Biology subjects

Mumby, P. J.

Publications and source records attributed to Mumby, P. J..

15 recordsLinked to original sources

bioRxiv2026

Juveniles exhibit lower heatwave tolerance than adults in a reef-building coral

Marine heatwaves cause widespread coral bleaching and mortality, yet thermal responses often differ between adult and juvenile corals, with the latter frequently being more tolerant. Whether the observed enhanced tolerance of juveniles reflects intrinsic physiological differences across life stages or simply reduced environmental stress due to shaded microhabitats occupied by juveniles, or a combination of both factors, remains unclear. To test whether colony size determines thermal responses and if a threshold size exists for tolerance, we exposed 89 colonies of the reef-building coral Acropora aff. digitifera to a 6-week, 32.5 C simulated marine heatwave under controlled light conditions, with cumulative stress reaching 20 C-weeks. Contrary to expectations, ~2 C-weeks less heat stress was required to trigger bleaching and mortality in coral juveniles compared to adults. Mortality divergence across colony sizes was greatest at ~10 C-weeks, when the smallest corals exceeded 80% mortality, whereas the largest colonies showed <10% mortality. A breakpoint in survival odds was apparent at 13.4 cm diameter, corresponding to the size at onset of sexual maturity in the native wild population for this species. These results indicate an ontogenetic shift in physiological heat tolerance, with larger reproductively mature colonies showing enhanced tolerance. The apparent survival advantage of juveniles in the reef frequently reported during bleaching events could be more likely due to micro-environmental buffering than intrinsic physiological tolerance. Our findings suggest that juvenile corals may be more vulnerable to climate change than previously thought, particularly as declining habitat complexity could reduce microhabitat refugia on future reefs.

ecology↗

bioRxiv2025

Beyond Coral Cover: A framework for assessing the condition of coral reef habitats and informing conservation targets

The goal of ecosystem management is to maintain healthy and resilient ecosystems over time. These attributes can be summarised under a general term widely used in management plans: ecosystem condition, defined as the overall quality of an ecosystem relative to a desired or reference state. However, measuring and monitoring ecosystem condition remains a challenge. Monitoring ecosystem condition requires a suite of ecological indicators that simultaneously capture the complexity and variability of ecological processes, while being informative and usable in management and decision-making contexts. Such indicators need to be holistic, measurable, sensitive and scalable. Here we outline a resilience-based monitoring framework for coral reefs that consolidates monitoring data and research insights into a relevant, integrated format. The framework includes indicators of ecosystem state (coral cover) and key processes (represented by recovery performance, macroalgae prevalence, community composition, and coral juvenile density). Indicators are generated and scaled from monitoring data by applying explicit, reef-specific thresholds, providing a simple but comprehensive set of ecosystem condition values. Using cases from the Great Barrier Reef, we demonstrate how the framework integrates these indicators for detailed assessments of reef habitat condition and its potential role in management. Based on these case studies, we discuss important considerations for applying this framework worldwide, acknowledging current limitations related to data availability, resolution, and the length of time series.

ecology↗

bioRxiv2025

Proximity and current alignment drives fertilisation success in a broadcast-spawning coral

As coral populations decline under climate change and other stressors, surviving corals will become increasingly isolated. While Allee effects that reduce gamete encounters and fertilisation success may lead to reproductive and recruitment failure, the critical population densities and distances between individuals required to maintain viable populations remains uncertain. Here, we investigate the links between colony isolation and fertilisation patterns using an experimentally manipulated patch of the broadcast spawning tabular coral, Acropora hyacinthus. Corals were arranged in a clustered radial design, with colonies arranged at increasing distances radiating downstream from a central spawning aggregation. Fertilisation and paternity assignment analyses were used to examine the influence of parental distance, current alignment, colony size, and genetic relatedness. Fertilisation success declined sharply with increasing distance among corals, and paternity assignments indicated most parents were located within 3 m of each other, underscoring the importance of colony proximity. Additionally, fertilisation success was highest for colonies positioned downstream of the central cluster, and 84% of sequenced progeny were sired by colonies located directly upstream. Simulations of natural reef spatial population distributions projected onto a virtual grid, incorporating empirically derived parentage distances, indicated that populations remained well-mixed at typical adult densities in nearby reefs. However, as densities decreased to 1 colony per 100 m-2 (i.e. 0.01 colonieslllm-2), reproductive isolation and the formation of patchy breeding units became prevalent. Overall, our findings highlight that the spatial arrangement and isolation of corals on reefs, and subsequent Allee effects on fertilisation, can jeopardise the reproductive success of broadcast spawning corals. Conservation efforts are needed to help maintain viable coral populations and successful reproductive aggregations for degraded reef systems.

