Habitat and morphological characteristics affect juvenile mortality in five coral reef damselfishes

Global decline in capacity of coral reefs to provide ecosystem services

Spatial distributions of coral reef fish species are potentially determined by habitat preferences and behavioural interactions. However, the relative importance of these factors and whether or not behavioural interactions reinforce or disrupt habitat associations are poorly understood. This paper explores the degree to which habitat and social preferences explain the association that three common coral reef cardinalfish species (Zoramia leptacanthus, Archamia zosterophora and Cheilodipterus quinquelineatus; family Apogonidae) have with coral substrata at Lizard Island, Great Barrier Reef. At diurnal resting sites, species were strongly associated with branching corals, with 80–90% of each species inhabiting one branching coral species, Porites cylindrica. Species were also highly gregarious, forming large con-specific and hetero-specific aggregations in coral heads, potentially reinforcing habitat associations. Three-way choice experiments were conducted to test fishes habitat preferences for living coral over dead substrata, for particular coral species, and the influence of gregarious behaviour on these habitat choices. The strength of habitat preferences differed among species, with Z. leptacanthus preferring live coral and P. cylindrica, A. zosterophora preferring P. cylindrica, whether live or dead and C. quinquelineatus exhibiting no preferences. All species were attracted to conspecifics, and for C. quinquelineatus and A. zosterophora, conspecific attraction resulted in stronger preferences for live corals. Gregarious behaviour also increased C. quinquelineatus associations with P. cylindrica. The relative strength of social attraction versus habitat preferences was investigated by comparing fish habitat preferences in the presence and/or absence of conspecifics. The presence of conspecifics on non-preferred rubble habitat reduced each species association with live coral. This study’s results indicate that in the field, habitat preferences and conspecific attraction combine to reinforce the association between cardinalfishes and a narrow range of coral substrata.

The effects of habitat availability and quality on small mammals abundance in the Brazilian Atlantic Forest

