Predicting coral community recovery using multi‐species population dynamics models

Capturing fine-scale coral dynamics with a metacommunity modelling framework

Natural systems exhibit high spatial variability across multiple scales. Models that can capture ecosystem dynamics across space and time by explicitly incorporating major biological mechanisms are crucial, both for management and for ecological insight. In the case of coral reef systems, much focus has been on modelling variability between reefs, despite substantial variability also existing within reefs. We developed C~scape, a coral metacommunity modelling framework that integrates the demography of corals with population-level responses to physical and environmental spatial layers, to facilitate spatiotemporal predictions of coral dynamics across reefs at fine (100s of metres to kilometres) scales. We used satellite-derived habitat maps to modulate community growth spatially, as a proxy for the many interacting physical and environmental factors-e.g., depth, light, wave exposure, temperature, and substrate type-that drive within-reef variability in coral demography. With a case study from the Great Barrier Reef, we demonstrate the model's capability for producing hindcasts of coral cover dynamics and show that overlooking within-reef variability may lead to misleading conclusions about metacommunity dynamics. C~scape provides a valuable framework for exploring a range of management and restoration scenarios at relevant spatial scales.

Natural coral recovery despite negative population growth

Demographic processes that ensure the recovery and resilience of marine populations are critical as climate change sends an increasing proportion on a trajectory of decline. Yet for some populations, recovery potential remains high. We conducted annual monitoring over 9 years (2012-2020) to assess the recovery of coral populations belonging to the genus Pocillopora. These populations experienced a catastrophic collapse following a severe typhoon in 2009. From the start of the monitoring period, high initial recruitment led to the establishment of a juvenile population that rapidly transitioned to sexually mature adults, which dominated the population within 6 years after the disturbance. As a result, coral cover increased from 1.1% to 20.2% during this time. To identify key demographic drivers of recovery and population growth rates (λ), we applied kernel-resampled integral projection models (IPMs), constructing eight successive models to examine annual change. IPMs were able to capture reproductive traits as key demographic drivers over the initial 3 years, while individual growth was a continuous key demographic driver throughout the entire monitoring period. IPMs further detected a pulse of reproductive output subsequent to two further Category 5 typhoon events during the monitoring period, exemplifying key mechanisms of resilience for coral populations impacted by disturbance. Despite rapid recovery, (i.e., increased coral cover, individual colony growth, low mortality), IPMs estimated predominantly negative values of λ, indicating a declining population. Indeed, while λ translates to a change in the number of individuals, the recovery of coral populations can also be driven by an increase in the size of surviving colonies. Our results illustrate that accumulating long-term data on historical dynamics and applying IPMs to extract demographic drivers are crucial for future predictions that are based on comprehensive and robust understandings of ecological change.

Corals survive severe bleaching event in refuges related to taxa, colony size, and water depth

Marine heatwaves are increasing in frequency and duration, threatening tropical reef ecosystems through intensified coral bleaching events. We examined a strikingly variable spatial pattern of bleaching in Moorea, French Polynesia following a heatwave that lasted from November 2018 to July 2019. In July 2019, four months after the onset of bleaching, we surveyed > 5000 individual colonies of the two dominant coral genera, Pocillopora and Acropora, at 10 m and 17 m water depths, at six forereef sites around the island where temperature was measured. We found severe bleaching increased with colony size for both coral genera, but Acropora bleached more severely than Pocillopora overall. Acropora bleached more at 10 m than 17 m, likely due to higher light availability at 10 m compared to 17 m, or greater daily temperature fluctuation at depth. Bleaching in Pocillopora corals did not differ with depth but instead varied with the interaction of colony size and Accumulated Heat Stress (AHS), in that larger colonies (> 30 cm) were more sensitive to AHS than mid-size (10-29 cm) or small colonies (5-9 cm). Our findings provide insight into complex interactions among coral taxa, colony size, and water depth that produce high spatial variation in bleaching and related coral mortality.

Natural recovery of corals after severe disturbance

Ecosystem recovery from human-induced disturbances, whether through natural processes or restoration, is occurring worldwide. Yet, recovery dynamics, and their implications for broader ecosystem management, remain unclear. We explored recovery dynamics using coral reefs as a case study. We tracked the fate of 809 individual coral recruits that settled after a severe bleaching event at Lizard Island, Great Barrier Reef. Recruited Acropora corals, first detected in 2020, grew to coral cover levels that were equivalent to global average coral cover within just 2 years. Furthermore, we found that just 11.5 Acropora recruits per square meter were sufficient to reach this cover within 2 years. However, wave exposure, growth form and colony density had a marked effect on recovery rates. Our results underscore the importance of considering natural recovery in management and restoration and highlight how lessons learnt from reef recovery can inform our understanding of recovery dynamics in high-diversity climate-disturbed ecosystems.

Coral recruitment: patterns and processes determining the dynamics of coral populations

Coral recruitment describes the addition of new individuals to populations, and it is one of the most fundamental demographic processes contributing to population size. As many coral reefs around the world have experienced large declines in coral cover and abundance, there has been great interest in understanding the factors causing coral recruitment to vary and the conditions under which it can support community resilience. While progress in these areas is being facilitated by technological and scientific advances, one of the best tools to quantify recruitment remains the humble settlement tile, variants of which have been in use for over a century. Here I review the biology and ecology of coral recruits and the recruitment process, largely as resolved through the use of settlement tiles, by: (i) defining how the terms 'recruit' and 'recruitment' have been used, and explaining why loose terminology has impeded scientific advancement; (ii) describing how coral recruitment is measured and why settlement tiles have value for this purpose; (iii) summarizing previous efforts to review quantitative analyses of coral recruitment; (iv) describing advances from hypothesis-driven studies in determining how refuges, seawater flow, and grazers can modulate coral recruitment; (v) reviewing the biology of small corals (i.e. recruits) to understand better how they respond to environmental conditions; and (vi) updating a quantitative compilation of coral recruitment studies extending from 1974 to present, thus revealing long-term global declines in density of recruits, juxtaposed with apparent resilience to coral bleaching. Finally, I review future directions in the study of coral recruitment, and highlight the need to expand studies to deliver taxonomic resolution, and explain why time series of settlement tile deployments are likely to remain pivotal in quantifying coral recruitment.