ecology↗

bioRxiv2025

Optimising fertilisation kinetics models for broadcast spawning corals in the genus Acropora

Synchronous spawning is a specialised adaptation to maximise fertilisation success in free spawning sessile invertebrates. There are many factors that drive and limit reproduction in such benthic invertebrates including localised hydrodynamic forcing, adult density dependence, and fine-scale gamete interactions, all of which are difficult to measure in situ. Therefore, measures to manage or restore reproductive populations of sessile invertebrates rely in part on adequate modelling of spawning processes at localised scales. Fertilisation kinetics of spawning events has been modelled for many free spawning marine invertebrate taxa, yet little work has been done to parameterise such models for hermaphroditic corals. This study used experimentally derived coral-specific parameters and optimisation protocols to improve model predictions of fertilisation outcomes for Acropora kenti (formerly A. "Maggie" tenuis) and A. digitifera. Three fine scale parameters that are difficult to measure experimentally - fertilisation efficiency (Fe), egg concentration (E0), and polyspermy block strength (tb) - were estimated using optimisation, and medians and 95% confidence intervals were derived for each parameter and species. For A. kenti the median optimised Fe value was 0.0194 (0.0027-0.0776), and tb was 0.1000 (0.1000-0.1000). For A. digitifera, the median optimised Fe value was 0.0013 (0.0002-0.0030), and tb was 10.0000 (2.4703- 10.0000). Further, sensitivity analyses suggest that kinetics models are the most sensitive to changes in Fe parameter values, as well as species-specific metrics like sperm swimming speed and egg size. Results will inform biophysical coral fertilisation models to better predict reproductive outcomes and support management decisions that safeguard natural reef recovery.

systems biology↗

bioRxiv2025

Impacts of wind-driven hydrodynamics on the early stages of coral development

Coral spawning has evolved to occur during relatively calm hydrodynamic conditions. However, moderate to high surface winds are often present on spawning nights in specific regions, with many unknown impacts to the early life-history stages of corals. Here, we mechanistically examine the sensitivity of fertilisation and larval development to increasing wind speeds for four common species of hermaphroditic corals on the Great Barrier Reef: Acropora kenti, A. millepora, A. spathulata, and Platygyra daedalea. Wind intensities relevant to coral spawning seasons were simulated by downscaling location-specific, historical wind speeds to laboratory flumes. Generally, fertilisation success declined as duration of exposure increased and was often lowest at the highest wind intensity equating to 15 knots in situ. Embryo damage, deformity, and fragmentation increased with exposure time, but varied across species. Four days following spawning, damaged and fragmented embryos had the highest mortality rates (76-82% and 70-73%) compared to intact embryos (26% and 52%) for A. kenti and A. spathulata, respectively. Experimental parameters were used to fit a 3D Fluid Dynamics model with outputs confirming that water surface elevations, velocity, and turbulence energy increased by up to 10%, 40%, and 50% respectively as winds intensified, likely explaining the physical drivers of the deleterious effects observed. Overall, results from this study indicate that suboptimal spawning conditions reduce propagule production, which may diminish recovery potential, thus require consideration when planning management strategies to safeguard coral reproduction.