<p><strong>Environmental disturbances driven by climate change are causing unprecedented degradation of natural systems across the globe. Rapid environmental changes limit our capacity to forecast future habitat conditions based on historical benchmarks as we face scenarios unlike any observed in the past. Tropical coral reefs are experiencing widespread biodiversity and habitat loss due to increasingly frequent marine heatwaves, intense storms, pathogens, pollutants, and human exploitation. Reef flattening has been observed across the entire range of latitudes where coral reefs develop. Coral reef fauna are specialised to inhabit one of the most structurally complex habitats in the world, making them particularly vulnerable to habitat degradation. The flattening of reef habitats changes system dynamics and jeopardizes the stability of the ecosystem services we rely on reefs to provide. In this thesis, I develop and explore ecosystem models that explicitly consider the influence of habitat quality on dynamic processes. Using parameters that simulate a generic reef ecosystem, I manipulate habitat quality in several ways, revealing key aspects of the interaction between fish communities and habitat quality with a focus on the provision of ecosystem services. These models can be used as predictive tools to inform ecosystem management strategies and determine trade-offs in decision-making, allowing us to plan for a future where coral reef ecosystems are likely to be drastically different from those of the past.</strong></p><p>To set the stage for this work, Chapter 1 begins with a comprehensive overview of coral reef ecosystems and the critical issues threatening their survival. The relationship between various ecological factors and their collective impacts on coral reefs is highlighted, focussing on trophic relationships and the consequences of disturbance. This is followed by a detailed examination of structural complexity in marine environments, emphasizing its crucial role as a structuring force in reef ecosystems. The next section dives into the functional ecology of reefs, reviewing observed impacts of habitat change on the functioning and structure of reef communities. Considering the myriad threats to reefs, current management efforts are explored, focusing on the role of ecosystem models in policy, strategic planning, and decision-making. Finally, I provide a framework for the research, detailing the primary objectives of each chapter and the work as a whole.</p><p>As ecosystem engineers on reefs, hard corals form complex, three-dimensional structures as they grow. These structures provide refuge from competitors, predators, and environmental stressors. By influencing predator-prey interactions, reef refuges promote juvenile survivorship and facilitate the transfer of energy up the food chain, allowing reefs to support abundant and diverse fish communities. In Chapter 2, I explore the impact of the refuge profile, a metric that quantifies both the abundance of predation refuges on a reef and the size range of fish that they can accommodate. Using a size-based ecosystem model, I evaluate how different sizes and distributions of refuges impact the ecosystem and affect the provision of ecosystem services. Model predictions indicate that refuges used by fish between 5 and 10 cm in length significantly increase fish biomass and fisheries yields, highlighting the importance of small-scale refuges for sustaining coral reef health. I also identify features of refuge profiles that maximise three valuable reef services: reef resilience, potential fisheries productivity, and ecotourism. These insights can inform the strategic design of artificial reefs to support ecosystem services through climate change.</p><p>Ecosystem models that capture trophic dynamics are valuable tools for predicting and managing the effects of exploitation and environmental change. Accounting for species interaction through food-web links reveals ecosystem-wide impacts of changes to dynamics processes, providing a more comprehensive view of potential outcomes of environmental change. Unfortunately, most of these frameworks require extensive data to set up, making them difficult to use for coral reefs and more difficult to generalize. Data collection, monitoring, and management enforcement are a consistent challenge for most of the world’s coral reefs, which develop along tropical coastlines, often in remote regions. Size-spectrum models offer a simpler perspective on trophic modelling, employing the assumption that predator-prey interactions are determined primarily by body size. However, there are no size-spectrum frameworks available for managers that incorporate a measure of habitat quality, a key component of reef ecosystems. Chapter 3 presents MizerReef, a novel R package that facilitates the development of dynamic, multi-species size-spectrum models specifically tailored for coral reef ecosystems. By incorporating the critical role of predation refuges, MizerReef enables users to simulate complex interactions among multiple species groups under various scenarios of habitat degradation. The chapter also presents some examples of package use and a set of steady-state parameters tuned for comparison to the size-spectrum model presented in Chapter 2. The MizerReef package offers a feasible pathway towards large-scale modelling of coral reef ecosystems to support management and maintain crucial services through climate change.</p><p>Physical traits, such as body shape and swimming ability, and behavioural traits, such as foraging strategy and activity pattern, shape the relationship between an organism and its environment. Functional structure, defined as the abundance and diversity of these traits within an environment, plays a pivotal role in how communities respond to disturbance and exploitation, influencing overall system stability. As reef habitat quality diminishes, functional structure also tends to change, and these shifts can have profound impacts on ecosystem service provision. Chapter 4 investigates how changes to the refuge profile impact ecosystem services and fish assemblage structure using a generic reef ecosystem model set up with MizerReef and several of the refuge profiles designated in Chapter 2. Predictions indicate that fish assemblage composition is dependent on the refuge profile. Profiles that supported the highest reef resilience in Chapter 2 were dominated by parrotfish, reinforcing the concept that reef resilience is supported by small-scale habitat structure. However, the productivity of the profile deemed best for fishing was also supported primarily by parrotfish, emphasizing the trade-offs involved in exploiting reefs with plentiful small predation refuges. Herbivores generally appear to benefit from habitat structure at any size while the productivity of larger piscivores is hindered by plentiful refuge. These results reveal a more resolved picture of how habitat quality affects reef communities, allowing us to fine-tune management strategies to support essential reef functions.</p><p>Coral reefs are subject to a multitude of stressors on local and global scales. Disturbances can cause rapid changes in the entire community, but also more subtle shifts that play out over decades. The process of reef flattening and recovery is continuous and dynamic and can result in a variety of stable ecosystem states. Considering the inherent limitations of steady-state dynamics in accounting for the episodic nature of disturbances and their impacts, Chapter 5 addresses the critical need to understand how coral reef ecosystems respond to acute environmental change. Using historical data, I develop a realistic timeline describing how the refuge profile changes following disturbance, with a particular focus on the consequences of mass bleaching events. This is used to create a new degradation dynamic for the MizerReef package that simulates changes to the refuge profile for three common disturbed coral reef states: coral rubble-dominated, macroalgae-dominated, and recovered. Predictions indicate that the assemblage composition of disturbed reefs is dependent on the recovery trajectory. Recovered reefs have the potential to support relatively stable fish assemblages, but macroalgal and rubble reefs become dominated by herbivores and generalist predators, respectively. This information can help managers plan for different degradation scenarios and demonstrates the potential for MizerReef to explore temporal dynamics.</p><p>This thesis encompasses a comprehensive exploration of the intricate relationships between habitat quality, community dynamics, and ecosystem service provision within a coral reef ecosystem model. Through a series of innovative modelling approaches, it sheds light on the role of structural complexity in sustaining reef biodiversity and the functionality of reef-associated communities. The findings underscore the urgent necessity for informed management strategies that prioritize habitat quality and structural complexity to mitigate the adverse effects of environmental disturbances. Ultimately, this thesis contributes to our understanding of coral reef ecosystems, providing a foundation for future efforts to preserve these critical habitats in the face of unprecedented global change.</p>

