or anaerobic metabolism. Continued exposure to elevated temperature for 108 days caused a reduction in body size compared with the control, but not in fish exposed to high temperature for 30 days or less. By contrast, exposure to elevated temperatures for any length of time had no effect on critical thermal maximum, which, combined with previous work, suggests a short-term physiological constraint of ∼37°C in this species. Our study shows that extended exposure to increased temperature can affect the development of juvenile fishes, with potential immediate and future consequences for individual performance.

Ocean acidification (OA) is predicted to affect the physiology of some fishes. To date, most studies have investigated this issue using stable pCO2 levels based on open ocean projections. Yet, most shallow, nearshore systems experience temporal and spatial pCO2 fluctuations. For example, pCO2 on coral reefs is highest at night and lowest during the day, but as OA progresses, both the average pCO2 and magnitude of fluctuations are expected to increase. We exposed four coral reef fishes - Lutjanus fulviflamma, Caesio cuning, Abudefduf whitleyi, and Cheilodipterus quinquelineatus - to ambient, stable elevated, or fluctuating elevated pCO2 conditions for 9-11 days. Then, we measured swimming performance, oxygen uptake rates, and haematological parameters during the day and at night. When compared to ambient pCO2 conditions, L. fulviflamma, C. cuning, and A. whitleyi exposed to fluctuating elevated pCO2 increased swimming performance, maximum oxygen uptake rates, and aerobic scope, regardless of time of day; whereas, the only nocturnal species studied, C. quinquelineatus, decreased maximum oxygen uptake rates and aerobic scope. Our findings suggest that exposure to fluctuating or stable elevated pCO2 can physiologically benefit some coral reef fishes; however, other species, such as the cardinalfish examined here, may be more sensitive to future OA conditions.

Ocean acidification, resulting from increasing atmospheric carbon dioxide (CO2) emissions, can affect the physiological performance of some fishes. Most studies investigating ocean acidification have used stable pCO(2) treatments based on open ocean predictions. However, nearshore systems can experience substantial spatial and temporal variations in pCO(2). Notably, coral reefs are known to experience diel fluctuations in pCO(2), which are expected to increase on average and in magnitude in the future. Though we know these variations exist, relatively few studies have included fluctuating treatments when examining the effects of ocean acidification conditions on coral reef species. To address this, we exposed two species of damselfishes, Amblyglyphidodon curacao and Acanthochromis polyacanthus, to ambient pCO(2), a stable elevated pCO(2) treatment, and two fluctuating pCO(2) treatments (increasing and decreasing) over an 8 h period. Oxygen uptake rates were measured both while fish were swimming and resting at low-speed. These 8 h periods were followed by an exhaustive swimming test (Ucrit) and blood draw examining swimming metrics and haematological parameters contributing to oxygen transport. When A. polyacanthus were exposed to stable pCO(2) conditions (ambient or elevated), they required more energy during the 8 h trial regardless of swimming type than fish exposed to either of the fluctuating pCO(2) treatments (increasing or decreasing). These results were reflected in the oxygen uptake rates during the Ucrit tests, where fish exposed to fluctuating pCO(2) treatments had a higher factorial aerobic scope than fish exposed to stable pCO(2) treatments. By contrast, A. curacao showed no effect of pCO(2) treatment on swimming or oxygen uptake metrics. Our results show that responses to stable versus fluctuating pCO(2) differ between species what is stressful for one species many not be stressful for another. Such asymmetries may have populationand community level impacts under higher more variable pCO(2) conditions in the future.

Competition for space affects patterns of habitat use and individual performance of coral-dwelling fishes; however, the physical attributes of corals that influence habitat preferences are uncertain. In this study, we investigated the influence of coral colony size and branching structure of 2 coral species, Acropora nasuta and Acropora spathulata, on habitat use and growth rate of 2 coral gobies, Gobiodon histrio and G. erythrospilus. First, we examined 2 key aspects of coral colony structure (interbranch depth and interbranch width) that may influence habitat preferences. We then used laboratory and field-based experiments to test the effects of coral species, coral colony size and branching structure on habitat preference and growth rates of G. histrio and G. erythrospilus. The preferred coral species, A. nasuta, had smaller interbranch width than A. spathulata. A binary-choice laboratory experiment demonstrated that both goby species preferred coral colonies with smaller interbranch width, except when they had the opportunity to occupy A. nasuta over A. spathulata. A field transplant experiment showed that both goby species grew faster on larger coral colonies and in colonies with smaller interbranch width. G. erythrospilus grew faster than G. histrio on A. spathulata, indicating that it suffers less fitness loss when occupying this alternative habitat. Our results show that coral physical attributes are important factors driving habitat preference of coral-dwelling gobies; however, there must also be additional factors that influence their habitat use. Declining average coral size and reduced habitat complexity on coral reefs could have significant impacts on the performance of fishes, affecting ecological processes such as competition.

Predicting the impacts of ocean warming and acidification on marine ecosystems requires an evolutionary perspective because, for most marine species, these environmental changes will occur over a number of generations. Acclimation through phenotypic plasticity and adaptation through genetic selection could help populations of some species cope with future warmer and more acidic oceans. Coral reef species are predicted to be some of the most vulnerable to climate change because they live close to their thermal limits. Yet, their evolutionary history may indicate that they possess adaptations that enable them to cope with a high CO2 environment. Here, we first explore the evolutionary history of reef fishes and how their history has shaped their physiological adaptations to environmental temperatures and pCO2. We examine current-day thermal and CO2 environments experienced by coral reef fishes and summarize experimental studies that have tested how they respond to elevated temperatures and pCO2 levels. We then examine evidence for acclimation and adaptation to projected ocean warming and acidification. Indeed, new studies have demonstrated the potential for transgenerational plasticity and heritable genetic variation that would allow some fishes to maintain performance as the oceans warm and become more acidic. We conclude by outlining management approaches – specifically those that can help preserve genetic variation by maintaining population size – to enhance the potential for genetic adaptation to climate change.