systems biology↗

bioRxiv2025

A rapidly closing window for coral persistence under global warming

Summary paragraphCoral reefs around the world are threatened by recurrent marine heatwaves causing mass coral bleaching and mortality1. Mitigating future warming impacts requires strategic management2 that adopts a long-term lens. Global analyses of projected heatwaves3,4 are critical for decision-making but how disturbance refugia, coral life-histories and adaptation interact with warming is unknown. Here, we simulate coral eco-evolutionary dynamics across >3,800 individual reefs of Australias iconic Great Barrier Reef under the current suite of climate projections5. We forecast a rapid coral decline before mid-century regardless of emissions scenario. Under the most likely warming6, corals may continue to decline throughout the century. However, corals may recover after mid-century provided that warming is sufficiently slow, allowing thermal adaptation to keep pace with temperature changes - as projected if warming does not exceed 2{degrees}C. Higher emission scenarios would drive most reefs to a near collapse. Future resilient reefs were mostly found in bleaching refugia, which also possessed a greater diversity of thermal phenotypes. Although cool-adapted corals disperse to thermal hotspots, there was no evidence of gene swamping undermining thermal adaptation. While opportunities exist to build management strategies that promote adaptation in thermal refugia and warm spots, curbing the rate of warming by 2050 is crucial for coral persistence.

ecology↗

bioRxiv2024

Allee effects, spawning asynchrony, and mixed reproductive modes in a common mass spawning coral

Understanding strategies of organisms that utilise multiple modes of reproduction presents a complex challenge for evolutionary biologists. Platygyra daedalea, a common reef-building coral with unclear reproductive boundaries between morphological species, illustrates these complexities. Here, we evaluate the contribution of these reproductive modes in the coral P. daedalea at Heron Island, on the southern Great Barrier Reef. We tagged and sequenced eighteen coral colonies, representing various degrees of spatial clustering, along a 130-m stretch of shallow reef slope. During spawning, divers collected eggs from each colony and placed them in mesh containers within the spawn slick, allowing free movement of sperm for fertilisation. High levels of spawning asynchrony were observed, potentially indicating distinct genetic clusters within the putative species, which resulted in low fertilisation success (1.5%). Notably, of those fertilised eggs, paternity assignments revealed that all resulting embryos were self-fertilised, with no cross-fertilisation occurring. The adult population showed evidence of two genetically distinct subpopulations, along with levels of spatial autocorrelation and inbreeding. This evidence supports the notion of small breeding populations within larger assemblages, density-dependent population effects, and localised recruitment. Selfing may serve as a reproductive assurance mechanism in such populations, which may be more hierarchically structured than previously thought. Given the lack of evidence for in situ outcrossed fertilisation in this natural coral population during split spawning, it appears that P. daedalea may rely on limited high-density patches of adults for successful cross-fertilisation, utilise atypical modes of reproduction when at low densities, and/or sustain its population through limited progeny.

ecology↗

bioRxiv2024

Broadscale reconnaissance of coral reefs from citizen science and deep learning

Coral reef managers require various forms of data. While monitoring is typically the preserve of scientists, larger scale reconnaissance data that can be used to inform spatial decisions does not usually require such precise measurement. There is an increasing need to collect such broadscale, up-to-date environmental data at massive scale to prioritise limited conservation resources in the face of global disturbances. Citizen science combined with novel technology presents an opportunity to achieve data collection at the required scale, but the accuracy and feasibility of new tools must be assessed. Here we show that a citizen science program that collects seascape images and analyses them using a combination of deep learning and online citizen scientists can produce accurate benthic cover estimates of key coral groups. The deep learning and citizen scientist analysis methods had different but complementary strengths depending on coral category. When the best performing analysis method was used for each category in all images, mean estimates from 8086 images of percent benthic cover of branching Acropora, plating Acropora, and massive-form coral were [~]99% accurate compared to expert assessment of the same images, and >95% accurate at all coral cover ranges tested. The effort to achieve 95% accuracy at a site - our ecologically relevant target based on the accuracy of other tools - was attainable based on citizen scientist involvement in pilot years of the program, with 18-80 images needed depending on coral type and reef state. Power analyses showed that sampling up to 114 images per site was needed to detect a 10% absolute difference in coral cover per category (power = 0.8), accounting for natural heterogeneity. However, the benthic cover of all other coral groups as a single category could only be estimated with 95% accuracy at 60% of survey sites and for images with 10-30% coral cover. Disaggregating this other coral group into more distinct coral categories may improve accuracy. Overall, citizen science can provide an accuracy that is acceptable for many end-users for select coral morphologies. Such a combination of emerging technology and citizen science presents an attainable tool for collecting inexpensive, widespread reconnaissance data of coral reefs that can complement higher resolution survey programs or be an accessible tool for resource-poor locations.

