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Australian Research Council; Lizard Island Reef Research Foundation, Grant/Award Number: Lizard Island Doctoral Fellowships to RAM and CJF; James Cook Univeristy, Grant/Award Number: James Cook University Postgraduate Research Schola

Coral reef ecosystems are at the forefront of biodiversity loss and climate change-mediated transformations. This is expected to have profound consequences for the functioning of these ecosystems. However, assessments of ecosystem function on reefs are often spatially limited, within biogeographic realms, or rely on presumed proxies such as traits. To address these shortcomings and assess the effects of biogeography and fish presence on the critical ecosystem function of macroalgal removal, we used assays of six algal genera across three reef habitats in two biogeographically distinct locations: Little Cayman in the Caribbean and Lizard Island on the Great Barrier Reef (GBR). Patterns of fish feeding and realised ecosystem function were strikingly similar between the two geographic locations, despite a threefold difference in the local diversity of nominally herbivorous fishes, a 2.4-fold difference in the diversity of fishes feeding and differences in the biogeographic history of the two locations. In both regions, a single species dominated the function: a surgeonfish, Naso unicornis, at the GBR location and, surprisingly, a triggerfish, Melichthys niger, at the Caribbean location. Both species, especially M. niger, were relatively rare, compared to other nominally herbivorous fishes, in censuses covering more than 14,000 m2 at each location. Our study provides novel insights into the critical function of macroalgal removal in hyperdiverse coral reef ecosystems, highlighting: (a) that function can transcend biogeographic, taxonomic and historical constraints; and (b) shortcomings in our assumptions regarding fish presence and realised ecosystem function on coral reefs.

International audience; Few studies assess the effects of recreational fishing in isolation from commercial fishing. We used meta-analysis to synthesise 4444 samples from 30 years (1987–2017) of fish surveys inside and outside a large network of highly protected reserves in the Ningaloo Marine Park, Western Australia, where the major fishing activity is recreational. Data were collected by different agencies, using varied survey designs and sampling methods. We contrasted the relative abundance and biomass of target and non-target fish groups between fished and reserve locations. We considered the influence of, and possible interactions between, seven additional variables: age and size of reserve, one of two reserve network configurations, reef habitat type, recreational fishing activity, shore-based fishing regulations and survey method. Taxa responded differently: the abundance and biomass inside reserves relative to outside was higher for targeted lethrinids, while other targeted (and non-targeted) fish groups were indistinguishable. Reef habitat was important for explaining lethrinid response to protection, and this factor interacted with reserve size, such that larger reserves were demonstrably more effective in the back reef and lagoon habitats. There was little evidence of changes in relative abundance and biomass of fishes with reserve age, or after rezoning and expansion of the reserve network. Our study demonstrates the complexities in quantifying fishing effects, highlighting some of the key factors and interactions that likely underlie the varied results in reserve assessments that should be considered in future reserve design and assessment.

Western Australia’s coral reefs have largely escaped the chronic pressures affecting other reefs around the world, but are regularly affected by seasonal storms and cyclones, and increasingly by heat stress and coral bleaching. Reef systems north of 18°S have been impacted by heat stress and coral bleaching during strong El Nino phases and those further south during strong La Nina phases. Cumulative heat stress and the extent of bleaching throughout the northern reefs in 2016 were higher than at any other time on record. To assess the changing regime of disturbance to reef systems across Western Australia (WA), we linked their site-specific exposure to damaging waves and heat stress since 1990 with mean changes in coral cover. Since 2010, there has been a noticeable increase in heat stress and coral bleaching across WA. Over half the reef systems have been severely impacted by coral bleaching since 2010, which was further compounded by cyclones at some reefs. For most (75%) reef systems with long-term data (5–26 yrs), mean coral cover is currently at (or near) the lowest on record and a full recovery is unlikely if disturbances continue to intensify with climate change. However, some reefs have not yet experienced severe bleaching and their coral cover has remained relatively stable or increased in recent years. Additionally, within all reef systems the condition of communities and their exposure to disturbances varied spatially. Identifying the communities least susceptible to future disturbances and linking them through networks of protected areas, based on patterns of larval connectivity, are important research and management priorities in coming years while the causes of climate change are addressed.

In 2016 we reported evidence for associative learning in plants (Gagliano et al., 2016). In view of the far-reaching implications of this finding we welcome the attempt made by Markel to replicate our study (Markel, 2020). However, as we discuss here, the protocol employed by Markel was unsuitable for testing for associative learning.

