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Insights into assemblages that can persist in extreme environments are still emerging. Ocean warming and acidification select against species with low physiological tolerance (trait-based 'filtering'). However, intraspecific trait variation can promote species adaptation and persistence, with potentially large effects on assemblage structure. By sampling nine coral traits (four morphological, four tissue and one skeletal) along an offshore-inshore gradient in temperature and pH, we show that distantly related coral species undergo consistent intraspecific changes as they cross into warm, acidic environments. Intraspecific variation and species turnover each favoured colonies with greater tissue biomass, higher symbiont densities and reduced skeletal investments, indicating strong filtering on colony physiology within and across species. Physiological tissue traits were highly variable within species and were independent of morphology, enabling morphologically diverse species to cross into sites of elevated temperature and acidity. Widespread intraspecific change can therefore counter the loss of biodiversity and morphological structure across a steep environmental gradient.

The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km2 ) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero. published

Scleractinian corals are colonial animals with a range of life history strategies, making up diverse species assemblages that define coral reefs. We tagged and tracked approximately 30 colonies from each of 11 species during seven trips spanning six years (2009-2015) in order to measure their vital rates and competitive interactions on the reef crest at Trimodal Reef, Lizard Island, Australia. Pairs of species were chosen from five growth forms where one species of the pair was locally rare (R) and the other common (C). The sampled growth forms were massive [Goniastrea pectinata (R) and G. retiformis (C)], digitate [Acropora humilis (R) and A. cf. digitifera (C)], corymbose [A. millepora (R) and A. nasuta (C)], tabular [A. cytherea (R) and A. hyacinthus (C)] and arborescent [A. robusta (R) and A. intermedia (C)]. An extra corymbose species with intermediate abundance, A. spathulata was included when it became apparent that A. millepora was too rare on the reef crest, making the 11 species in total. The tagged colonies were visited each year in the weeks prior to spawning. During visits, two or more observers each took 2-3 photographs of each tagged colony from directly above and on the horizontal plane with a scale plate to track planar area. Dead or missing colonies were recorded and new colonies tagged in order to maintain approximately 30 colonies per species throughout the six years of the study. In addition to tracking tagged corals, 30 fragments were collected from neighboring untagged colonies of each species for counting numbers of eggs per polyp (fecundity); and fragments of untagged colonies were brought into the laboratory where spawned eggs were collected for biomass and energy measurements. We also conducted surveys at the study site to generate size structure data for each species in several of the years. Each tagged colony photograph was digitized by at least two people. Therefore, we could examine sources of error in planar area for both photographers and outliners. Competitive interactions were recorded for a subset of species by measuring the margins of tagged colony outlines interacting with neighboring corals. The study was abruptly ended by Tropical Cyclone Nathan (Category 4) that killed all but nine of the over 300 tagged colonies in early 2015. Nonetheless, these data will be of use to other researchers interested in coral demography and coexistence, functional ecology, and parametrizing population, community and ecosystem models. The data set is not copyright restricted, and users should cite this paper when using the data. Publisher PDF

Biotic responses to global change include directional shifts in organismal traits. Body size, an integrative trait that determines demographic rates and ecosystem functions, is often thought to be shrinking in the Anthropocene. Here, we assess the prevalence of body size change in six taxon groups across 5,032 assemblage time-series spanning 1960-2020. Using the Price equation to partition this change into within-species body size versus compositional changes, we detect prevailing decreases in body size through time. Change in assemblage composition contributes more to body size changes than within-species trends, but both components show substantial variation in magnitude and direction. The biomass of assemblages remains remarkably stable as decreases in body size trade-off with increases in abundance.One-Sentence SummaryVariable within-species and compositional trends combine into shrinking body size, abundance increases and stable biomass.

Coral bleaching and mortality can show significant spatial and taxonomic heterogeneity at local scales, highlighting the need to understand the fine-scale drivers and impacts of thermal stress. In this study, we used structure-from-motion photogrammetry to track coral bleaching, mortality, and changes in community composition during the 2019 marine heatwave in Kāne‘ohe Bay, Hawai‘i. We surveyed 30 shallow reef patches every 3 weeks for the duration of the bleaching event (August-December) and one year after, resulting in a total of 210 large-area, high-resolution photomosaics that enabled us to follow the fate of thousands of coral colonies through time. We also measured environmental variables such as temperature, sedimentation, depth, and wave velocity at each of these sites, and extracted estimates of habitat complexity (rugosity R and fractal dimension D) from digital elevation models to better understand their effects on patterns of bleaching and mortality. We found that up to 80% of corals experienced moderate to severe bleaching in this period, with peak bleaching occurring in October when heat stress (DHW) reached its maximum. Mortality continued to accumulate as bleaching levels dropped, driving large declines in more heat-susceptible species (77% loss ofPocilloporacover) and moderate declines in heat-tolerant species (19% and 23% forPorites compressaandMontipora capitata, respectively). Declines in live coral were accompanied by a rapid increase in algal cover across the survey sites. Spatial differences in bleaching were significantly linked to habitat complexity and coral species composition, with reefs that were dominated byPocilloporaexperiencing the most severe bleaching. Mortality was also influenced by species composition, fractal dimension, and site-level differences in thermal stress. Our results show that spatial heterogeneity in the impacts of bleaching are driven by a mix of environmental variation, habitat complexity, and differences in assemblage composition.