Coral reef communities between 26.8 °N and 18.6 °N latitude in the Saudi Arabian Red Sea were surveyed to provide baseline data and an assessment of fine-scale biogeography of communities in this region. Forty reefs along 1100 km of coastline were surveyed using depth-stratified visual transects of fish and benthic communities. Fish abundance and benthic cover data were analyzed using multivariate approaches to investigate whether coral reef communities differed with latitude. A total of 215 fish species and 90 benthic categories were recorded on the surveys. There were no significant differences among locations in fish abundance, species richness, or among several diversity indices. Despite known environmental gradients within the Red Sea, the communities remained surprisingly similar. The communities do, however, exhibit subtle changes across this span of reefs that likely reflect the constrained distributions of several species of reef fish and benthic fauna.

Although competition is recognized as a core ecological process, its prevalence and importance in coral reef fish communities have been debated. Here we compile and synthesize the results of 173 experimental tests of competition from 72 publications. We show that evidence for competition is pervasive both within and between species, with 72% of intraspecific tests and 56% of interspecific tests demonstrating a demographically significant consequence of competition (e.g., a decrease in recruitment, survival, growth, or fecundity). We highlight several factors that can interact with the effects of competition and make it more difficult to detect in field experiments. In light of this evidence, we discuss the role of competition in shaping coral reef fish communities and competition's status as one of several processes that contribute to species coexistence. Finally, we consider some of the complex ways that climate change may influence competition, and we provide suggestions for future research.

Elevated CO2 levels have been shown to affect metabolic performance in some coral reef fishes. However, all studies to date have employed stable elevated CO2 levels, whereas reef habitats can experience substantial diel fluctuations in pCO2 ranging from ±50 to 600 μatm around the mean, fluctuations that are predicted to increase in magnitude by the end of the century. Additionally, past studies have often investigated the effect of elevated CO2 in isolation, despite the fact that ocean temperatures will increase in tandem with CO2 levels. Here, we tested the effects of stable (1000 μatm) versus diel-cycling (1000 ± 500 μatm) elevated CO2 conditions and elevated temperature (+2 °C) on metabolic traits of juvenile spiny damselfish, Acanthochromis polyacanthus. Resting oxygen uptake rates (ṀO2) were higher in fish exposed to stable elevated CO2 conditions when compared to fish from stable control conditions, but were restored to control levels under diel CO2 fluctuations. However, the benefits of diel CO2 fluctuations were diminished at elevated temperature. Factorial aerobic scope showed a similar pattern, but neither maximal ṀO2 nor absolute aerobic scope was affected by CO2 or temperature. Our results suggest that diel CO2 cycles can ameliorate the increased metabolic cost associated with elevated CO2, but elevated temperature diminishes the benefits of diel CO2 cycles. Thus, previous studies may have misestimated the effect of ocean acidification on the metabolic performance of reef fishes by not accounting for environmental CO2 fluctuations. Our findings provide novel insights into the interacting effects of diel CO2 fluctuations and temperature on the metabolic performance of reef fishes.

Elevated temperature can have detrimental effects on the physiological performance of many marine organisms. However, phenotypic plasticity may enable some populations to maintain their performance under thermal stress. Two longitudinally separated populations of the coral reef fish, Acanthochromis polyacanthus from the Great Barrier Reef have shown differing capacities for thermal plasticity - the southernmost Heron Island population restored aerobic scope within one generation at a higher temperature, whereas the northernmost Palm Island population restored aerobic scope only when two generations were exposed to warmer conditions. We recently discovered an epigenetic signature associated with transgenerational plasticity in the Palm Island population. Here, we aimed to determine if epigenetic changes are also associated with the within-generational plasticity observed in the Heron Island population and, if so, how this epigenetic signature compares to the Palm Island transgenerational epigenome. By sequencing and analyzing the genome-wide DNA methylome of fish reared at control (+0 degrees C) or elevated temperatures (+1.5 and +3 degrees C) since early life, we identified 480 differentially methylated genomic regions and 372 adjacent protein-coding genes associated with within-generational plasticity in the Heron Island population. Functions related to insulin, cardiovascular capacity, development, and heat response were significantly enriched in differentially methylated genes, suggesting that these functions are the core mechanisms for within-generational restoration of aerobic scope. Comparison to the differentially methylated genes identified from F2 Palm Island population revealed little overlap of genes and enriched functions, indicating that distinct genetic toolkits may be used for within- and between-generational plasticity to ocean warming in the same species from different latitudes.