Canopy-forming macroalgae can construct extensive meadow habitats in tropical seascapes occupied by fishes that span a diversity of taxa, life-history stages and ecological roles. Our synthesis assessed whether these tropical macroalgal habitats have unique fish assemblages, provide fish nurseries and support local fisheries. We also applied a meta-analysis of independent surveys across 23 tropical reef locations in 11 countries to examine how macroalgal canopy condition is related to the abundance of macroalgal-associated fishes. Over 627 fish species were documented in tropical macroalgal meadows, with 218 of these taxa exhibiting higher local abundance within this habitat (cf. nearby coral reef) during at least one life-history stage. Major overlap (40%-43%) in local fish species richness among macroalgal and seagrass or coral reef habitats suggest macroalgal meadows may provide an important habitat refuge. Moreover, the prominence of juvenile fishes suggests macroalgal meadows facilitate the triphasic life cycle of many fishes occupying diverse tropical seascapes. Correlations between macroalgal canopy structure and juvenile abundance suggests macroalgal habitat condition can influence levels of replenishment in tropical fish populations, including the majority of macroalgal-associated fishes that are targeted by commercial, subsistence or recreational fisheries. While many macroalgal-associated fishery species are of minor commercial value, their local importance for food and livelihood security can be substantial (e.g. up to 60% of landings in Kenyan reef fisheries). Given that macroalgal canopy condition can vary substantially with sea temperature, there is a high likelihood that climate change will impact macroalgal-associated fish and fisheries.

This research is supported by an Australian Government Research Training Program (RTP) Scholarship, as well as with funding provided by the Linnean Society of New South Wales. We also wish to thank Kelsey Sanborn for assistance in the field.

Submerged reef ecosystems can be very diverse and may serve as important refugia for shallow-water conspecifics. This study quantified the benthic and fish communities of two proximate, predominantly mesophotic coral ecosystems (MCEs), Glomar Shoal and Rankin Bank, which are geographically isolated from other similar features in the region. Glomar Shoal is identified as a key ecological feature (KEF) in the North West Marine Region of Australia. Multibeam surveys were performed to characterise the seafloor and to derive secondary environmental variables, used to explain patterns in benthic and fish communities. Towed video surveys quantified benthic cover, and stereo baited remote underwater stations were used to survey fish abundance and diversity. Surveys were completed in depths of ~ 20–115 m. The two MCEs exhibited distinct communities; Rankin Bank consistently had higher cover (up to 30×) of benthic taxa across depths, and fish communities that were twice as abundant and 1.5× more diverse than Glomar Shoal. The location of the MCEs, depth and rugosity were most influential in structuring benthic communities. Phototrophic taxa, specifically macroalgae and hard corals, had up to 22 × higher cover at Rankin Bank than at Glomar Shoal and were dominant to 80 m (compared to 60 m at Glomar Shoal), presumably due to greater light penetration (lower turbidity) and lower sand cover at greater depths. The 20% coral cover at Rankin Bank was comparable to that reported for shallow reefs. The cover of sand, hard corals and sponges influenced fish communities, with higher abundance and diversity of fish associated with shallow hard coral habitats. This study demonstrated that the two MCEs were unique within the local context, and when coupled with their geographical isolation and biodiversity, presents compelling support for the additional recognition of Rankin Bank as a KEF.

Because water is essential to life, organisms have evolved a wide range of strategies to cope with water limitations, including actively searching for their preferred moisture levels to avoid dehydration. Plants use moisture gradients to direct their roots through the soil once a water source is detected, but how they first detect the source is unknown. We used the model plant Pisum sativum to investigate the mechanism by which roots sense and locate water. We found that roots were able to locate a water source by sensing the vibrations generated by water moving inside pipes, even in the absence of substrate moisture. When both moisture and acoustic cues were available, roots preferentially used moisture in the soil over acoustic vibrations, suggesting that acoustic gradients enable roots to broadly detect a water source at a distance, while moisture gradients help them to reach their target more accurately. Our results also showed that the presence of noise affected the abilities of roots to perceive and respond correctly to the surrounding soundscape. These findings highlight the urgent need to better understand the ecological role of sound and the consequences of acoustic pollution for plant as well as animal populations.

Dredging can have significant impacts on aquatic environments, but the direct effects on fish have not been critically evaluated. Here, a meta-analysis following a conservative approach is used to understand how dredging-related stressors, including suspended sediment, contaminated sediment, hydraulic entrainment and underwater noise, directly influence the effect size and the response elicited in fish across all aquatic ecosystems and all life-history stages. This is followed by an in-depth review summarizing the effects of each dredging-related stressor on fish. Across all dredging-related stressors, studies that reported fish mortality had significantly higher effect sizes than those that describe physiological responses, although indicators of dredge impacts should endeavour to detect effects before excessive mortality occurs. Studies examining the effects of contaminated sediment also had significantly higher effect sizes than studies on clean sediment alone or noise, suggesting additive or synergistic impacts from dredging-related stressors. The early life stages such as eggs and larvae were most likely to suffer lethal impacts, while behavioural effects were more likely to occur in adult catadromous fishes. Both suspended sediment concentration and duration of exposure greatly influenced the type of fish response observed, with both higher concentrations and longer exposure durations associated with fish mortality. The review highlights the need for in situ studies on the effects of dredging on fish which consider the interactive effects of multiple dredging-related stressors and their impact on sensitive species of ecological and fisheries value. This information will improve the management of dredging projects and ultimately minimize their impacts on fish.