Disturbance-Induced Changes in Population Size Structure Promote Coral Biodiversity

AbstractReef-building coral assemblages are typically species rich, yet the processes maintaining high biodiversity remain poorly understood. Disturbance has long been thought to promote coral species coexistence by reducing the strength of competition (i.e., the intermediate disturbance hypothesis [IDH]). However, such disturbance-induced effects are insufficient to inhibit competitive exclusion. Nevertheless, there are other mechanisms by which disturbance and, more generally, environmental variation can favor coexistence. Here, we develop a size-structured, stochastic coral competition model calibrated with field data from two common colony morphologies to investigate the effects of hydrodynamic disturbance on community dynamics. We show that fluctuations in wave action can promote coral species coexistence but that this occurs via interspecific differences in size-dependent mortality rather than solely via stochastic fluctuations in competition (i.e., free space availability). While this mechanism differs from that originally envisioned in the IDH, it is nonetheless a mechanism by which intermediate levels of disturbance do promote coexistence. Given the sensitivity of coexistence to disturbance frequency and intensity, anthropogenic changes in disturbance regimes are likely to affect coral assemblages in ways that are not predictable from single-population models.

Divergent recovery trajectories of intertidal and subtidal coral communities highlight habitat-specific recovery dynamics following bleaching in an extreme macrotidal reef environment

Coral reefs face an uncertain future punctuated by recurring climate-induced disturbances. Understanding how reefs can recover from and reassemble after mass bleaching events is therefore important to predict their responses and persistence in a rapidly changing ocean. On naturally extreme reefs characterized by strong daily temperature variability, coral heat tolerance can vary significantly over small spatial gradients but it remains poorly understood how this impacts bleaching resilience and recovery dynamics, despite their importance as resilience hotspots and potential refugia. In the macrotidal Kimberley region in NW Australia, the 2016 global mass bleaching event had a strong habitat-specific impact on intertidal and subtidal coral communities at our study site: corals in the thermally variable intertidal bleached less severely and recovered within six months, while 68% of corals in the moderately variable subtidal died. We therefore conducted benthic surveys 3.5 years after the bleaching event to determine potential changes in benthic cover and coral community composition. In the subtidal, we documented substantial increases in algal cover and live coral cover had not fully recovered to pre-bleaching levels. Furthermore, the subtidal coral community shifted from being dominated by branching Acropora corals with a competitive life history strategy to opportunistic, weedy Pocillopora corals which likely has implications for the functioning and stress resilience of this novel coral community. In contrast, no shifts in algal and live coral cover or coral community composition occurred in the intertidal. These findings demonstrate that differences in coral heat tolerance across small spatial scales can have large consequences for bleaching resilience and that spatial patchiness in recovery trajectories and community reassembly after bleaching might be a common feature on thermally variable reefs. Our findings further confirm that reefs adapted to high daily temperature variability play a key role as resilience hotspots under current climate conditions, but their ability to do so may be limited under intensifying ocean warming.

Effects of Madagascar marine reserves on juvenile and adult coral abundance, and the implication for population regulation

Recruitment is a critical component in the dynamics of coral assemblages, and a key question is to determine the degree to which spatial heterogeneity of adults is influenced by pre-vs. post-settlement processes. We analyzed the density of juvenile and adult corals among 18 stations located at three regions around Madagascar, and examined the effects of Marine Protected Areas (MPAs). Our survey did not detect a positive effect of MPAs on juveniles, except for Porites at the study scale. The MPA effect was more pronounced for adults, notably for Acropora, Montipora, Seriatopora, and Porites at the regional scale. For most dominant genera, densities of juveniles and adults were positively correlated at the study scale, and at least at one of the three regions. These outcomes suggest recruitment-limitation relationships for several coral taxa, although differences in post-settlement events may be sufficiently strong to distort the pattern established at settlement for other populations. The modest benefits of MPAs on the density of juvenile corals demonstrated here argue in favor of strengthening conservation measures more specifically focused to protect recruitment processes.

Net effects of life-history traits explain persistent differences in abundance among similar species

Life-history traits are promising tools to predict species commonness and rarity because they influence a population's fitness in a given environment. Yet, species with similar traits can have vastly different abundances, challenging the prospect of robust trait-based predictions. Using long-term demographic monitoring, we show that coral populations with similar morphological and life-history traits show persistent (decade-long) differences in abundance. Morphological groups predicted species positions along two, well known life-history axes (the fast-slow continuum and size-specific fecundity). However, integral projection models revealed that density-independent population growth (λ) was more variable within morphological groups, and was consistently higher in dominant species relative to rare species. Within-group λ differences projected large abundance differences among similar species in short timeframes, and were generated by small but compounding variation in growth, survival, and reproduction. Our study shows that easily measured morphological traits predict demographic strategies, yet small life-history differences can accumulate into large differences in λ and abundance among similar species. Quantifying the net effects of multiple traits on population dynamics is therefore essential to anticipate species commonness and rarity.