Extreme thermal events are increasing in frequency and duration as the climate continues to warm, with potential detrimental effects on marine organisms. However, the effects of heatwaves may differ among geographically separated populations depending on their capacity for thermal plasticity. Here, we compared the response to simulated summer heatwave temperatures (+1.5 and +3.0 ˚C above average) in two populations of a coral reef damselfish with different capacities for thermal plasticity. We found that the more thermally tolerant population had greater plasticity of gene expression and had significantly more downregulated genes, which may provide more energy to repair damage associated with thermal stress and to maintain basic functions at these extreme temperatures. In contrast, the thermally sensitive population exhibited higher basal levels of heat shock proteins and had three times fewer changes in gene expression overall. The limited changes in gene regulation suggest that individuals have reduced genome plasticity to tolerate thermal fluctuations and consequently may not have enough energy to repair damage and resume cellular homeostasis at extreme temperatures. Thus, we have identified the molecular signatures of how two genetically distinct fish populations cope with an extreme thermal event, and why they differ in their capacity for thermal plasticity.

Tropical reefs have experienced an unprecedented loss of live coral in the past few decades and the biodiversity of coral-dependent species is under threat. Many reef fish species decline in abundance as coral cover is lost, yet the mechanisms responsible for these losses are largely unknown. A commonly hypothesised cause of fish decline is the loss of shelter space between branches as dead corals become overgrown by algae. Here we tested this hypothesis by quantifying changes in predator-avoidance behaviour of a common damselfish, Pomacentrus moluccensis, before and after the death of their coral colony. Groups of P. moluccensis were placed on either healthy or degraded coral colonies, startled using a visual stimulus and their sheltering responses compared over a 7-week period. P. moluccensis stopped sheltering amongst the coral branches immediately following the death of the coral, despite the presence of ample shelter space. Instead, most individuals swam away from the dead coral, potentially increasing their exposure to predators. It appears that the presence of live coral rather than shelter per se is the necessary cue that elicits the appropriate behavioural response to potential predators. The disruption of this link poses an immediate threat to coral-associated fishes on degrading reefs.

Recent studies show that daily variation in pCO2 levels can modify the life-history and calcification responses of marine organisms to ocean acidification. The early life stages of coral reef fish exhibit varied growth, survival and otolith development responses to elevated pCO2, yet no studies to date have considered the substantial diel pCO2 cycles that occur in shallow reef habitats. Here, we reared three clutches of juvenile Acanthochromis polyacanthus and Amphiprion percula under control (500 µatm), stable, elevated (1000 µatm) and diel cycling, elevated (1000 ± 300 and 1000 ± 500 µatm) pCO2 for 11 and 6 weeks, respectively. Survival was unaffected by exposure to either elevated stable or diel cycling pCO2 conditions in both species. For A. polyacanthus there was a non-significant trend of decreased standard length and wet weight under stable, elevated pCO2 conditions, whereas values in both the diel cycling treatments were closer to those observed under control conditions. A similar non-significant trend was observed for Am. percula, except that exposure to stable, elevated pCO2 conditions resulted in slightly longer and heavier fish. Finally, otolith size, shape and symmetry in both species were unaffected by exposure to either elevated stable or diel cycling pCO2 conditions. Overall, our results suggest that the growth, survival and otolith development of juvenile coral reef fishes under ocean acidification is unlikely to be affected, in isolation, by diel cycles in pCO2.

While there is increasing evidence for habitat specialization in coral reef fishes, the extent to which different corals support different fish communities is not well understood. Here we quantitatively assess the relative importance of different coral species in structuring fish communities and evaluate whether sampling scale and coral colony size affect the perceived strength of fish-habitat relationships. Fish communities present on colonies of eight coral species (Porites cylindrica, Echinopora horrida, Hydnophora rigida, Stylophora pistillata, Seriatopora hystrix, Acropora formosa, A. tenuis and A. millepora) were examined in the Lizard Island lagoon, Great Barrier Reef, Australia. Additionally, the differences in fish communities supported by three coral species (P. cylindrica, E. horrida, H. rigida) were investigated at three spatial scales of sampling (2x2 m, 1x1 m, 0.5x0.5 m). Substantial differences in fish communities were observed across the different coral species, with E. horrida and H. rigida supporting the most fish species and individuals. Coral species explained more of the variability in fish species richness (20.9–53.6%), than in fish abundance (0–15%). Most coral species supported distinctive fish communities, with dissimilarities ranging from 50 to 90%. For three focal coral species, a greater amount of total variation in fish species richness and fish abundance was evident at a larger scale of sampling. Together, these results indicate that the structure of reef fish communities is finely tuned to coral species. Loss of preferred coral species could have profound effects on reef fish biodiversity, potentially more so than would be predicted on the basis of declining coral cover alone.

Increased oceanic uptake of atmospheric carbon dioxide (CO2) is a threat to marine organisms and ecosystems. Among the most dramatic consequences predicted to date are behavioural impairments in marine fish which appear to be caused by the interference of elevated CO2 with a key neurotransmitter receptor in the brain. In this study, we tested the effects of elevated CO2 on the foraging and shelter-seeking behaviours of the reef-dwelling epaulette shark, Hemiscyllium ocellatum. Juvenile sharks were exposed for 30 d to control CO2 (400 µatm) and two elevated CO2 treatments (615 and 910 µatm), consistent with medium- and high-end projections for ocean pCO2 by 2100. Contrary to the effects observed in teleosts and in some other sharks, behaviour of the epaulette shark was unaffected by elevated CO2. A potential explanation is the remarkable adaptation of H. ocellatum to low environmental oxygen conditions (hypoxia) and diel fluctuations in CO2 encountered in their shallow reef habitat. This ability translates into behavioural tolerance of near-future ocean acidification, suggesting that behavioural tolerance and subsequent adaptation to projected future CO2 levels might be possible in some other fish, if adaptation can keep pace with the rate of rising CO2 levels.