ecology↗

bioRxiv2024

Marine spatial planning to enhance coral adaptive potential

Ocean warming interacts with local stressors to negatively affect coral reefs. The adaptive capacity of reefs to survive these stressors is driven by ecological and evolutionary processes occurring at multiple spatial scales. Marine protected area (MPA) networks are one solution that can address both local and regional threats, yet the impacts of MPA network design on adaptive processes remains unclear. In this paper, we used an eco-evolutionary model to simulate hypothetical MPA configurations in the Caribbean, Southwest Pacific and Coral Triangle under projected warming. We found that protecting thermal refugia (i.e., cooler reefs) largely benefited corals inside the refugia while other reefs declined. In contrast, protecting a diverse habitat portfolio led to increased coral cover both inside and outside of the MPA network. We then quantified the thermal habitat and connectivity representations of reefs both inside and outside existing MPA networks across each region. Most strikingly, reefs in current MPA networks in the Southwest Pacific and Coral Triangle are approximately 2 {degrees}C cooler than reefs outside the MPA networks, while the Caribbeans MPA network is approximately 1 {degrees}C warmer than reefs outside the network, based on mean temperatures from 2008-2018. These results suggest that the Caribbean MPA network is poised to protect sources of warm-adapted larvae but not destinations, and the opposite is true of the Southwest Pacific and Coral Triangle. Our results suggest that 1) by protecting sites with particular temperature and connectivity characteristics, marine spatial planning may alter eco-evolutionary processes to enhance or inhibit the adaptive capacity of a reef network and 2) the distribution, extent, and effectiveness of local interventions have the potential to affect regional distributions of coral cover beyond what would be expected from local benefits alone, due to the potentially wide-reaching effects of larval dispersal and gene flow.

ecology↗

bioRxiv2024

Reproducing within-reef variability in coral dynamics with a metacommunity modelling framework

Reef systems span spatial scales from 10s to 100s and even 1000s of kilometres, with substantial spatial variability across these scales. Managing and predicting the future of coral reefs requires insights into reef functioning at all spatial scales. However, investigations of reef functioning often consider individual reefs as the smallest unit (10s of kilometres), despite substantial spatiotemporal variability occurring within-reefs (100s of meters). 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 simulate a mosaic of interacting coral communities across a heterogenous seascape. Coral communities are linked using biophysical connectivity modelling. Coral community growth is modelled with a logistic growth model, with the intrinsic growth parameter determined from taxa-specific Integral Projection Models to incorporate demographic mechanisms. Site-specific coral habitat parameters, derived from satellite-based geomorphic and benthic habitat maps, define the maximum coral cover and are used to modulate community growth spatially and temporally as a function of the available space suitable for corals. These parameters are 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. Using a case study from the Great Barrier Reef, we show that modulating community growth using site-specific habitat parameters enables more accurate hindcasts of coral cover dynamics, while overlooking within-reef variability may lead to misleading conclusions about metacommunity dynamics. More generally, C[~]scape provides a valuable framework for predicting spatiotemporal dynamics of coral communities within and between reefs, offering a mechanistic approach to test a range of management and restoration options.