Age-specific sensitivity analysis of stable, stochastic and transient growth for stage-classified populations

Sensitivity analysis in ecology and evolution is a valuable guide to rank demographic parameters depending on their relevance to population growth. Here, we propose a method to make the sensitivity analysis of population growth for matrix models solely classified by stage more fine-grained by considering the effect of age-specific parameters. The method applies to stable population growth, the stochastic growth rate, and transient growth. The method yields expressions for the sensitivity of stable population growth to age-specific survival and fecundity from which general properties are derived about the pattern of age-specific selective forces molding senescence in stage-classified populations.

Tracking changes in social-ecological systems along environmental disturbances with the ocean health index

The well-being of coastal communities is intimately tied to a healthy ocean, but coastal social-ecological systems are among the most vulnerable to global change. Improving the resilience of coastal communities requires an understanding of how local social-ecological systems respond to shocks to better inform decision-making and adapt local management interventions. However, assessments of social-ecological changes throughout a disturbance regime are scarce at the local level, although critical for efficient natural resource management and sustainable use of ocean ecosystem services. Here, we apply the Ocean Health Index (OHI) to assess the status of the marine social-ecological system of a tropical island (Moorea, French Polynesia), and track changes of the system before, during and after a disturbance regime. Our results show that while there are signs of social-ecological recovery, coastal protection was most affected along the disturbance, and that there is room for improvement toward biodiversity conservation. In addition, our study highlights some context-specific challenges associated with local OHI assessments, particularly those driven by limited fisheries data and appropriate reference point selection for coastal protection. Our results demonstrate the value of localized, regular OHI assessments through time to track changes in marine social-ecological systems, while uncovering important data gaps, to inform management at appropriate scales for decision-making.

Priority effects in coral-macroalgae interactions can drive alternate community paths in the absence of top-down control

The outcomes of species interactions can vary greatly in time and space with the outcomes of some interactions determined by priority effects. On coral reefs, benthic algae rapidly colonize disturbed substrate. In the absence of top-down control from herbivorous fishes, these algae can inhibit the recruitment of reef-building corals, leading to a persistent phase shift to a macroalgae-dominated state. Yet, corals may also inhibit colonization by macroalgae, and thus the effects of herbivores on algal communities may be strongest following disturbances that reduce coral cover. Here, we report results from experiments conducted on the fore reef of Moorea, French Polynesia, where we: 1) tested the ability of macroalgae to invade coral-dominated and coral-depauperate communities under different levels of herbivory, 2) explored the ability of juvenile corals (Pocillopora spp.) to suppress macroalgae, and 3) quantified the direct and indirect effects of fish herbivores and corallivores on juvenile corals. We found that macroalgae proliferated when herbivory was low but only in recently disturbed communities where coral cover was also low. When coral cover was < 10%, macroalgae increased 20-fold within one year under reduced herbivory conditions relative to high herbivory controls. Yet, when coral cover was high (50%), macroalgae were suppressed irrespective of the level of herbivory despite ample space for algal colonization. Once established in communities with low herbivory and low coral cover, macroalgae suppressed recruitment of coral larvae, reducing the capacity for coral replenishment. However, when we experimentally established small juvenile corals (2 cm diameter) following a disturbance, juvenile corals inhibited macroalgae from invading local neighborhoods, even in the absence of herbivores, indicating a strong priority effect in macroalgae-coral interactions. Surprisingly, fishes that initially facilitated coral recruitment by controlling algae had a net negative effect on juvenile corals via predation. Corallivores reduced growth rates of corals exposed to fishes by ~ 30% relative to fish exclosures despite increased competition with macroalgae within the exclosures. These results highlight that different processes are important for structuring coral reef ecosystems at different successional stages and underscore the need to consider multiple ecological processes and historical contingencies to predict coral community dynamics.

Post-settlement demographics of reef building corals suggest prolonged recruitment bottlenecks

For many organisms, early life stages experience significantly higher rates of mortality relative to adults. However, tracking early life stage individuals through time in natural settings is difficult, limiting our understanding of the duration of these ‘mortality bottlenecks’, and the time required for survivorship to match that of adults. Here, we track a cohort of juvenile corals (1–5 cm maximum diameter) from 12 taxa at a remote atoll in the Central Pacific from 2013 to 2017 and describe patterns of annual survivorship. Of the 537 juveniles initially detected, 219 (41%) were alive 4 years later, 163 (30%) died via complete loss of live tissue from the skeleton, and the remaining 155 (29%) died via dislodgement. The differing mortality patterns suggest that habitat characteristics, as well as species-specific features, may influence early life stage survival. Across most taxa, survival fit a logistic model, reaching > 90% annual survival within 4 years. These data suggest that mortality bottlenecks characteristic of ‘recruitment’ extend up to 5 years after individuals can be visually detected. Ultimately, replenishment of adult coral populations via sexual reproduction is needed to maintain both coral cover and genetic diversity. This study provides key insights into the dynamics and time scales that characterize these critical early life stages.

The war of corals: patterns, drivers and implications of changing coral competitive performances across reef environments

Amidst global environmental changes, predicting species' responses to future environments is a critical challenge for preserving biodiversity and associated human benefits. We explored the original idea that coral competitive performances, the ability of corals to preempt ecological space on the reef through territorial warfare, serve as indicators of species' ecological niches and environmental windows, and therefore, responses to future environments. Our surveys indicated that coral performances varied with taxonomic identity, size and position along environmental gradients, highlighting complex interplays between life-history, warfare-strategy and niche segregation. Our results forewarn that growing alterations of coastal environments may trigger shifts in coral dominance, with the decline of major reef-building taxa like acroporids, and emphasize the importance of limiting human impacts for coastal resilience. Our empirical approach untangles the complexity of species' battle-like interactions and can help identify winners and losers in various communities caught in the interplay between ecological niches, environmental windows and global changes.