Latitudinal gradients in water temperature may be useful for predicting the likely responses of marine species to global warming. The ranges of coral reef fishes extend into the warmest oceanic waters on the planet, but the comparative life-history traits across their full latitudinal range are unknown. Here, we examined differences in early life-history traits of 2 coral reef fishes, the damselfish Pomacentrus moluccensis and the wrasse Halichoeres melanurus, among 8 locations across 21 degrees of latitude, from northern Papua New Guinea (2.3 degrees S) to the southern Great Barrier Reef (23.3 degrees S). Water temperature during larval development ranged between 25.6 and 29.8 degrees C among sites, with the warmest sites closest to the equator. Recently settled juveniles were collected and otolith microstructure was analysed to estimate pelagic larval duration (PLD), daily growth, and size at settlement. Latitudinal comparisons revealed a non-linear relationship between temperature and each of PLD, larval growth and size at settlement. PLD declined with increasing temperature up to approx. 28 to 29 degrees C, above which it stabilised in P. moluccensis and increased in H. melanurus. Larval growth increased with increasing temperature up to approx. 28 to 29 degrees C before stabilising in P. moluccensis and decreasing in H. melanurus. Size at settlement tended to be highest at mid-latitudes, but overall declined with increasing temperature above 28.5 degrees C in both species. These results indicate that the thermal optima for growth and development is reached or surpassed at low latitudes, such that populations at these latitudes may be particularly vulnerable to global warming.

Atmospheric CO2 levels have been increasing at an unprecedented rate due to anthropogenic activity. Consequently, ocean pCO2 is increasing and pH decreasing, affecting marine life, including fish. For many coastal marine fishes, selection of the adult habitat occurs at the end of the pelagic larval phase. Fish larvae use a range of sensory cues, including sound, for locating settlement habitat. This study tested the effect of elevated CO2 on the ability of settlement-stage temperate fish to use auditory cues from adult coastal reef habitats. Wild late larval stages of painted goby (Pomatoschistus pictus) were exposed to control pCO2 (532 μatm, pH 8.06) and high pCO2 (1503 μatm, pH 7.66) conditions, likely to occur in nearshore regions subjected to upwelling events by the end of the century, and tested in an auditory choice chamber for their preference or avoidance to nighttime reef recordings. Fish reared in control pCO2 conditions discriminated reef soundscapes and were attracted by reef recordings. This behaviour changed in fish reared in the high CO2 conditions, with settlement-stage larvae strongly avoiding reef recordings. This study provides evidence that ocean acidification might affect the auditory responses of larval stages of temperate reef fish species, with potentially significant impacts on their survival. Fundação para a Ciência e a Tecnologia (FCT) info:eu-repo/semantics/publishedVersion

The effects of ocean acidification (OA) on the structure and complexity of coastal marine biogenic habitat have been broadly overlooked. Here we explore how declining pH and carbonate saturation may affect the structural complexity of four major biogenic habitats. Our analyses predict that indirect effects driven by OA on habitat-forming organisms could lead to lower species diversity in coral reefs, mussel beds and some macroalgal habitats, but increases in seagrass and other macroalgal habitats. Available in situ data support the prediction of decreased biodiversity in coral reefs, but not the prediction of seagrass bed gains. Thus, OA-driven habitat loss may exacerbate the direct negative effects of OA on coastal biodiversity; however, we lack evidence of the predicted biodiversity increase in systems where habitat-forming species could benefit from acidification. Overall, a combination of direct effects and community-mediated indirect effects will drive changes in the extent and structural complexity of biogenic habitat, which will have important ecosystem effects. How ocean acidification will impact coastal biogenic habitats is unclear. This study predicts that indirect effects on habitat-forming organisms, combined with direct effects on biodiversity, will cause changes in structural complexity and extent of these habitats.

International audience; Pivotal to projecting the fate of coral reefs is the capacity of reef-building corals to acclimatize and adapt to climate change. Transgenerational plasticity may enable some marine organisms to acclimatize over several generations and it has been hypothesized that epigenetic processes and microbial associations might facilitate adaptive responses. However, current evidence is equivocal and understanding of the underlying processes is limited. Here, we discuss prospects for observing transgenerational plasticity in corals and the mechanisms that could enable adaptive plasticity in the coral holobiont, including the potential role of epigenetics and coral-associated microbes. Well-designed and strictly controlled experiments are needed to distinguish transgenerational plasticity from other forms of plasticity, and to elucidate the underlying mechanisms and their relative importance compared with genetic adaptation.

While global extinctions of marine species are infrequent, local extinctions are becoming common. However, the role of habitat degradation and resource specialisation in explaining local extinction is unknown. On coral reefs, coral bleaching is an increasingly frequent cause of coral mortality that can result in dramatic changes to coral community composition. Coral-associated fishes are often specialised on a limited suite of coral species and are therefore sensitive to these changes. This study documents the local extinction of a corallivorous reef fish, Oxymonacanthus longirostris, following a mass bleaching event that altered the species composition of associated coral communities. Local extinction only occurred on reefs that also completely lost a key prey species, Acropora millepora, even though coral cover remained high. In an experimental test, fish continued to select bleached A. millepora over the healthy, but less-preferred prey species that resisted bleaching. These results suggest that behavioural inflexibility may limit the ability of specialists to cope with even subtle changes to resource availability.

Laboratory experiments have shown that the behaviour of reef fishes can be impaired by the CO2 levels projected to occur in the ocean by the end of this century. Research now shows that reef fishes at natural volcanic CO2 seeps also exhibit behavioural abnormalities, and that behaviour does not acclimate with extended exposure to high CO2. Fish communities are therefore likely to face a serious threat from CO2-induced behavioural abnormalities in the future as ocean acidification becomes widespread.