Identifying and protecting nursery habitats for species is a key conservation strategy for the long-term sustainability of populations. In tropical ecosystems, macroalgal habitats have recently been identified as nurseries for fish of commercial and conservation significance. Here, we explore how local-scale variations in seaweed habitat quality interact with large-scale climatic conditions (Southern Oscillation Index, SOI) to influence the recruitment of three tropical fish species (Lethrinus spp.), often targeted by fishers. New fish recruits and juveniles of all species were almost exclusively found in macroalgal nursery habitats, while adults of two of these species were predominantly found on adjacent coral reefs. Annual supply rates of new recruits were found to be strongly correlated to variations in the SOI, with La Nina conditions associated with higher recruitment. However, local rates of recruitment were generally poor predictors of older juvenile abundance. Instead, local juvenile abundance was more closely related to structural characteristics of macroalgae nursery habitat quality (density, canopy height, canopy cover) and/or predator biomass, at the time of survey, with species-specific habitat associations apparent. Given the dynamic nature of fish recruitment supply to the SOI, coupled with the effects of climatic and oceanic processes on the structure of macroalgal patches, these results suggest protection of macroalgal nursery habitats that maintain high canopy density, height and cover is critical to supporting the conservation of fish populations.

Tropical cyclones generate extreme waves that can damage coral reef communities. Recovery typically requires up to a decade, driving the trajectory of coral community structure. Coral reefs have evolved over millennia with cyclones. Increasingly, however, processes of recovery are interrupted and compromised by additional pressures (thermal stress, pollution, diseases, predators). Understanding how cyclones interact with other pressures to threaten coral reefs underpins spatial prioritization of conservation and management interventions. Models that simulate coral responses to cumulative pressures often assume that the worst cyclone wave damage occurs within ~100 km of the track. However, we show major coral loss at exposed sites up to 800 km from a cyclone that was both strong (high sustained wind speeds=33 m/s) and big (widespread circulation~300 km), using numerical wave models and field data from northwest Australia. We then calculate the return time of big and strong cyclones, big cyclones of any strength and strong cyclones of any size, for each of 150 coral reef ecoregions using a global data set of past cyclones from 1985 to 2015. For the coral ecoregions that regularly were exposed to cyclones during that time, we find that 75% of them were exposed to at least one cyclone that was both big and strong. Return intervals of big and strong cyclones are already less than 5 years for 13 ecoregions, primarily in the cyclone-prone NW Pacific, and less than 10 years for an additional 14 ecoregions. We identify ecoregions likely at higher risk in future given projected changes in cyclone activity. Robust quantification of the spatial distribution of likely cyclone wave damage is vital not only for understanding past coral response to pressures, but also for predicting how this may change as the climate continues to warm and the relative frequency of the strongest cyclones rises.

Coral reefs have been heavily affected by elevated sea-surface temperature (SST) and coral bleaching since the late 1980s; however, until recently coastal reefs of north-western Australia have been relatively unaffected compared to Timor Sea and eastern Australian reefs. We compare SST time series with changes in coral cover spanning a period of up to 36 years to describe temporal and spatial variability in bleaching and associated coral mortality throughout the Pilbara–Ningaloo region. Declines in coral cover ranged from 12.5 to 51.3%, with relative declines ranging from 38 to 92%. Since 2013, coral cover throughout the region has declined to historically low levels at four of five subregions, with impaired recovery occurring at two subregions. Observations are consistent with global trends of repeated severe heat waves, coral bleaching and acute declines in coral cover. Locations within this study region have already experienced multiple coral-bleaching events within a period of less than 5 years. There is a high likelihood that reefs in the western Pilbara and northern Ningaloo regions will experience more frequent marine heatwaves, coral bleaching and mortality events in the future. Action, therefore, needs to be taken now to support the resilience of coral reef ecosystems in the region, which is arguably the most important coral-reef province on Australia’s western coast.

Understanding the dynamics of juvenile fish populations is a key component to understanding variation in adult populations, however, juvenile fish are frequently found in a variety of structurally complex habitats which are often not easily sampled. The use of baited (BRUV) and unbaited (RUV) remote underwater stereo-video to study juvenile fish populations is uncommon and thus far, no study has directly compared the efficacy of these two methods solely for juvenile fish assemblages. The macro-tidal Kimberley region in the north-west of Australia is challenging to sample using diver-based methods due to the strong currents and prevalence of saltwater crocodiles (Crocodylus porosus). We sampled 60 Stereo-RUVs and 60 Stereo-BRUVs across four shallow-water (1-6 m) benthic habitats: coral, mangrove, macroalgae, and seagrass, to contrast the effect of the presence or absence of bait, deployment period, in-water visibility and tidally driven water speed on estimates of relative total abundance, species richness, and composition of the juvenile fish assemblage. No difference was detected in the ability of stereo-BRUV or stereo-RUV to quantify the relative total abundance, species richness, or assemblage composition of juvenile fish. We also found little effect of in-water visibility or tidally driven water speed, likely as a result of stratifying our sampling to slack water periods. We found that a deployment period of 10 min for Stereo-BRUVs and 15 min for Stereo-RUVs was optimum for sampling the juvenile fish assemblage across all four contrasting habitats. Since no statistical significance was observed between 10 and 15 min, we recommend that Stereo-RUVs deployed for 15 min during tidal slack water conditions are an optimum way to provide consistent results for comparisons of juvenile fish assemblage metrics across the benthic habitats studied within this region. The controlled video methodologies described here provided an opportunity to access un-sampled juvenile fish habitats and assemblages where traditional diver-based methodologies are impossible. Applying these methods broadly can help to improve our understanding of the status of juvenile fish and infer the reproductive success and viability of their populations across a range of habitat and environments.