ecology↗

bioRxiv2023

Unexpectedly high coral heat tolerance at thermal refugia

Marine heatwaves and mass bleaching have led to global declines in coral reefs. Corals can adapt, yet, to what extent local variations in thermal stress regimes influence heat tolerance and adaptive potential remains uncertain. Here we identify persistent local-scale thermal refugia and hotspots among the reefs of a remote Pacific archipelago, based on 36 years of satellite-sensed temperatures. Theory suggests that hotspots should promote coral heat tolerance through acclimatisation and directional selection. While historic patterns of mass bleaching and marine heatwaves align with this expectation, we find a contrasting pattern for a single species, Acropora digitifera, exposed to a marine heatwave experiment. Higher heat tolerance at thermal refugia (+0.7 {degrees}C-weeks) and correlations with other traits suggest that non-thermal selective pressures may also influence heat tolerance. We also uncover widespread heat tolerance variability, indicating climate adaptation potential. Compared to the least-tolerant 10% of the A. digitifera population, the most-tolerant 10% could withstand an additional heat stress of 5.2 and 4.1 {degrees}C-weeks for thermal refugia and hotspots, respectively. Despite expectations, local-scale thermal refugia can harbour higher heat tolerance, and mass bleaching patterns do not necessarily predict species responses. This has important implications for designing climate-smart initiatives to tackle global-scale adaptive management problems.

ecology↗

bioRxiv2021

Fine-tuning heat stress algorithms to optimise global predictions of mass coral bleaching

Increasingly severe marine heatwaves under climate change threaten the persistence of many marine ecosystems. Mass coral bleaching events, caused by periods of anomalously warm sea surface temperatures (SST), have led to catastrophic levels of coral mortality globally. Remotely monitoring and forecasting such biotic responses to heat stress is key for effective marine ecosystem management. The Degree Heating Week (DHW) metric, designed to monitor coral bleaching risk, reflects the duration and intensity of heat stress events, and is computed by accumulating SST anomalies (HotSpot) relative to a stress threshold over a 12-week moving window. Despite significant improvements in the underlying SST datasets, corresponding revisions of the HotSpot threshold and accumulation window are still lacking. Here, we fine-tune the operational DHW algorithm to optimise coral bleaching predictions using the 5km satellite-based SSTs (CoralTemp v3.1) and a global coral bleaching dataset (37,871 observations, National Oceanic and Atmospheric Administration). After developing 234 test DHW algorithms with different combinations of HotSpot threshold and accumulation window, we compared their bleaching-prediction ability using spatiotemporal Bayesian hierarchical models and sensitivity-specificity analyses. Peak DHW performance was reached using HotSpot thresholds less than or equal to Maximum Monthly Mean SST and accumulation windows of 4 - 8 weeks. This new configuration correctly predicted up to an additional 310 bleaching observations compared to the operational DHW algorithm, an improved hit rate of 7.9 %. Given the detrimental impacts of marine heatwaves across ecosystems, heat stress algorithms could also be fine-tuned for other biological systems, improving scientific accuracy, and enabling ecosystem governance.

ecology↗

bioRxiv2021

Evolution and connectivity influence the persistence and recovery of coral reefs under climate change in the Caribbean, Southwest Pacific, and Coral Triangle

Corals are experiencing unprecedented decline from climate change-induced mass bleaching events. Dispersal not only contributes to coral reef persistence through demographic rescue but can also hinder or facilitate evolutionary adaptation. Locations of reefs that are likely to survive future warming therefore remain largely unknown, particularly within the context of both ecological and evolutionary processes across complex seascapes that differ in temperature range, strength of connectivity, network size, and other characteristics. Here, we used eco-evolutionary simulations to examine coral adaptation to warming across reef networks in the Caribbean, the Southwest Pacific, and the Coral Triangle. We assessed the factors associated with coral persistence in multiple reef systems to understand which results are general and which are sensitive to particular geographic contexts. We found that evolution can be critical in preventing extinction and facilitating the long-term recovery of coral communities in all regions. Furthermore, the strength of immigration to a reef (destination strength) and current sea surface temperature robustly predicted reef persistence across all reef networks and across temperature projections. However, we found higher initial coral cover, slower recovery, and more evolutionary lag in the Coral Triangle, which has a greater number of reefs and more larval settlement than the other regions. We also found the lowest projected future coral cover in the Caribbean. These findings suggest that coral reef persistence depends on ecology, evolution, and habitat network characteristics, and that, under an emissions stabilization scenario (RCP 4.5), recovery may be possible over multiple centuries.