The temperature dependence of aerobic scope has been suggested to be a major determinant of how marine animals will cope with future rises in environmental temperature. Here, we present data suggesting that in some animals, the temperature dependence of anaerobic scope (i.e., the capacity for surviving severe hypoxia) may determine present-day latitudinal distributions and potential for persistence in a warmer future. As a model for investigating the role of anaerobic scope, we studied two sibling species of coral-dwelling gobies, Gobiodon histrio, and G. erythrospilus, with different latitudinal distributions, but which overlap in equal abundance at Lizard Island (14°40'S) on the Great Barrier Reef. These species did not differ in the temperature dependence of resting oxygen consumption or critical oxygen concentration (the lowest oxygen level where resting oxygen consumption can be maintained). In contrast, the more equatorial species (G. histrio) had a better capacity to endure anaerobic conditions at oxygen levels below the critical oxygen concentration at the high temperatures (32-33 °C) more likely to occur near the equator, or in a warmer future. These results suggest that anaerobic scope, in addition to aerobic scope, could be important in determining the impacts of global warming on some marine animals.

Parental effects have been shown to buffer the negative effects of within-generation exposure to ocean acidification (OA) conditions on the offspring of shallow water marine organisms. However, it remains unknown if parental effects will be impacted by the presence of diel CO 2 cycles that are prevalent in many shallow water marine habitats. Here, we examined the effects that parental exposure to stable elevated (1000 µatm) and diel-cycling elevated (1000 ± 300 µatm) CO 2 had on the survival and growth of juvenile coral reef anemonefish, Amphiprion melanopus . Juvenile survival was unaffected by within-generation exposure to either elevated CO 2 treatment but was significantly increased (8%) by parental exposure to diel-cycling elevated CO 2 . Within-generation exposure to stable elevated CO 2 caused a significant reduction in juvenile growth (10.7–18.5%); however, there was no effect of elevated CO 2 on growth when diel CO 2 cycles were present. Parental exposure to stable elevated CO 2 also ameliorated the negative effects of elevated CO 2 on juvenile growth, and parental exposure to diel CO 2 cycles did not alter the effects of diel CO 2 cycles on juveniles. Our results demonstrate that within-generation exposure to diel-cycling elevated CO 2 and parental exposure to stable elevated CO 2 had similar outcomes on juvenile condition. This study illustrates the importance of considering natural CO 2 cycles when predicting the long-term impacts of OA on marine ecosystems.

Equatorial populations of marine species are predicted to be most impacted by global warming because they could be adapted to a narrow range of temperatures in their local environment. We investigated the thermal range at which aerobic metabolic performance is optimum in equatorial populations of coral reef fish in northern Papua New Guinea. Four species of damselfishes and two species of cardinal fishes were held for 14 days at 29, 31, 33, and 34 °C, which incorporated their existing thermal range (29-31 °C) as well as projected increases in ocean surface temperatures of up to 3 °C by the end of this century. Resting and maximum oxygen consumption rates were measured for each species at each temperature and used to calculate the thermal reaction norm of aerobic scope. Our results indicate that one of the six species, Chromis atripectoralis, is already living above its thermal optimum of 29 °C. The other five species appeared to be living close to their thermal optima (ca. 31 °C). Aerobic scope was significantly reduced in all species, and approached zero for two species at 3 °C above current-day temperatures. One species was unable to survive even short-term exposure to 34 °C. Our results indicate that low-latitude reef fish populations are living close to their thermal optima and may be more sensitive to ocean warming than higher-latitude populations. Even relatively small temperature increases (2-3 °C) could result in population declines and potentially redistribution of equatorial species to higher latitudes if adaptation cannot keep pace.

Habitat degradation often results in resident displacement. One potentially important determinant of the lethality of such displacement is the nature of interactions between displaced individuals and the occupants of nearby, intact habitat. Here, we show that displaced individuals of the coral-dwelling fish Dascyllus aruanus have very low potential to join a new group due to targeted and cooperative aggression by conspecific resident group members. Residents were found to be relatively non-aggressive towards familiar displaced individuals seeking group re-entry but highly aggressive towards displaced unfamiliar prospective group members. The extent of individual resident aggression towards unfamiliar individuals correlated with group-based dominance rank, resident-to-intruder size similarity, and social group size, such that higher ranking resident group members disproportionately contributed to intruder defence. Subsequent group re-entry by displaced familiar individuals was observed 100% of the time, compared to an 18% group entry success rate for displaced unfamiliar individuals. Results indicate that pre-existing social bonds and associated cooperative aggression can generate greater habitat-disturbance lethality for displaced inhabitants than that predicted by mobility potential and alternative habitat availability alone. This implies that social group entry rules may be an important determinant of population resilience to patchy habitat disturbance.