Tropical reefs have been subjected to a range of anthropogenic pressures such as global climate change, overfishing and eutrophication that have raised questions about the prominence of macroalgae on tropical reefs, whether they pose a threat to biodiversity, and how they may influence the function of tropical marine ecosystems. We synthesise current understanding of the structure and function of tropical macroalgal reefs and how they may support various ecosystem goods and services. We then forecast how key stressors may alter the role of macroalgal reefs in tropical seascapes of the Anthropocene. High levels of primary productivity from tropical canopy macroalgae, which rivals that of other key producers (e.g., corals and turf algae), can be widely dispersed across tropical seascapes to provide a boost of secondary productivity in a range of biomes that include coral reefs, and support periodic harvests of macroalgal biomass for industrial and agricultural uses. Complex macroalgal reefs that comprise a mixture of canopy and understorey taxa can also provide key habitats for a diverse community of epifauna, as well as juvenile and adult fishes that are the basis for important tropical fisheries. Key macroalgal taxa (e.g., Sargassum) that form complex macroalgal reefs are likely to be sensitive to future climate change. Increases in maximum sea temperature, in particular, could depress biomass production and/or drive phenological shifts in canopy formation that will affect their capacity to support tropical marine ecosystems. Macroalgal reefs can support a suite of tropical marine ecosystem functions when embedded within an interconnected mosaic of habitat types. Habitat connectivity is, therefore, essential if we are to maintain tropical marine biodiversity alongside key ecosystem goods and services. Consequently, complex macroalgal reefs should be treated as a key ecological asset in strategies for the conservation and management of diverse tropical seascapes. A plain language summary is available for this article.

Within the complex food webs that occur on coral reefs, mesopredatory fish consume small-bodied prey and transfer accumulated biomass to other trophic levels. We estimated biomass, growth and mortality rates of three common mesopredators from Ningaloo Reef in Western Australia to calculate their annual turnover rates and potential contribution to local trophic dynamics. Biomass estimates of the serranid Epinephelus rivulatus (4.46 ± 0.76 g m−2) were an order of magnitude greater than two smaller-bodied mesopredatory fishes, Pseudochromis fuscus (0.10 ± 0.03 g m−2) and Parapercis clathrata (0.23 ± 0.31 g m−2). Growth parameters generated from a von Bertalanffy growth function fitted to size-at-age data, however, indicated that mortality rates for the three mesopredators were similar and that 32–55 % of fish survived each year. Consequently, interspecific differences in annual turnover rates among E. rivulatus (1.9 g m−2 yr−1), Pa. clathrata (0.10 g m−2 yr−1) and Ps. fuscus (0.07 g m−2 yr−1) were an artefact of differences in local biomass estimates. The rapid turnover estimates for E. rivulatus suggest this species is an important conduit of energy within the isolated patch reef habitat where it is typically found, while Ps. fuscus and Pa. clathrata channel smaller amounts of energy from specific habitats in the Ningaloo lagoon. Apparent differences in habitat, diet and turnover rates of the three species examined provide an insight into the different roles these species play in coral reef food webs and suggest that life-history traits allow for variability in the local and spatial contribution of these species at Ningaloo Reef. Moreover, calculating turnover rates of a broader suite of fish species from a range of trophic groups will help better define the role of fishes in coral reef trophic dynamics.

We thank staff at the Department of Parks and Wildlife Exmouth for field support, AIMS 2013 Appropriation funding 3.3.5 and the Australian Research Council for financial support.

The diets of four common mesopredator fishes were examined in the back-reef habitat of a subtropical fringing reef system during the summer months. Quantitative gut content analyses revealed that crustaceans, represented >60% of ingested prey (% mass) by the latticed sand-perch Parapercis clathrata, brown dottyback Pseudochromis fuscus and half-moon grouper Epinephelus rivulatus. Dietary analyses also provided insights into ontogenetic shifts. Juvenile P. fuscus ingested large numbers of crustaceans (amphipods and isopods); these small prey were rarely found in larger individuals (

The nervous system of animals serves the acquisition, memorization and recollection of information. Like animals, plants also acquire a huge amount of information from their environment, yet their capacity to memorize and organize learned behavioral responses has not been demonstrated. In Mimosa pudica-the sensitive plant-the defensive leaf-folding behaviour in response to repeated physical disturbance exhibits clear habituation, suggesting some elementary form of learning. Applying the theory and the analytical methods usually employed in animal learning research, we show that leaf-folding habituation is more pronounced and persistent for plants growing in energetically costly environments. Astonishingly, Mimosa can display the learned response even when left undisturbed in a more favourable environment for a month. This relatively long-lasting learned behavioural change as a result of previous experience matches the persistence of habituation effects observed in many animals.