Habitat association in populations on landscapes with continuous-valued heterogeneous habitat quality

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 612:167-192 (2019) - DOI: https://doi.org/10.3354/meps12874 Global baselines and benchmarks for fish biomass: comparing remote reefs and fisheries closures Tim R. McClanahan1,*, Robert E. Schroeder2, Alan M. Friedlander3,4, Laurent Vigliola5, Laurent Wantiez6, Jennifer E. Caselle7, Nicholas A. J. Graham8, Shaun Wilson9,10, Graham J. Edgar11, Rick D. Stuart-Smith11, Remy M. Oddenyo12, J. E. Cinner13 1Wildlife Conservation Society, Marine Programs, Bronx, NY 10460, USA 2National Oceanic and Atmospheric Administration Fisheries, Honolulu, HI 96818, USA 3Pristine Seas, National Geographic Society, Washington, DC 20036, USA 4Fisheries Ecology Research Lab, University of Hawaii, Honolulu, HI 96822, USA 5Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Laboratoire Excellence LABEX Corail, 98851 Noumea, New Caledonia, France 6Institut De Sciences Exactes Et Appliquées (ISEA), EA7484, University of New Caledonia, 98851 Noumea, New Caledonia, France 7Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA 8Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK 9Department of Biodiversity Conservation and Attractions, Kensington, WA 6151, Australia 10Oceans Institute, University of Western Australia, Crawley, WA 6009, Australia 11Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia 12Wildlife Conservation Society, Coral Reef Conservation Program, Mombasa 80107, Kenya 13Australian Research Council, James Cook University, Townsville, QLD 4811, Australia *Corresponding author: tmcclanahan@wcs.org ABSTRACT: Baselines and benchmarks (B&Bs) are needed to evaluate the ecological status and fisheries potential of coral reefs. B&Bs may depend on habitat features and energetic limitations that constrain biomass within the natural variability of the environment and fish behaviors. To evaluate if broad B&Bs exist, we compiled data on the biomass of fishes in ~1000 reefs with no recent history of fishing in 19 ecoregions. These reefs spanned the full longitude and latitude of Indian and Pacific Ocean reefs and included older high-compliance fisheries closures (>15 yr closure) and remote reef areas (>9 h travel time from fisheries markets). There was no significant change in biomass over the 15 to 48 yr closure period but closures had only ~40% of the biomass (740 kg ha-1, lower confidence interval [LCI] = 660 kg ha-1, upper confidence interval [UCI] = 810 kg ha-1, n = 157) of remote tropical reefs (1870 [1730, 2000] kg ha-1, n = 503). Remote subtropical reefs had lower biomass (950 [860, 1040] kg ha-1, n = 329) than tropical reefs. Closures and remote reef fish biomass responded differently to environmental variables of coral cover, net primary productivity, and light, indicating that remote reefs are more limited by productivity and habitat than closures. Closures in fished seascapes are unlikely to achieve the biomass and community composition of remote reefs, which suggests fisheries benchmarks will differ substantially from wilderness baselines. A fishery benchmark (B0) of ~1000 kg ha-1 adjusted for geography is suggested for fisheries purposes. For ecological purposes, a wilderness baseline of ~1900 kg ha-1 is appropriate for including large and mobile species not well protected by closures. KEY WORDS: Baselines · Coral reef fish · Fisheries and ecological indicators · Pristine or virgin biomass · Sustainability Full text in pdf format Supplementary material PreviousNextCite this article as: McClanahan TR, Schroeder RE, Friedlander AM, Vigliola L and others (2019) Global baselines and benchmarks for fish biomass: comparing remote reefs and fisheries closures. Mar Ecol Prog Ser 612:167-192. https://doi.org/10.3354/meps12874 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 612. Online publication date: March 07, 2019 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2019 Inter-Research.