Long-term ecological research and the COVID-19 anthropause: A window to understanding social-ecological disturbance

The period of disrupted human activity caused by the COVID-19 pandemic, coined the "anthropause," altered the nature of interactions between humans and ecosystems. It is uncertain how the anthropause has changed ecosystem states, functions, and feedback to human systems through shifts in ecosystem services. Here, we used an existing disturbance framework to propose new investigation pathways for coordinated studies of distributed, long-term social-ecological research to capture effects of the anthropause. Although it is still too early to comprehensively evaluate effects due to pandemic-related delays in data availability and ecological response lags, we detail three case studies that show how long-term data can be used to document and interpret changes in air and water quality and wildlife populations and behavior coinciding with the anthropause. These early findings may guide interpretations of effects of the anthropause as it interacts with other ongoing environmental changes in the future, particularly highlighting the importance of long-term data in separating disturbance impacts from natural variation and long-term trends. Effects of this global disturbance have local to global effects on ecosystems with feedback to social systems that may be detectable at spatial scales captured by nationally to globally distributed research networks.

A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress

Urbanized coral reefs experience anthropogenic disturbances caused by coastal development, pollution, and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity.There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are structured both at the community and functional levels. As such, it is unclear how they will respond to future disturbance events.Here, we examine the patterns of coral reef community change and determine whether ecosystem functions provided by specialist species are lost post-disturbance. We present a comparison of community and functional trait-based changes for scleractinian coral genera and reef fish species assemblages subject to coastal development, coastal modification, and mass bleaching between two time periods, 1975-1976 and 2018, in Nakagusuku Bay, Okinawa, Japan.We observed an increase in fish habitat generalists, a dominance shift from branching to massive/sub-massive corals and increasing site-based coral genera richness between years. Fish and coral communities significantly reassembled, but functional trait-based multivariate space remained constant, indicating a turnover of species with similar traits. A compression of coral habitat occurred, with shallow (<5 m) and deep (>8 m) coral genera shifting towards the mid-depths (5-8 m).We show that although reef species assemblages altered post disturbance, new communities retained similar ecosystem functions. This result could be linked to the stressors experienced by urban reefs, which reflect those that will occur at an increasing frequency globally in the near future. Yet, even after shifts to disturbed communities, these fully functioning reef systems may maintain high conservation value.

Scaling up calcification, respiration, and photosynthesis rates of six prominent coral taxa

Coral reefs provide a range of important services to humanity, which are underpinned by community-level ecological processes such as coral calcification. Estimating these processes relies on our knowledge of individual physiological rates and species-specific abundances in the field. For colonial animals such as reef-building corals, abundance is frequently expressed as the relative surface cover of coral colonies, a metric that does not account for demographic parameters such as coral size. This may be problematic because many physiological rates are directly related to organism size, and failure to account for linear scaling patterns may skew estimates of ecosystem functioning. In the present study, we characterize the scaling of three physiological rates - calcification, respiration, and photosynthesis - considering the colony size for six prominent, reef-building coral taxa in Mo'orea, French Polynesia. After a seven-day acclimation period in the laboratory, we quantified coral physiological rates for three hours during daylight (i.e., calcification and gross photosynthesis) and one hour during night light conditions (i.e., dark respiration). Our results indicate that area-specific calcification rates are higher for smaller colonies across all taxa. However, photosynthesis and respiration rates remain constant over the colony-size gradient. Furthermore, we revealed a correlation between the demographic dynamics of coral genera and the ratio between net primary production and calcification rates. Therefore, intraspecific scaling of reef-building coral physiology not only improves our understanding of community-level coral reef functioning but it may also explain species-specific responses to disturbances.

Size-dependent mortality of corals during marine heatwave erodes recovery capacity of a coral reef

For many long-lived taxa, such as trees and corals, older, and larger individuals often have the lowest mortality and highest fecundity. However, climate change-driven disturbances such as droughts and heatwaves may fundamentally alter typical size-dependent patterns of mortality and reproduction in these important foundation taxa. Working in Moorea, French Polynesia, we investigated how a marine heatwave in 2019, one of the most intense marine heatwaves at our sites over the past 30 years, drove patterns of coral bleaching and mortality. The marine heatwave drove island-wide mass coral bleaching that killed up to 76% and 65% of the largest individuals of the two dominant coral genera, Pocillopora and Acropora, respectively. Colonies of Pocillopora and Acropora ≥30 cm diameter were ~3.5× and ~1.3×, respectively, more likely to die than colonies <30-cm diameter. Typically, annual mortality in these corals is concentrated on the smallest size classes. Yet, this heatwave dramatically reshaped this pattern, with heat stress disproportionately killing larger coral colonies and equalizing annual mortality rates across the size spectrum. This shift in the size-mortality relationship reduced the overall fecundity of these genera by >60% because big corals are disproportionately important for reproduction on reefs. Additionally, the survivorship of microscopic coral recruits, critical for the recovery of corals following disturbances, declined to 2%, over an order of magnitude lower compared to a year without elevated thermal stress, where 33% of coral recruits survived. While other research has shown that larger corals can bleach more frequently than smaller corals, we show the severe impact this phenomenon can have at the reef-wide scale. As marine heatwaves become more frequent and intense, disproportionate mortality of the largest, most fecund corals and near-complete loss of entire cohorts of newly-settled coral recruits will likely reduce the recovery capacity of these iconic ecosystems.