We thank P. Tinkler and staff of the Exmouth Office of the Department of Environment and Conservation Western Australia for field assistance; A. Heyward, R. Lowe, and C. Simpson for helpful discussions; the Australian Research Council, Australian Institute of Marine Science, Western Australian Marine Science Institute, and the Department of Environment and Conservation Western Australia for funding; and two anonymous reviewers for helpful comments. Data collection was conducted in the traditional country of the Jinigudira and Bayungu tribes of the Thalanyji people.

Fish predation is often cited as a key process in structuring sea urchin populations on coral reefs, with population outbreaks often being related to the removal of key predators through overfishing. However, moderate–high densities of the sea urchin Echinometra mathaei have been reported on a reef with relatively intact predator assemblages; Ningaloo Reef, Western Australia. This study examined the relationship between the densities of E. mathaei and its potential predators, to gain some insight into the potential role of predation in structuring E. mathaei populations on Ningaloo Reef. To identify potential urchin predators we recorded predation events on tethered E. mathaei using stationary video cameras. Seven fish species preyed on the tethered urchins with two labrid species, Coris aygula and Choerodon rubescens, accounting for 65% of all observed predation events. There was, however, no evidence for the role of predation in determining E. mathaei populations either within or among habitats. Despite the densities of E. mathaei varying from 0.1 to 219.7 ind 100 m− 2 among habitats, the density and biomass of potential urchin predators displayed limited variation among habitats. Furthermore, the density of E. mathaei was positively related to that of their predators on the reef slope and the back reef. While the overall density of potential predators (53.3 ind ha− 1) was comparable to other protected reefs, the suite of predators differed from that of other regions. In particular, large triggerfish species (f. Balistidae), the dominant predators of E. mathaei on other Indo-Pacific reefs, were rare or absent. While the lack of these species may have contributed to the moderate–high densities of E. mathaei on Ningaloo Reef, other factors such as larval supply, food availability and habitat characteristics may be important. Irrespective of the mechanisms, moderate–high densities of E. mathaei should not be universally viewed as an indicator of reef degradation.

Gagliano et al. (Learning by association in plants, 2016) reported associative learning in pea plants. Associative learning has long been considered a behavior performed only by animals, making this claim particularly newsworthy and interesting. In the experiment, plants were trained in Y-shaped mazes for 3 days with fans and lights attached at the top of the maze. Training consisted of wind consistently preceding light from either the same or the opposite arm of the maze. When plant growth forced a decision between the two arms of the maze, fans alone were able to influence growth direction, whereas the growth direction of untrained plants was not affected by fans. However, a replication of their protocol failed to demonstrate the same result, calling for further verification and study before mainstream acceptance of this paradigm-shifting phenomenon. This replication attempt used a larger sample size and fully blinded analysis., eLife digest Associative learning is a simple learning ability found in most animals, which involves linking together two different cues. For example, the dogs in Pavlov’s famous experiment were trained to associate sound with the arrival of food, and eventually started salivating upon hearing the sound alone. Plants, like animals, are capable of complex behaviors. The snapping leaves of a Venus fly trap or the sun-tracking abilities of sunflowers are examples of instinctive responses to environmental cues that have evolved over many generations. Whether or not plants can learn during their lifetimes has remained unknown. A handful of studies have tested for associative learning in plants, the most convincing of which was published in 2016. In this study, pea plants were exposed to two signals: light, the plant version of dog food, and wind, equivalent to the sound in Pavlov’s experiment. Just as dogs salivate in response to food, plants instinctively grow towards light, whereas air flow does not affect the direction of growth. The plants were grown inside Y-shaped mazes and their ‘selection’ of one particular arm was used as a ‘read-out’ of learned behavior. The experiments trained growing plants by exposing them to wind and light from either the same direction or opposite directions. Once the plants were at the point of ‘choosing’ between the two arms, they were exposed to wind in the absence of light. Wind by itself appeared to influence the direction the trained plants took, with wind attracting plants trained with wind and light together and repelling plants trained with wind and light apart. Untrained plants remained unaffected, making random selections. These observations were interpreted as the strongest evidence of associative learning in plants and if true would have great scientific and philosophical significance. Kasey Markel therefore set out to confirm and expand on these findings by replicating the 2016 study. As many conditions as possible were kept identical, such as the training regime. The new experiments also used more plants and, most importantly, were done ‘blind’ meaning the people recording the data did not know how the plants had been trained. This ensured the expectations of the researcher would not influence the final results. The new study found no evidence for associative learning, but did not rule it out altogether. This is because some experimental details in the first study remained unknown, such as the exact model of lights and fans originally used. This work demonstrates the importance of replicating scientific experiments. In the future, Markel hopes their results will pave the way for further, rigorous testing of the hypothesis that plants can learn.