The influence of habitat quality on a species' demographics is critical for understand- ing its ecology and effective conservation. However, quantifying habitat quality is problematic because it may comprise of abiotic components at different spatial scales and also be influenced by biotic processes. This study investigated the relationship between reef-associated Caribbean fishes and habitat quality at 2 spatial scales: (1) multiple characteristics of Montastraea annularis coral colonies (<1 m 2 ) and (2) coral density in a 5 × 5 m plot around each microhabitat. Further- more, the influence on habitat quality of 2 biotic factors (predation pressure and interactions between competitively superior territorial damselfishes and other species) was considered. A total of 102 M. annularis colonies within thirty 25 m 2 plots were surveyed on a Belizean forereef. Gen- eralised linear mixed-effect models demonstrated that both damselfishes and other reef - associated species were correlated with colony-scale habitat quality (more abundant on taller, refuge-rich colonies). Adult reef-associated species were also correlated with larger-scale habitat quality, being more abundant on colonies with high densities of other Montastraea colonies within 25 m 2 (probably higher quality home ranges). However, the presence of damselfishes was associ- ated with reduced abundances of other reef-associated species on M. annularis colonies, reflect- ing the importance of both biotic and abiotic controls of habitat quality. On reefs, coral mortality will reduce the density of optimal colonies and potentially increase the proportion occupied by damselfishes. This may lead to smaller populations of inferior competitors as they are increasingly displaced onto sub-optimal microhabitats.

Fish often evade predators with a fast-start escape response. Studies typically examine this behaviour in still water despite water motion being an inherent feature of aquatic ecosystems. In shallow habitats, waves create complex flows that likely influence escape performance, particularly in small fishes with low absolute swimming speeds relative to environmental flows. I examined how wave-driven water flow affects the behaviour and kinematics of escape responses in juveniles of three coral reef damselfishes (Pomacentridae) with different body morphologies. Tropical damselfishes have similar fin and body shapes during early development, with the exception of body depth, a trait deemed important for postural control and stability. Wave-driven flow increased response latency in two of the three species tested: fish with a fusiform body responded 2.9 times slower in wave-driven flow than in still water, whereas this difference was less pronounced in fish with an intermediate body depth (1.9 times slower response) and absent in fish with a laterally compressed body. The effect of wave-driven flow on swimming performance (cumulative escape distance and turning rate) was variable and depended on the timing and trajectory of escape responses in relation to the wave phase. Given intense predation pressure on juvenile coral reef fishes during settlement, interspecific differences in how wave-driven flow affects their ability to escape predators could influence the distribution and abundance of species across spatial and temporal scales.

What controls distribution of larval and juvenile yellow perch? The role of habitat characteristics and spatial processes in a large, shallow lake

This article proposes a mechanism that triggers first maturation and spawning in coral reef (bony) fish, which allows for predicting their length at first maturity. Thus, mean lengths at first maturity (Lm) and the corresponding maximum lengths (Lmax) in 207 populations of 131 species of coral reef fish were assembled and used to test the hypotheses that (a) there is, in coral reef fish, a single value of a size-related parameter acting as a trigger for their maturation and eventual spawning, and (b) that this single value is statistically the same as that published previously for other bony fish. The results, based on the assembled Lm and Lmax data and on estimates of the parameter D, which link the length of fish with the relative surface of their gills, covered 44 families and Lmax values ranging from 1.8 to 181.6 cm and confirmed that the threshold in (a) exists. Also, we assessed (in b) that this threshold value, i.e., LmaxD/LmD = 1.35 (±0.02), is not statistically different from similar estimates for other groups of teleosts, notably semelparous salmonids, cichlids, sturgeons and Chinese and Turkish freshwater and marine fish. One implication is that given ocean warming and deoxygenation, coral reef fish will not only be smaller than they currently are, but also mature and spawn at smaller sizes, and thus produce fewer, smaller eggs.

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m2 quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities.