A molecular census of early-life stage scleractinian corals in shallow and mesophotic zones

The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield against disturbances and help replenish deteriorated shallower reefs. In this study, we characterized spatial (horizontal and vertical) and seasonal patterns of diversity in coral recruits from Dabaisha and Guiwan reefs at Ludao, Taiwan. Concrete blocks supporting terra-cotta tiles were placed at shallow (15m) and mesophotic (40m) depths, during 2016-2018. Half of the tiles were retrieved and replaced biannually over three 6-month surveys (short-term); the remainder retrieved at the end of the 18-month (long-term) survey. 451 recruits were located using fluorescent censusing and identified by DNA barcoding. Barcoding the mitochondrial cytochrome oxidase I (COI) gene resulted in 17 molecular operational taxonomic units (MOTUs). To obtain taxonomic resolution to the generic level, Pocillopora were phylotyped using the mitochondrial open reading frame (ORF), resolving eight MOTUs. Acropora, Isopora, and Montipora recruits were identified by the nuclear PaxC intron, yielding ten MOTUs. Overall, 35 MOTUs were generated and were comprised primarily of Pocillopora and, in fewer numbers, Acropora, Isopora, Pavona, Montipora, Stylophora, among others. 40% of MOTUs recruited solely within mesophotic reefs while 20% were shared by both depth zones. MOTUs recruiting across a broad depth distribution appear consistent with the hypothesis of mesophotic reefs acting as a refuge for shallow-water coral reefs. In contrast, Acropora and Isopora MOTUs were structured across depth zones representing an exception to this hypothesis. This research provides an imperative assessment of coral recruitment in understudied mesophotic reefs and imparts insight into the refuge hypothesis.

Scaling the effects of ocean acidification on coral growth and coral-coral competition on coral community recovery

Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, French Polynesia. Focusing on the dominant coral genera from the fore reef, Pocillopora, Acropora, Montipora and Porites, model efficacy first was evaluated through the comparison of simulated and empirical dynamics from 2010-2016, when the reef was recovering from sequential acute disturbances (a crown-of-thorns seastar outbreak followed by a cyclone) that reduced coral cover to ~0% by 2010. The model then was used to evaluate how the effects of OA (1,100-1,200 µatm pCO₂) on coral growth and competition among corals affected recovery rates (as assessed by changes in % cover y^-1) of each coral population between 2010-2016. The model indicated that recovery rates for the fore reef community was halved by OA over 7 years, with cover increasing at 11% y^-1 under ambient conditions and 4.8% y^-1 under OA conditions. However, when OA was implemented to affect coral growth and not competition among corals, coral community recovery increased to 7.2% y^-1, highlighting mechanisms other than growth suppression (i.e., competition), through which OA can impact recovery. Our study reveals the potential for IBMs to assess the impacts of OA on coral communities at temporal and spatial scales beyond the capabilities of experimental studies, but this potential will not be realized unless empirical analyses address a wider variety of response variables representing ecological, physiological and functional domains.

Juvenile corals underpin coral reef carbonate production after disturbance

Sea-level rise is predicted to cause major damage to tropical coastlines. While coral reefs can act as natural barriers for ocean waves, their protection hinges on the ability of scleractinian corals to produce enough calcium carbonate (CaCO₃ ) to keep up with rising sea levels. As a consequence of intensifying disturbances, coral communities are changing rapidly, potentially reducing community-level CaCO₃ production. By combining colony-level physiology and long-term monitoring data, we show that reefs recovering from major disturbances can produce 40% more CaCO₃ than currently estimated due to the disproportionate contribution of juvenile corals. However, the buffering effect of highly productive juvenile corals is compromised by recruitment failures, which have been more frequently observed after large-scale, repeated bleaching events. While the size structure of corals can bolster a critical ecological function on reefs, climate change impacts on recruitment may undermine this buffering effect, thus further compromising the persistence of reefs and their provision of important ecosystem services.

Apoptosis and cell proliferation during metamorphosis of the planula larva of Clytia hemisphaerica (Hydrozoa, Cnidaria)

BACKGROUND

Metamorphosis in marine species is characterized by profound changes at the ecophysiological, morphological, and cellular levels. The cnidarian Clytia hemisphaerica exhibits a triphasic life cycle that includes a planula larva, a colonial polyp, and a sexually reproductive medusa. Most studies so far have focused on the embryogenesis of this species, whereas its metamorphosis has been only partially studied.

RESULTS

We investigated the main morphological changes of the planula larva of Clytia during the metamorphosis, and the associated cell proliferation and apoptosis. Based on our observations of planulae at successive times following artificial metamorphosis induction using GLWamide, we subdivided the Clytia's metamorphosis into a series of eight morphological stages occurring during a pre-settlement phase (from metamorphosis induction to planula ready for settlement) and the post-settlement phase (from planula settlement to primary polyp). Drastic morphological changes prior to definitive adhesion to the substrate were accompanied by specific patterns of stem-cell proliferation as well as apoptosis in both ectoderm and endoderm. Further waves of apoptosis occurring once the larva has settled were associated with morphogenesis of the primary polyp.

CONCLUSION

Clytia larval metamorphosis is characterized by distinct patterns of apoptosis and cell proliferation during the pre-settlement phase and the settled planula-to-polyp transformation.