Species habitat associations are often complex, making it difficult to assess their influence on populations. Among coral reef fishes, habitat requirements vary among species and with ontogeny, but the relative importance of nursery and adult-preferred habitats on future abundances remain unclear. Moreover, adult populations may be influenced by recruitment of juveniles and assessments of habitat importance should consider relative effects of juvenile abundance. We conducted surveys across 16 sites and 200 km of reef to identify the microhabitat preferences of juveniles, sub-adults and adults of the damselfish Pomacentrus moluccensis . Microhabitat preferences at different life-history stages were then combined with 6 years of juvenile abundance and microhabitat availability data to show that the availability of preferred juvenile microhabitat (corymbose corals) at the time of settlement was a strong predictor of future sub-adult and adult abundance. However, the influence of nursery microhabitats on future population size differed spatially and at some locations abundance of juveniles and adult microhabitat (branching corals) were better predictors of local populations. Our results demonstrate that while juvenile microhabitats are important nurseries, the abundance of coral-dependent fishes is not solely dependent on these microhabitats, especially when microhabitats are readily available or following large influxes of juveniles.

The spring and summer of 2010/11 saw an exceptionally strong La Nina push warm waters from Indonesia down the Western Australian coastline, resulting in a host of extraordinary biological oddities including significant bleaching of Western Australian corals. Here, we report a 79–92 % decline in coral cover for a location in the Ningaloo Marine Park where sustained high water temperatures over an 8-month period left just 1–6 % of corals alive. The severity of bleaching provided an opportunity to investigate the resilience of different taxonomic groups and colony size classes to an acute but protracted episode of thermal stress. While the sub-dominant community of massive growth forms fared reasonably well, the dominant Acropora and Montipora assemblages all died, with the exception of the

Lipofuscin, an autofluorescent biomarker of physiological wear-and-tear, was concentrated in those areas of a fish's midbrain responsible for visual performance, suggesting a potentially strong link between physiological specialization, ecological adaptation and senescence.

The number of relatively untouched coral reefs worldwide is rapidly decreasing. Nevertheless, one coral reef ecosystem remains relatively intact: the largest west-continental reef ecosystem in the world, Ningaloo Reef in Western Australia. This study investigated the status of 2 potential bio-indicators for coral reef decline, macroalgae and sea urchin densities, on this reef. Sur- prisingly, both were abundant, with the presence of extensive macroalgal beds in the sandy lagoon and a sea urchin-dominated reef slope. The algal distribution on Ningaloo reflected marked cross- shelf variation in the composition of fish functional groups, with only the back reef and the reef slope exhibiting high grazing rates (completely scraped every 43 and 59 d, respectively). Estimated bioero- sion rates by fishes ranged between 1 and 2.3 kg m -2 yr -1 . Echinoids only played a significant role in bioerosion on the reef slopes owing to their high abundance in that habitat (>12 individuals m -2 ). Here, estimated echinoid erosion equalled that of the most abundant excavating parrotfish, Chloru- rus sordidus. High echinoid and macroalgal abundances on this relatively intact reef system highlight the need for caution when using these metrics for evaluating reef ecosystem condition.

Accelerating coastal development and shipping activities dictate that dredging operations will intensify, increasing potential impacts to fishes. Coastal fishes have high economic, ecological, and conservation significance and there is a need for evidence-based, quantitative guidelines on how to mitigate the impacts of dredging activities. We assess the potential risk from dredging to coastal fish and fisheries on a global scale. We then develop quantitative guidelines for two management strategies: threshold reference values and seasonal restrictions. Globally, threatened species and nearshore fisheries occur within close proximity to ports. We find that maintaining suspended sediment concentrations below 44 mg/L (15–121 bootstrapped CI) and for less than 24 hours would protect 95% of fishes from dredging-induced mortality. Implementation of seasonal restrictions during peak periods of reproduction and recruitment could further protect species from dredging impacts. This study details the first evidence-based defensible approach to minimize impacts to coastal fishes from dredging activities.

Ocean acidification is one of the key threats facing coral reef ecosystems, but there are few estimates of spatial and temporal variability in pH among reef habitats. The present study documents levels of spatial variability in pH among coral reef habitats (9 to 10), among locations separated by 100’s km of latitude and between east (Great Barrier Reef, GBR) and west (Ningaloo Reef) coasts of Australia. Differences were found in pH between inshore and offshore waters along Ningaloo Reef (means 8.45, 8.53, respectively). Replicate assessments here ranged from 8.22 to 8.64. On the GBR, the range of values over all habitats and replicates was 0.39 pH units (7.98 to 8.37). There were minor but significant differences of 0.05 pH units between 5 consecutive days for habitats on average. Highest pH was recorded in filamentous algal beds maintained by the damselfish Dischistodus perspicillatus. Lowest pH was found in water extracted from sand-dwelling goby holes. While there were marked changes in pH over a 48-h sampling period among 4 habitats at Lizard Island (GBR), there was little evidence of a diel trend. Understanding how pH varies at scales that are relevant to organisms that live on shallow coral reefs is crucial for the design and interpretation of experiments that test the effects on organisms of the changes in water chemistry predicted to affect oceans in the future.

The ubiquitous coenzyme Q (CoQ) is a powerful antioxidant defence against cellular oxidative damage. In fishes, differences in the isoprenoid length of CoQ and its associated antioxidant efficacy have been proposed as an adaptation to different thermal environments. Here, we examine this broad contention by a comparison of the CoQ composition and its redox status in a range of coral reef fishes. Contrary to expectations, most species possessed CoQ 8 and their hepatic redox balance was mostly found in the reduced form. These elevated concentrations of the ubiquinol antioxidant are indicative of a high level of protection required against oxidative stress. We propose that, in contrast to the current paradigm, CoQ variation in coral reef fishes is not a generalized adaptation to thermal conditions, but reflects species-specific ecological habits and physiological constraints associated with oxygen demand.