ecology↗

bioRxiv2020

Cumulative impacts across Australia's Great Barrier Reef: A mechanistic evaluation

Cumulative impacts assessments on marine ecosystems have been hindered by the difficulty of collecting environmental data and identifying drivers of community dynamics beyond local scales. On coral reefs, an additional challenge is to disentangle the relative influence of multiple drivers that operate at different stages of coral ontogeny. We integrated coral life history, population dynamics and spatially-explicit environmental drivers to assess the relative and cumulative impacts of multiple stressors across 2,300 km of the worlds largest coral reef ecosystem, Australias Great Barrier Reef (GBR). Using literature data, we characterized relationships between coral life history processes (reproduction, larval dispersal, recruitment, growth and mortality) and environmental variables. We then simulated coral demographics and stressor impacts at the organism (coral colony) level on >3,800 individual reefs linked by larval connectivity, and exposed to temporally- and spatially-realistic regimes of acute (crown-of-thorns starfish outbreaks, cyclones and mass coral bleaching) and chronic (water quality) stressors. Model simulations produced a credible reconstruction of recent (2008-2020) coral trajectories consistent with monitoring observations, while estimating the impacts of each stressor at reef and regional scales. Overall, corals declined by one third across the GBR, from an average [~]29% to [~]19% hard coral cover. By 2020, less than 20% of the GBR had coral cover higher than 30%. Global annual rates of coral mortality were driven by bleaching (48%) ahead of cyclones (41%) and starfish predation (11%). Beyond the reconstructed status and trends, the model enabled the emergence of complex interactions that compound the effects of multiple stressors while promoting a mechanistic understanding of coral cover dynamics. Drivers of coral cover growth were identified; notably, water quality (suspended sediments) was estimated to delay recovery for at least 25% of inshore reefs. Standardized rates of coral loss and recovery allowed the integration of all cumulative impacts to determine the equilibrium cover for each reef. This metric, combined with maps of impacts, recovery potential, water quality thresholds and reef state metrics, facilitates strategic spatial planning and resilience-based management across the GBR.

ecology↗

bioRxiv2018

Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals

AimWidespread coral bleaching, crown-of-thorns seastar outbreaks, and tropical storms all threaten foundational coral species of the Great Barrier Reef, with impacts differing over time and space. Yet, dispersal via larval propagules could aid reef recovery by supplying new settlers and enabling the spread of adaptive variation among regions. Documenting and predicting spatial connections arising from planktonic larval dispersal in marine species, however, remains a formidable challenge.\n\nLocationThe Great Barrier Reef, Australia\n\nMethodsContemporary biophysical larval dispersal models were used to predict longdistance multigenerational connections for two common and foundational coral species (Acropora tenuis and Acropora millepora). Spatially extensive genetic surveys allowed us to infer signatures of asymmetric dispersal for these species and evaluate concordance against expectations from biophysical models using coalescent genetic simulations, directions of inferred gene flow, and spatial eigenvector modelling.\n\nResultsAt long distances, biophysical models predicted a preponderance of north to south connections and genetic results matched these expectations: coalescent genetic simulations rejected an alternative scenario of historical isolation; the strongest signals of inferred gene flow were from north to south; and asymmetric eigenvectors derived from north to south connections in the biophysical models were significantly better predictors of spatial genetic patterns than eigenvectors derived from symmetric null spatial models.\n\nMain conclusionsResults are consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality of connections. For A. tenuis and A. millepora, northern and central reefs have been important sources to downstream southern reefs over the recent evolutionary past and should continue to provide southward gene flow. Endemic genetic diversity of southern reefs suggests substantial local recruitment and lack of long distance gene flow from south to north.

ecology↗