Different population trajectories of two reef-building corals with similar life-history traits

Increases in the frequency and intensity of acute and chronic disturbances are causing declines of coral reefs world‐wide. Although quantifying the responses of corals to acute disturbances is well documented, detecting subtle responses of coral populations to chronic disturbances is less common, but can also result in altered population and community structures.

We investigated the population dynamics of two key reef‐building Merulinid coral species, Dipsastraea favus and Platygyra lamellina, with similar life‐history traits, in the Gulf of Eilat and Aqaba, Red Sea from 2015 to 2018, to assess potential differences in their population trajectories.

Demographic processes, which included rates of survival, growth, reproduction and recruitment were used to parametrize integral projection models and estimate population growth rates and the likely population trajectories of both coral species.

The survival and reproduction rates of both D. favus and P. lamellina were positively related to coral colony size, and elasticity analyses showed that large colonies most influenced population dynamics. Although both species have similar life‐history traits and growth morphologies and are generally regarded as ‘stress‐tolerant’, the populations showed contrasting trajectories—D. favus appears to be increasing whereas P. lamellina appears to be decreasing.

As many corals have long‐life expectancies, the process of local and regional decline might be subtle and slow. Ecological assessments based on total living coral coverage, morphological groups or functional traits might overlook subtle, species‐specific trends. However, demographic approaches capable of detecting subtle species‐specific population changes can augment ecological studies and provide valuable early warning signs of decline before major coral loss becomes evident.

Stony coral populations are more sensitive to changes in vital rates in disturbed environments

Reef-building corals, like many long-lived organisms, experience environmental change as a combination of separate but concurrent processes, some of which are gradual yet long-lasting, while others are more acute but short-lived. For corals, some chronic environmental stressors, such as rising temperature and ocean acidification, are thought to induce gradual changes in colonies' vital rates. Meanwhile, other environmental changes, such as the intensification of tropical cyclones, change the disturbance regime that corals experience. Here, we use a physiologically structured population model to explore how chronic environmental stressors that impact the vital rates of individual coral colonies interact with the intensity and magnitude of disturbance to affect coral population dynamics and cover. We find that, when disturbances are relatively benign, intraspecific density dependence driven by space competition partially buffers coral populations against gradual changes in vital rates. However, the impact of chronic stressors is amplified in more highly disturbed environments, because disturbance weakens the buffering effect of space competition. We also show that coral cover is more sensitive to changes in colony growth and mortality than to external recruitment, at least in open populations, and that space competition and size structure mediate the extent and pace of coral population recovery following a large-scale mortality event. Understanding the complex interplay among chronic environmental stressors, mass-mortality events, and population size structure sharpens our ability to manage and to restore coral-reef ecosystems in an increasingly disturbed future.

Recovery disparity between coral cover and the physical functionality of reefs with impaired coral assemblages

The ecology and structure of many tropical coral reefs have been markedly altered over the past few decades. Although long-term recovery has been observed in terms of coral cover, it is not clear how novel species configurations shape reef functionality in impaired reefs. The identities and life-history strategies of the corals species that recover are essential for understanding reef functional dynamics. We used a species identity approach to quantify the physical functionality outcomes over a 13 year period across 56 sites in the Mexican Caribbean. This region was affected by multiple stressors that converged and drastically damaged reefs in the early 2000s. Since then, the reefs have shown evidence of a modest recovery of coral cover. We used Bayesian linear models and annual rates of change to estimate temporal changes in physical functionality and coral cover. Moreover, a functional diversity framework was used to explore changes in coral composition and the traits of those assemblages. Between 2005 and 2018, physical functionality increased at a markedly lower rate compared to that of coral cover. The disparity between recovery rates depended on the identity of the species that increased (mainly non-framework and foliose-digitate corals). No changes in species dominance or functional trait composition were observed, whereas non-framework building corals consistently dominated most reefs. Although the observed recovery of coral cover and functional potential may provide some ecological benefits, the long-term effects on reef frameworks remain unclear, as changes in the cover of key reef-building species were not observed. Our findings are likely to be representative of many reefs across the wider Caribbean basin, as declines in coral cover and rapid increases in the relative abundance of weedy corals have been reported regionally. A coral identity approach to assess species turnover is needed to understand and quantify changes in the functionality of coral reefs.

Landscape-scale patterns of nutrient enrichment in a coral reef ecosystem: implications for coral to algae phase shifts

Nutrient pollution is altering coastal ecosystems worldwide. On coral reefs, excess nutrients can favor the production of algae at the expense of reef-building corals, yet the role of nutrients in driving community changes such as shifts from coral to macroalgae is not well understood. Here we investigate the potential role of anthropogenic nutrient loading in driving recent coral-to-macroalgae phase shifts on reefs in the lagoons surrounding the Pacific island of Moorea, French Polynesia. We use nitrogen (N) tissue content and stable isotopes (δ¹⁵ N) in an abundant macroalga (Turbinaria ornata) together with empirical models of nutrient discharge to describe spatial and temporal patterns of nutrient enrichment in the lagoons. We then employ time series data to test whether recent increases in macroalgae are associated with nutrients. Our results revealed that patterns of N enrichment were linked to several factors, including rainfall, wave-driven circulation, and distance from anthropogenic nutrient sources, especially human sewage. Reefs near large watersheds, where inputs of N from sewage and agriculture are high, have been consistently enriched in N for at least the last decade. In many of these areas, corals have decreased and macroalgae have increased, while reefs with lower levels of N input have maintained high cover of coral and low cover of macroalgae. Importantly, these patchy phase shifts to macroalgae have occurred despite substantial island-wide increases in the density and biomass of herbivorous fishes over the time period. Together, these results indicate that nutrient loading may be an important driver of coral-to-macroalgae phase shifts in the lagoons of Moorea even though the reefs harbor an abundant and diverse herbivore assemblage. These results emphasize the important role that bottom-up factors can play in driving coral-to-macroalgae phase shifts and underscore the critical importance of watershed management for reducing inputs of nutrients and other land-based pollutants to coral reef ecosystems.