Ecosystem reconfigurations arising from climate-driven changes in species distributions are expected to have profound ecological, social, and economic implications. Here we reveal a rapid climate-driven regime shift of Australian temperate reef communities, which lost their defining kelp forests and became dominated by persistent seaweed turfs. After decades of ocean warming, extreme marine heat waves forced a 100-kilometer range contraction of extensive kelp forests and saw temperate species replaced by seaweeds, invertebrates, corals, and fishes characteristic of subtropical and tropical waters.This community-wide tropicalization fundamentally altered key ecological processes, suppressing the recovery of kelp forests., This work was funded by the Australian Research Council (T.W., G.A.K.), the Hermon Slade Foundation (T.W., S.B.), a U.K. Natural Environment Research Council Independent Research Fellowship (D.A.S.), the Australian Institute of Marine Science (T.W., M.D., B.R.), the Australian National University (C.J.F.), the Western Australian Museum (J.F.), the Department of Parks and Wildlife (T.H.H., S.W.), CSIRO Oceans and Atmosphere (R.C.B., F.D., M.A.V.), Fisheries Research and Development Corporation project no. 2008/013 (R.K.H., G.A.K.), The Marsden Fund of The Royal Society of New Zealand (M.S.T.), and the WA Strategic Research Fund for the Marine Environment (R.B., M.A.V., J.F.).

Vertebrate animals localize sounds by comparing differences in the acoustic signal between the two ears and, accordingly, ear structures such as the otoliths of fishes are expected to develop symmetrically. Sound recently emerged as a leading candidate cue for reef fish larvae navigating from open waters back to the reef. Clearly, the integrity of the auditory organ has a direct bearing on what and how fish larvae hear. Yet, the link between otolith symmetry and effective navigation has never been investigated in fishes. We tested whether otolith asymmetry influenced the ability of returning larvae to detect and successfully recruit to favourable reef habitats. Our results suggest that larvae with asymmetrical otoliths not only encountered greater difficulties in detecting suitable settlement habitats, but may also suffer significantly higher rates of mortality. Further, we found that otolith asymmetries arising early in the embryonic stage were not corrected by any compensational growth mechanism during the larval stage. Because these errors persist and phenotypic selection penalizes asymmetrical individuals, asymmetry is likely to play an important role in shaping wild fish populations.

Most colour patterns in animals represent an elegant compromise between conspicuousness to ensure effective communication with preferred receivers and camouflage to avoid attracting the attention of unwanted predators. Many species, including several coral reef fishes, overcome this conflict by using ultraviolet (UV) colouration and signalling, as these colours are visible only over short distances and are often invisible to their predators. Despite a great interest in their behavioural significance and ecological influence on survival, little is known about when these colours first develop on the bodies of free-living animals. Here we show for the first time that the UV facial patterns of a coral reef fish do not develop in captivity but only when juveniles experience the socio-behavioural conditions of their natural environment. Using field and laboratory experiments, we determined that the onset and early development of these UV facial markings did not occur at metamorphosis. Instead, juveniles developed the UV markings during their first two weeks on the reef. Exposure to different reef environments revealed significant plasticity in the development of these markings. The direct or indirect (through intraspecific interactions) exposure to predators is a likely candidate trigger for the plastic development of these UV markings in the wild.

Life history theory predicts a range of directional generic responses in life history traits with increasing organism size. Among these are the relationships between size and longevity, mortality, growth rate, timing of maturity, and lifetime reproductive output. Spanning three orders of magnitude in size, coral reef fishes provide an ecologically diverse and species-rich vertebrate assemblage in which to test these generic responses. Here we examined these relationships by quantifying the life cycles of three miniature species of coral reef fish from the genus Eviota (Gobiidae) and compared their life history characteristics with other reef fish species. We found that all three species of Eviota have life spans of

The 1998 global coral bleaching event was the largest recorded historical disturbance of coral reefs and resulted in extensive habitat loss. Annual censuses of reef fish community structure over a 12-year period spanning the bleaching event revealed a marked phase shift from a prebleach to postbleach assemblage. Surprisingly, we found that the bleaching event had no detectable effect on the abundance, diversity or species richness of a local cryptobenthic reef fish community. Furthermore, there is no evidence of regeneration even after 5–35 generations of these short-lived species. These results have significant implications for our understanding of the response of coral reef ecosystems to global warming and highlight the importance of selecting appropriate criteria for evaluating reef resilience.