Coral reef ecosystems are experiencing a global decline in coral cover, with direct effects on reef fishes. A decline in habitat may lead to crowding of live coral specialists into remnant habitat patches, intensifying intraspecific competition. Increased local densities of conspecifics are known to negatively affect key demographic processes, but the magnitude of density effects and the role of crowding in response to habitat loss are poorly understood. In this study we examined habitat use and relationships between habitat availability and population density in a coral-dwelling damselfish — Chrysiptera parasema. First, we conducted habitat use and availability surveys to establish the level of habitat selectivity. We then investigated the evidence for crowding due to habitat loss by comparing densities within juvenile aggregations on natural reefs with high and low cover of the preferred habitat. Finally, we used a manipulative patch-reef experiment to measure the potential effects of crowding on mortality of juvenile C. parasema. Surveys revealed that 97% of juvenile C. parasema were associated with Acropora corals. Furthermore, C. parasema densities were closely related to the cover of bottlebrush Acropora, the preferred growth form. Contrary to predictions, there was no evidence of crowding on natural reefs with low coral cover, but rather, reefs with abundant Acropora cover supported larger aggregations with double the density of juveniles. We hypothesized that low densities of C. parasema on natural reefs with low coral cover could be explained by intense intraspecific competition. Experimental manipulations showed that juvenile mortality was density-dependent, with mortality 20% higher on high-density experimental patch-reefs compared to low-density reefs. Behavioural observations on the patch-reefs revealed that the frequency of agonistic interactions and distance to shelter were both unrelated to conspecific densities, highlighting the need for further research into mechanisms underpinning density dependent mortality. These results suggest that intraspecific competition may play an important role in reducing reef fish abundance as a consequence of habitat loss. Given that coral reef systems are currently under threat, with a global decline in coral cover, this study adds to the growing body of knowledge of how disturbances to habitat may affect reef fish communities.

Biological impacts of ocean acidification have mostly been studied using future levels of CO without consideration of natural variability or how this modulates both duration and magnitude of CO exposure. Here we combine results from laboratory studies on coral reef fish with diurnal in situ CO data from a shallow coral reef, to demonstrate how natural variability alters exposure times for marine organisms under increasingly high-CO conditions. Large in situ CO variability already results in exposure of coral reef fish to short-term CO levels higher than laboratory-derived critical CO levels (∼600 μatm). However, we suggest that the in situ exposure time is presently insufficient to induce negative effects observed in laboratory studies. Our results suggest that both exposure time and the magnitude of CO levels will be important in determining the response of organisms to future ocean acidification, where both will increase markedly with future increases in CO. Key Points Seawater CO2 variability alters in situ CO2 exposure time and magnitude Fish are presently exposed to short-term CO2 levels above critical values Acidification experiments should consider both CO2 level and exposure times

Many animals preferentially select a habitat from a range of those potentially available. However, the consequences of these preferences for distribution and abundance, and the underlying basis of habitat preferences are often unknown. The present study, conducted at Great Keppel Island, Australia, examined how distribution and abundance of an obligate corallivorous filefish, Oxymonacanthus longirostris, relates to coral architecture and diversity. The main drivers of the distribution and abundance of O. longirostris among reefs were coral species richness and availability of branching coral. Feeding territories had a higher percentage of Acropora coral than surrounding habitat. In addition, feeding territories had a higher percentage of the structurally important branching coral, Acropora nobilis, and a primary prey species, Acropora millepora. A series of pair-wise choice experiments in which both structural complexity and coral tissue quality were independently manipulated showed that habitat choice was primarily based on structural complexity and shelter characteristics. In addition, the choice for the preferred coral (A. nobilis) was stronger in the presence of a piscivorous fish. These results indicate that species-diverse coral habitats, which provide sufficient structural complexity along with nutritionally important prey, are essential for population persistence of this small, corallivorous reef fish.

In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic diversity. Analyses of a 436 base pair fragment of the mtDNA control region revealed that the endemic C. joculator exhibited high haplotype (h > 0.98 at both locations) and nucleotide (Christmas p% = 3.63, Cocos p% = 9.99) diversity. Similarly, isolated populations of widespread angelfishes (C. bispinosa and C. flavicauda) had high haplotype (h > 0.98) and nucleotide (p% = 2.81 and p% = 5.78%, respectively) diversity. Therefore, in contrast to terrestrial patterns, endemic and isolated populations of widespread angelfishes do not have low genetic diversity, rather their haplotype and nucleotide diversities were among the highest reported for marine fishes. High genetic diversity should reduce extinction risk in these species as it could provide the evolutionary potential to adapt to the rapidly changing environmental conditions forecast for coral reefs.

We tested the effect of near-future CO2 levels (a parts per thousand 490, 570, 700, and 960 mu atm CO2) on the olfactory responses and activity levels of juvenile coral trout, Plectropomus leopardus, a piscivorous reef fish that is also one of the most important fisheries species on the Great Barrier Reef, Australia. Juvenile coral trout reared for 4 weeks at 570 mu atm CO2 exhibited similar sensory responses and behaviors to juveniles reared at 490 mu atm CO2 (control). In contrast, juveniles reared at 700 and 960 mu atm CO2 exhibited dramatically altered sensory function and behaviors. At these higher CO2 concentrations, juveniles became attracted to the odor of potential predators, as has been observed in other reef fishes. They were more active, spent less time in shelter, ventured further from shelter, and were bolder than fish reared at 490 or 570 mu atm CO2. These results demonstrate that behavioral impairment of coral trout is unlikely if pCO(2) remains below 600 mu atm; however, at higher levels, there are significant impacts on juvenile performance that are likely to affect survival and energy budgets, with consequences for predator-prey interactions and commercial fisheries.