Diversity, structure and demography of coral assemblages on underwater lava flows of different ages at Reunion Island and implications for ecological succession hypotheses

Understanding colonization of new habitats and ecological successions is key to ecosystem conservation. However, studies on primary successions are scarce for reef-building corals, due to the rarity of newly formed substratum and the long-term monitoring efforts required for their long life cycle and slow growth rate. We analysed data describing the diversity, structure and demography of coral assemblages on lava flows of different ages and coral reefs at Reunion Island, to evaluate the strength and mechanisms of succession, and its agreement to the theoretical models. No significant differences were observed between the two habitats for most structure and demographic descriptors. In contrast, species richness and composition differentiated coral reefs from lava flows, but were not related to the age of the lava flow. We observed a strong dominance of Pocillopora colonies, which underline the opportunistic nature of this taxa, with life-history traits advantageous to dominance on primary and secondary successional stages. Although some results argue in favor of the tolerance model of succession, the sequences of primary successions as theorized in other ecosystems were difficult to observe, which is likely due to the high frequency and intensity of disturbances at Reunion, that likely distort or set back the expected successional sequences.

Considering the rates of growth in two taxa of coral across Pacific islands

Reef-building coral taxa demonstrate considerable flexibility and diversity in reproduction and growth mechanisms. Corals take advantage of this flexibility to increase or decrease size through clonal expansion and loss of live tissue area (i.e. via reproduction and mortality of constituent polyps). The biological lability of reef-building corals may be expected to map onto varying patterns of demography across environmental contexts which can contribute to geographic variation in population dynamics. Here we explore the patterns of growth of two common coral taxa, corymbose Pocillopora and massive Porites, across seven islands in the central and south Pacific. The islands span a natural gradient of environmental conditions, including a range of pelagic primary production, a metric linked to the relative availability of inorganic nutrients and heterotrophic resources for mixotrophic corals, and sea surface temperature and thermal histories. Over a multi-year sampling interval, most coral colonies experienced positive growth (greater planar area of live tissue in second relative to first time point), though the distributions of growth varied across islands. Island-level median growth did not relate simply to estimated pelagic primary productivity or temperature. However, at locations that experienced an extreme warm-water event during the sampling interval, most Porites colonies experienced net losses of live tissue and nearly all Pocillopora colonies experienced complete mortality. While descriptive statistics of demographics offer valuable insights into trends and variability in colony change through time, simplified models predicting growth patterns based on summarized oceanographic metrics appear inadequate for robust demographic prediction. We propose that the complexity of life history strategies among colonial reef-building corals introduces unique demographic flexibility for colonies to respond to a wide breadth of environmental conditions.

Projected shifts in coral size structure in the Anthropocene

Changes in the size structure of coral populations have major consequences for population dynamics and community function, yet many coral reef monitoring projects do not record this critical feature. Consequently, our understanding of current and future trajectories in coral size structure, and the demographic processes underlying these changes, is still emerging. Here, we provide a conceptual summary of the benefits to be gained from more comprehensive attention to the size of coral colonies in reef monitoring projects, and we support our argument through the use of case-history examples and a simplified ecological model. We neither seek to review the available empirical data, or to rigorously explore causes and implications of changes in coral size, we seek to reveal the advantages to modifying ongoing programs to embrace the information inherent in changing coral colony size. Within this framework, we evaluate and forecast the mechanics and implications of changes in the population structure of corals that are transitioning from high to low abundance, and from large to small colonies, sometimes without striking effects on planar coral cover. Using two coral reef locations that have been sampled for coral size, we use demographic data to underscore the limitations of coral cover in understanding the causes and consequences of long-term declining coral size, and abundance. A stage-structured matrix model is used to evaluate the demographic causes of declining coral colony size and abundance, particularly with respect to the risks of extinction. The model revealed differential effects of mortality, growth and fecundity on coral size distributions. It also suggested that colony rarity and declining colony size in association with partial tissue mortality and chronic declines in fecundity, can lead to a demographic bottleneck with the potential to prolong the existence of coral populations when they are characterized by mostly very small colonies. Such bottlenecks could have ecological importance if they can delay extinction and provide time for human intervention to alleviate the environmental degradation driving reductions in coral abundance.

Combining agent-based, trait-based and demographic approaches to model coral-community dynamics

The complexity of coral-reef ecosystems makes it challenging to predict their dynamics and resilience under future disturbance regimes. Models for coral-reef dynamics do not adequately account for the high functional diversity exhibited by corals. Models that are ecologically and mechanistically detailed are therefore required to simulate the ecological processes driving coral reef dynamics. Here, we describe a novel model that includes processes at different spatial scales, and the contribution of species' functional diversity to benthic-community dynamics. We calibrated and validated the model to reproduce observed dynamics using empirical data from Caribbean reefs. The model exhibits realistic community dynamics, and individual population dynamics are ecologically plausible. A global sensitivity analysis revealed that the number of larvae produced locally, and interaction-induced reductions in growth rate are the parameters with the largest influence on community dynamics. The model provides a platform for virtual experiments to explore diversity-functioning relationships in coral reefs.