The distribution and abundance of small cryptic reef fishes were quantified among microhabitats and reef zones at both exposed and sheltered sites at Lizard Island, Great Barrier Reef. A total of 1042 individuals from 44 species in 8 families were sampled. Marked variation in abun- dance, species numbers, size-class distribution and species composition were displayed among reef zones at exposed sites; in contrast, comparatively little variation was found in sheltered sites. The exposed, wave-swept front flat reef zone was clearly the most depauperate and species-poor zone with calmer back reef, lagoonal and reef base zones containing the highest numbers of individuals and species. Larger, heavier individuals predominated in exposed wave-swept reef zones whereas smaller, lighter individuals were commonly found in calmer waters. Sheltered sites exhibited little variation among zones. In these sites, microhabitat appeared to play a much greater role in shaping community composition. Overall, 68.5% of all individuals (70.1% at exposed and 65.4% at sheltered sites) were collected from sand/rubble microhabitats as opposed to 31.5% from open reef microhab- itats. Assemblages at exposed and sheltered sites exhibited little taxonomic overlap, even of highly abundant species. These results indicate that wave energy plays a significant role in structuring small cryptic coral reef fish communities, with microhabitat type playing a key role in the absence of wave energy.

An examination of the trophic status of a cryptobenthic reef fish community from the central Great Barrier Reef was carried out to evaluate the potential role of cryptobenthic fishes in coral reef ecosystems. Using frequency of occurrence data, dietary analyses revealed a diverse range of trophic groups, although detritivory (in 10 out of 16 species and 39.3% of individuals) and carnivory (5 of 16 species and 40.5% of individuals) clearly dominate as trophic modes. Herbivory (1 species; 2.4% of individuals) is only a minor component in the community trophic structure. Of the 18 dietary categories identified, detritus and copepods were the only constituents represented in all 16 species examined. Although the degree of dietary specialization varied among taxa, the 2 most abundant species, Eviota queenslandica and Istigobius goldmanni, utilised the broadest range of dietary items. Morphology reflected the trophic partitioning among fishes: carnivores were invariably 38 mm TL with GLRs generally exceeding >1.0. The trophic composition and numerical strength of the cryptobenthic fish fauna suggests that cryptobenthic reef fishes have the potential to make a significant contribution to reef trophodynamics along a number of trophic pathways. This prompts a re-evaluation of the roles of reef fishes in the functioning of coral reefs, particularly those related to the recycling of primary production through detrital pathways.

Eyespots on the body of many animals have long been assumed to confer protection against predators, but empirical evidence has recently demonstrated that this may not always be the case and suggested that such markings may also serve other purposes. Clearly, this raises the unresolved question of what functions do these markings have and do they contribute to an individual's evolutionary fitness in the wild. Here, we examined the occurrence of eyespots on the dorsal fin of a coral reef damselfish (Pomacentrus amboinensis), where these markings are typical of the juvenile stage and fade away as the fish approaches sexual maturation to then disappear completely in the vast majority of, but not all, adult individuals. By exploring differences in body shape among age and gender groups, we found that individuals retaining the eyespot into adulthood are all sexually mature males, suggesting that these eyespots may be an adult deceptive signal. Interestingly, the body shape of these individuals resembled more closely that of immature females than mature dominant males. These results suggest that eyespots have multiple roles and their functional significance changes within the lifetime of an animal from being a juvenile advertisement to a deceptive adult signal. Male removal experiments or colour manipulations may be necessary to establish specific functions.

Marine ecosystems are facing increasing exposure to a range of stressors and declines in critical ecological functions. The likelihood of further loss of functions and resilience is dependent, in part, on the extent of functional redundancy (i.e. the capacity of one species to functionally compensate for the loss of another species) within critical functional groups. We used multiple metrics; species richness, generic richness, abundance and reserve capacity (i.e. the relative number of individuals available to fulfil the function if the numerically dominant species is lost), as indicators to assess the potential functional redundancy of four functional groups of herbivorous fishes (browsers, excavators, grazers and scrapers) in two of the worlds' most intact coral reef ecosystems: the Great Barrier Reef (GBR) and Ningaloo Reef in Western Australia. We found marked variations in potential redundancy among habitats within each reef system and functional groups. Despite negligible fishing of herbivorous fishes, coastal habitats in both reef systems had lower functional redundancy compared to offshore locations for all herbivorous fishes collectively and the four functional groups independently. This pattern was consistent in all four indicators of redundancy. The potential vulnerability of these coastal habitats is highlighted by recent shifts from coral to macroalgal dominance on several coastal reefs of the GBR. Our approach provides a simple yet revealing evaluation of potential functional redundancy. Moreover, it highlights the spatial variation in potential vulnerability and resilience of reef systems.

The dynamic nature of coral reefs offers a rare opportunity to examine the response of ecosystems to disruption due to climate change. In 1998, the Great Barrier Reef experienced widespread coral bleaching and mortality. As a result, cryptobenthic fish assemblages underwent a dramatic phase-shift. Thirteen years, and up to 96 fish generations later, the cryptobenthic fish assemblage has not returned to its pre-bleach configuration. This is despite coral abundances returning to, or exceeding, pre-bleach values. The post-bleach fish assemblage exhibits no evidence of recovery. If these short-lived fish species are a model for their longer-lived counterparts, they suggest that (1) the full effects of the 1998 bleaching event on long-lived fish populations have yet to be seen, (2) it may take decades, or more, before recovery or regeneration of these long-lived species will begin, and (3) fish assemblages may not recover to their previous composition despite the return of corals.