Neurosensory and behavioural disruptions are some of the most consistently reported responses upon exposure to ocean acidification-relevant CO2 levels, especially in coral reef fishes. The underlying cause of these disruptions is thought to be altered current across the GABAA receptor in neuronal cells due to changes in ion gradients (HCO3− and/or Cl−) that occur in the body following compensation for elevated ambient CO2. Despite these widely-documented behavioural disruptions, the present study is the first to pair a behavioural assay with measurements of relevant intracellular and extracellular acid-base parameters in a coral reef fish exposed to elevated CO2. Spiny damselfish (Acanthochromis polyacanthus) exposed to 1900 μatm CO2 for 4 days exhibited significantly increased intracellular and extracellular HCO3− concentrations and elevated brain pHi compared to control fish, providing evidence of CO2 compensation. As expected, high CO2 exposed damselfish spent significantly more time in a chemical alarm cue (CAC) than control fish, supporting a potential link between behavioural disruption and CO2 compensation. Using HCO3− measurements from the damselfish, the reversal potential for GABAA (EGABA) was calculated, illustrating that biophysical properties of the brain during CO2 compensation could change GABAA receptor function and account for the behavioural disturbances noted during exposure to elevated CO2.

Exposure to pollution and environmental change can alter the behaviour of aquatic animals and here we review recent evidence that exposure to elevated CO₂ and reduced sea water pH alters the behaviour of tropical reef fish and hermit crabs. Three main routes through which behaviour might be altered are discussed; elevated metabolic load, 'info-disruption' and avoidance behaviour away from polluted locations. There is clear experimental evidence that exposure to high CO₂ disrupts the ability to find settlement sites and shelters, the ability to detect predators and the ability to detect prey and food. In marine vertebrates and marine crustaceans behavioural change appears to occur via info-disruption. In hermit crabs and other crustaceans impairment of performance capacities might also play a role. We discuss the implications for such behavioural changes in terms of potential impacts at the levels of population health and ecosystem services, and consider future directions for research.

While it is generally assumed that specialist species are more vulnerable to disturbance compared with generalist counterparts, this has rarely been tested in coastal marine ecosystems, which are increasingly subject to a wide range of natural and anthropogenic disturbances. Habitat specialists are expected to be more vulnerable to habitat loss because habitat availability exerts a greater limitation on population size, but it is also possible that specialist species may escape effects of disturbance if they use habitats that are generally resilient to disturbance. This study quantified specificity in use of different coral species by six coral-dwelling damselfishes (Chromis viridis, C. atripectoralis, Dascyllus aruanus, D. reticulatus, Pomacentrus moluccensis, and P. amboinensis) and related habitat specialization to proportional declines in their abundance following habitat degradation caused by outbreaks of the coral eating starfish, Acanthaster planci. The coral species preferred by most coral-dwelling damselfishes (e.g., Pocillopora damicornis) were frequently consumed by coral eating crown-of-thorns starfish, such that highly specialized damselfishes were disproportionately affected by coral depletion, despite using a narrower range of different coral species. Vulnerability of damselfishes to this disturbance was strongly correlated with both their reliance on corals and their degree of habitat specialization. Ongoing disturbances to coral reef ecosystems are expected, therefore, to lead to fundamental shifts in the community structure of fish communities where generalists are favored over highly specialist species.

Changes in coral health may have significant impacts on fishes that shelter within live coral habitats. However, disturbances can be spatially patchy and it is unclear whether fishes subject to degradation of their immediate habitat are able to move and exploit alternative nearby healthy habitat patches. This study experimentally investigated the response of a common coral-dwelling damselfish (Dascyllus aruanus) to bleaching and mortality of host coral colonies. Three factors were considered that may influence the initiation and success of movement among habitat patches; i) condition of the host colony, ii) the availability of preferred habitat, and iii) the presence of conspecifics on alternative coral habitat. D. aruanus remained associated with bleached coral colonies and only moved to alternate habitats once the host coral died. On colonies that suffered complete mortality, 67% of associated fish vacated and migrated to healthy coral colonies. The remaining individuals persisted on dead colonies as a result of competition from aggressive resident fish on neighbouring healthy colonies, but relocated once offered an alternative colony without any competitive resident fish. When relocating in degraded reefs, 64% of the fish were successful in migrating to alternative healthy habitats. For these fish the selection of new habitat was based mostly on the presence of conspecifics, with 91% of fish relocating to healthy coral colonies containing conspecifics. The importance of conspecifics presence was further demonstrated by tank experiments where fish selected to associate with habitat containing conspecifics over unoccupied dead or healthy habitat. Movement of coral-dwelling fishes following disturbances will allow individuals to mediate the impact of host coral degradation by relocating to more suitable habitats. However, the potential for relocation will decline as disturbances become more severe and widespread, thereby increasing the distance to suitable habitats and reducing the availability of preferred habitat types. Furthermore, increased densities within habitat patches may increase competitive effects, with potential consequences for growth, survival and reproductive success.

1. With the global increase in CO2 emissions, there is a pressing need for studies aimed at understanding the effects of ocean acidification on marine ecosystems. Several studies have reported that exposure to CO2 impairs chemosensory responses of juvenile coral reef fishes to predators. Moreover, one recent study pointed to impaired responses of reef fish to auditory cues that indicate risky locations. These studies suggest that altered behaviour following exposure to elevated CO2 is caused by a systemic effect at the neural level. 2. The goal of our experiment was to test whether juvenile damselfish Pomacentrus amboinensis exposed to different levels of CO2 would respond differently to a potential threat, the sight of a large novel coral reef fish, a spiny chromis, Acanthochromis polyancanthus, placed in a watertight bag. 3. Juvenile damselfish exposed to 440 (current day control), 550 or 700 μatm CO2 did not differ in their response to the chromis. However, fish exposed to 850 μatm showed reduced antipredator responses; they failed to show the same reduction in foraging, activity and area use in response to the chromis. Moreover, they moved closer to the chromis and lacked any bobbing behaviour typically displayed by juvenile damselfishes in threatening situations. 4. Our results are the first to suggest that response to visual cues of risk may be impaired by CO2 and provide strong evidence that the multi-sensory effects of CO2 may stem from systematic effects at the neural level.