Background: Bontosua Island, located in the Spermonde Archipelago, is one of the strategic and historical islands in the region. The island plays a vital role in ecosystem conservation efforts by the local community, who are committed to preserving their natural environment. With dynamic ecosystem conditions, it is essential to understand the seabed cover and biodiversity on the island to support more effective conservation efforts. Methods: This study was conducted from March to September 2022 to mark the seabed cover of Bontosua Island and understand the relationships between coral reef fish species and the ecosystem. The method used was a stationary visual census, followed by descriptive analysis and one-way ANOVA to assess the biodiversity and diversity of coral reefs. Findings: The results showed a total of 1,306 coral reef fish from 9 families with 63 species identified, including the families Chaetodontidae, Serranidae, Lutjanidae, Haemulidae, Lethrinidae, Scaridae, Acanthuridae, and Siganidae. The families with the highest citations were Scaridae, Acanthuridae, and Siganidae. The highest coral reef fish were found in the north, west, and southwest of the island, where live coral areas are more dominant. Conclusion: This study shows that Bontosua Island has significant coral reef diversity, and certain areas, such as the north and southwest sides, have higher reported fish. These findings indicate the importance of these areas in conservation efforts. Novelty/Originality: This study provides a comprehensive picture of the seabed cover and coral reef fish diversity in Bontosua Island, which has yet to be widely discussed in previous studies. These findings provide a scientific basis for more targeted conservation strategies and help improve understanding of the dynamics of coral reef ecosystems in the Spermonde Islands.. Novelty/Originality of this article: This study proposes developing a community-based coral reef monitoring system that integrates local knowledge with digital mapping technology, aiming to increase the effectiveness of conservation and management efforts of marine resources on small islands.

Spatial variation and habitat preference of reef fish and gastropod assemblages from two coastal habitats in subtropical reef, Port Shelter, Hong Kong.

Coral reefs contain a disproportionately high amount of marine biodiversity and support millions of people worldwide by providing food security and livelihoods. This coupled relationship between reefs and people is increasingly threatened globally by climate change and globalization, as well as locally by overfishing, habitat destruction, and nutrient pollution. Biomonitoring the varied ecological outcomes of these threats and estimating how conservation and management interventions mitigate them are crucial scientific endeavors for understanding the socio-ecological complexity of coral reef dynamics. Common ecological indicators of reef health, however, are theoretically and taxonomically limited when used alone, thus a combination of modeling and methodological approaches is needed for comprehensive assessments of coral reef patterns and processes. In addition, there are under-discussed power dynamics and equity implications of biomonitoring, especially when novel technologies are employed. Here, we address these research gaps with field data collected from coral reefs in Indonesia using visual surveys of fishes and corals and environmental DNA (eDNA) surveys of coral reef animals more broadly. We also evaluate potential equity outcomes of eDNA frameworks and implementations using critical discourse analysis. Engaging with multiple disciplinary paradigms, the aims of this dissertation are to understand the biophysical and human-mediated pathways shaping coral reef fish and habitat assemblages, evaluate the utility of eDNA for uncovering spatial patterns in coral reef biodiversity, and critically examine how the discourses and practices of the eDNA field may lead to inequitable outcomes. Chapter 1 contextualizes the results presented in Chapters 2, 3, and 4. It outlines the global magnitude of coral reef biodiversity and its threats, describes the common bioindicators used to evaluate management practices and ecosystem processes, gives rationale for using an eDNA approach, and establishes the importance of scrutinizing eDNA’s social dimensions. Key information about Indonesia’s coral reefs is also summarized. In Chapter 2, we used structural equation models (SEMs) to evaluate the relative influences of biophysical and human-mediated pathways affecting coral reef fishes and habitats. SEMs are a form of path analysis that allows multiple competing hypotheses about a system to be evaluated within the same theoretical and statistical framework. SEMs allows for understanding coral reef processes because they organize field data from reefs in terms of their causal proximity to each other. In our SEMs, we used visual survey data collected on coral reef fishes and habitat conditions across four regions of Indonesia that vary in their management designations. We also incorporated additional socio-environmental

Ujung Kulon National Park (TNUK) employs a management with the zonation system established to maintain the sustainability of resources, one of them are coral reef fish. This study aimed to identify the influence of management status on coral reef fish. Field observations were conducted on 14-22 October 2017 in Ujung Kulon using underwater visual census method, by recording the fish found in observation transects. The coral reef fish most frequently found in Core Zone was Caesionidae, while in The Marine Protection Zone is Acanthuridae. The Core Zone has higher species richness, and more abundance of coral reef fish than the Marine Protection Zone, although only species richness parameter shows a significant difference based on statistical tests. The management status that regulates the activities in each zoning has an impact on the coral reef ecosystem, including coral reef fish communities in it. Coral reef fish in the Core Zone have more diverse species than the Marine Protection Zone, because the coral reefs in the Core Zone are more preserved than the Marine Protection Zone.