Cross-Shelf Variation in Coral Community Response to Disturbance on the Great Barrier Reef

Changes in coral reef health and status are commonly reported using hard coral cover, however such changes may also lead to substantial shifts in coral community composition. Here we assess the extent to which coral communities departed from their pre-disturbance composition following disturbance (disassembly), and reassembled during recovery (reassembly) along an environmental gradient across the continental shelf on Australia’s Great Barrier Reef. We show that for similar differences in coral cover, both disassembly and reassembly were greater on inshore reefs than mid- or outer-shelf reefs. This pattern was mostly explained by spatial variation in the pre-disturbance community composition, of which 28% was associated with chronic stressors related to water quality (e.g., light attenuation, concentrations of suspended sediments and chlorophyll). Tropical cyclones exacerbated the magnitude of community disassembly, but did not vary significantly among shelf positions. On the outer shelf, the main indicator taxa (tabulate Acropora) were mostly responsible for community dissimilarity, whereas contribution to dissimilarity was distributed across many taxa on the inner shelf. Our results highlight that community dynamics are not well captured by aggregated indices such as coral cover alone, and that the response of ecological communities to disturbance depends on their composition and exposure to chronic stressors.

Experimental support for alternative attractors on coral reefs

Ecological theory predicts that under the same environmental conditions, an ecosystem could have more than one community state that is maintained by reinforcing feedbacks. If so, a sufficiently large disturbance can flip the system to a less desired community that is difficult to reverse. Here, we demonstrate that a coral reef can become trapped in a seaweed-dominated state in the same conditions under which corals thrive. The implications are profound, particularly in light of the increasing occurrence of shifts to seaweed on coral reefs worldwide. Our results indicate that anticipatory management strategies that lessen the chance of a switch to seaweeds will be more effective than those aimed at restoring the coral community after a shift.

Ecological theory predicts that ecosystems with multiple basins of attraction can get locked in an undesired state, which has profound ecological and management implications. Despite their significance, alternative attractors have proven to be challenging to detect and characterize in natural communities. On coral reefs, it has been hypothesized that persistent coral-to-macroalgae “phase shifts” that can result from overfishing of herbivores and/or nutrient enrichment may reflect a regime shift to an alternate attractor, but, to date, the evidence has been equivocal. Our field experiments in Moorea, French Polynesia, revealed the following: (i) hysteresis existed in the herbivory–macroalgae relationship, creating the potential for coral–macroalgae bistability at some levels of herbivory, and (ii) macroalgae were an alternative attractor under prevailing conditions in the lagoon but not on the fore reef, where ambient herbivory fell outside the experimentally delineated region of hysteresis. These findings help explain the different community responses to disturbances between lagoon and fore reef habitats of Moorea over the past several decades and reinforce the idea that reversing an undesired shift on coral reefs can be difficult. Our experimental framework represents a powerful diagnostic tool to probe for multiple attractors in ecological systems and, as such, can inform management strategies needed to maintain critical ecosystem functions in the face of escalating stresses.

Spatial Patterns and Short-term Changes of Coral Assemblages Along a Cross-shelf Gradient in the Southwestern Lagoon of New Caledonia

Coral reef assemblages generally form gradients of spatial structures which are governed by a variety of interacting physical and biological processes that vary in intensity, frequency, and spatial scale. Assessing the structure of contemporary reef assemblages may help to understand future changes and to identify appropriate conservation actions. The spatial distribution and interannual variability (from 2006 to 2008) of coral assemblages were investigated at 10 stations in the southwestern lagoon of New Caledonia, and the strength of the cross-shelf gradient was evaluated. Coral cover, generic richness, and abundance of adult and juvenile assemblages were highly variable within and among the three major reef habitats (fringing, mid-shelf, and barrier reefs). Abundance increased with distance from shore, whereas generic richness and cover were not correlated with shelf position. Assemblage composition was generally related to habitat, even though some mid-shelf and fringing reef assemblages resembled those observed on other habitats. A significant correlation between juvenile and adult distributions was recorded, suggesting that adult assemblages are partly controlled by the short-term history of recruitment patterns. The interannual variation of coral assemblages was far less pronounced, with significant changes only detected at some mid-shelf and barrier reefs, for a few genera characterised by high turn-over.

Exposure, vulnerability, and resiliency of French Polynesian coral reefs to environmental disturbances

Preserving coral reef resilience is a major challenge in the Anthropocene, yet recent studies demonstrate failures of reef recovery from disturbance, globally. The wide and vigorous outer-reef system of French Polynesia presents a rare opportunity to assess ecosystem resilience to disturbances at a large-scale equivalent to the size of Europe. In this purpose, we analysed long-term data on coral community dynamics and combine the mixed-effects regression framework with a set of functional response models to evaluate coral recovery trajectories. Analyses of 14 years data across 17 reefs allowed estimating impacts of a cyclone, bleaching event and crown-of-thorns starfish outbreak, which generated divergence and asynchrony in coral community trajectory. We evaluated reef resilience by quantifying levels of exposure, degrees of vulnerability, and descriptors of recovery of coral communities in the face of disturbances. Our results show an outstanding rate of coral recovery, with a systematic return to the pre-disturbance state within only 5 to 10 years. Differences in the impacts of disturbances among reefs and in the levels of vulnerability of coral taxa to these events resulted in diverse recovery patterns. The consistent recovery of coral communities, and convergence toward pre-disturbance community structures, reveals that the processes that regulate ecosystem recovery still prevail in French Polynesia.