Predicted future CO2 levels can affect reproduction, growth, and behaviour of many marine organisms. However, the capacity of species to adapt to predicted changes in ocean chemistry is largely unknown. We used a unique field-based experiment to test for differential survival associated with variation in CO2 tolerance in a wild population of coral-reef fishes. Juvenile damselfish exhibited variation in their response to elevated (700 μatm) CO2 when tested in the laboratory and this influenced their behaviour and risk of mortality in the wild. Individuals that were sensitive to elevated CO2 were more active and move further from shelter in natural coral reef habitat and, as a result, mortality from predation was significantly higher compared with individuals from the same treatment that were tolerant of elevated CO2. If individual variation in CO2 tolerance is heritable, this selection of phenotypes tolerant to elevated CO2 could potentially help mitigate the effects of ocean acidification.

Two of the major threats to coral reefs are increasing sea surface temperature and ocean acidification, both of which result from rising concentrations of atmospheric carbon dioxide (CO2). Recent evidence suggests that both increased water temperature and elevated levels of dissolved CO2 can change the behaviors of fishes in ways that reduce individual fitness, however the interacting effects of these variables are unknown. We used a fully factorial experiment to test the independent and interactive effects of temperature (3 levels: 28.5, 30, and 31.5 °C) and pCO2 (3 levels: averaging 420, 530, and 960 μatm) on food consumption and activity level of juvenile anemonefish Amphiprion melanopus (Bleeker 1852). Experimental levels were consistent with current-day ocean conditions and predictions for mid-century and late-century based on atmospheric CO2 projections. Sibling fish were reared for 21 days from the end of their larval phase in each of the nine treatments, at which time behavioral observations were conducted. Food consumption and foraging activity decreased at the highest temperature. In isolation, CO2 level did not significantly affect behavior; however, there was an interaction with temperature. While rearing at high temperature (31.5 °C) and control (420 μatm) or moderate (530 μatm) CO2 resulted in a reduction of food consumption and foraging activity, rearing at high temperature and high CO2 (960 μatm) resulted in an elevation in these behaviors. Maintaining food consumption and foraging activity in high temperature and CO2 conditions may reduce energy efficiency if the thermal optimum for food assimilation and growth has been exceeded. Maintaining foraging effort might increase predation vulnerability. These results suggest that changes in foraging behaviors caused by the interactive effects of increased SST and CO2 could have significant effects on the growth and survival of juvenile reef fishes by late century.

Increased habitat diversity is often predicted to promote the diversity of animal communities because a greater variety of habitats increases the opportunities for species to specialize on different resources and coexist. Although positive correlations between the diversities of habitat and associated animals are often observed, the underlying mechanisms are only now starting to emerge, and none have been tested specifically in the marine environment. Scleractinian corals constitute the primary habitat-forming organisms on coral reefs and, as such, play an important role in structuring associated reef fish communities. Using the same field experimental design in two geographic localities differing in regional fish species composition, we tested the effects of coral species richness and composition on the diversity, abundance, and structure of the local fish community. Richness of coral species overall had a positive effect on fish species richness but had no effect on total fish abundance or evenness. At both localities, certain individual coral species supported similar levels of fish diversity and abundance as the high coral richness treatments, suggesting that particular coral species are disproportionately important in promoting high local fish diversity. Furthermore, in both localities, different microhabitats (coral species) supported very different fish communities, indicating that most reef fish species distinguish habitat at the level of coral species. Fish communities colonizing treatments of higher coral species richness represented a combination of those inhabiting the constituent coral species. These findings suggest that mechanisms underlying habitat-animal interaction in the terrestrial environment also apply to marine systems and highlight the importance of coral diversity to local fish diversity. The loss of particular key coral species is likely to have a disproportionate impact on the biodiversity of associated fish communities.

Understanding the degree of connectivity between coastal and island landscapes and nearby coral reefs is vital to the integrated management of terrestrial and marine environments in the tropics. Coral reef fish are capable of navigating appropriate settlement habitats following their pelagic larval phase, but the mechanisms by which they do this are unclear. The importance of olfactory cues in settlement site selection has been demonstrated, and there is increasing evidence that chemical cues from terrestrial sources may be important for some species. Here, we test the olfactory preferences of eight island-associated coral reef fish recruits and one generalist species to discern the capacity for terrestrial cue recognition that may aid in settlement site selection. A series of pairwise choice experiments were used to evaluate the potential role that terrestrial, water-borne olfactory cues play in island–reef recognition. Olfactory stimuli tested included near-shore water, terrestrial rainforest leaf litter, and olfactory cues collected from different reef types (reefs surrounding vegetated islands, and reefs with no islands present). All eight island-associated species demonstrated high levels of olfactory discrimination and responded positively toward olfactory cues indicating the presence of a vegetated island. We hypothesize that although these fish use a suite of cues for settlement site recognition, one mechanism in locating their island/reef habitat is through the olfactory cues produced by vegetated islands. This research highlights the role terrestrial olfactory cues play in large-scale settlement site selection and suggests a high degree of ecosystem connectivity.