The structural complexity of coral reefs provides important ecosystem functions, such as wave attenuation for coastal protection, surfaces for coral growth, and habitat for other organisms. Corals build much of this structure, but an understanding of how colonies of different species and sizes contribute to complexity is lacking. We quantified three interdependent descriptors of complexity—rugosity, fractal dimension, and height range—for reef patches as well as the corals growing upon them in Kāne‘ohe Bay (O‘ahu, Hawai‘i). Despite similar levels of reef-scale complexity throughout the bay, we found marked differences in how species contribute to this complexity. Variation in complexity among species was closely tied to colony morphology, but not to colony size. Together, our results show that no one species is sufficient to generate the full spectrum of habitat complexities we see on coral reefs, which has direct implications for reef recovery and restoration.

Climate change is causing the distribution and abundance of many organisms to change. In particular, organisms typical of the tropics are increasing in abundance in many subtropical regions, a process known as tropicalization. Here, we examine changes in coral abundance and assemblage structure in the Solitary Islands Marine Park (SIMP), over a 23-year period between 1990 and 2013–14. Total coral cover decreased at all six islands sampled with a concomitant decline in total coral cover at the regional scale (i.e. between sampling occasions). When coral taxa were classified as either cosmopolitan or subtropical, cosmopolitan corals decreased in cover at the regional scale. In contrast, subtropical coral cover did not change at the regional scale because large increases in cover at some islands, such as North Solitary Island, were matched by decreases at other islands. Of 16 common coral taxa examined at the regional level, one declined and two increased in cover with no change in the remaining 13 taxa. In particular, there was no increase in the abundance of coral taxa typically associated with tropical reefs. Similarly, multivariate analyses of coral assemblage structure using these 16 common taxa indicated changes in two of the six island assemblages but, again, provided no evidence for tropicalization. Modelling suggested very low probabilities of larval dispersal from the southern Great Barrier Reef to the SIMP suggesting that limited connectivity with tropical coral populations is one possible cause of the lack of tropicalization in the coral assemblages. We therefore conclude that, despite significant increases in mean sea surface temperature over the last few decades, there has been no tropicalization of the coral fauna in the SIMP. Furthermore, the small proportional reduction in total coral cover, despite the occasional incidence of coral bleaching, coral disease outbreaks and a number of large storms, suggest that the reefs of the SIMP were in reasonably good health at the time of the final survey in 2014. Our results suggest that factors other than temperature, in particular, a lack of dispersal, are limiting the expansion of tropical corals along the east coast of Australia.

14 pages, 5 figures, 1 table, supporting information https://doi.org/10.1111/ele.13718.-- Data availability statement: The data and code related to the manuscript have been placed in the Dryad Digital Repository: https://doi.org/10.5061/dryad.69p8cz91g, Quantifying changes in functional community structure driven by disturbance is critical to anticipate potential shifts in ecosystem functioning. However, how marine heatwaves (MHWs) affect the functional structure of temperate coral‐dominated communities is poorly understood. Here, we used five long‐term (> 10 years) records of Mediterranean coralligenous assemblages in a multi‐taxa, trait‐based analysis to investigate MHW‐driven changes in functional structure. We show that, despite stability in functional richness (i.e. the range of species functional traits), MHW‐impacted assemblages experienced long‐term directional changes in functional identity (i.e. their dominant trait values). Declining traits included large sizes, long lifespans, arborescent morphologies, filter‐feeding strategies or calcified skeletons. These traits, which were mostly supported by few sensitive and irreplaceable species from a single functional group (habitat‐forming octocorals), disproportionally influence certain ecosystem functions (e.g. 3D‐habitat provision). Hence, MHWs are leading to assemblages that are deficient in key functional traits, with likely consequences for the ecosystem functioning, We acknowledge the funding of the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019‐000928‐S). This research has also been partially funded by the HEATMED project (RTI2018‐095346‐B‐I00, MCIU/AEI/FEDER, UE), Interreg Med Programme (Projects MPA‐ENGAGE; 5216 | 5MED18_3.2_M23_007 and MPA‐Adapt, 1MED15_3.2_M2_337) 85% cofunded by the European Regional Development Fund, the MIMOSA project funded by the Foundation Prince Albert II Monaco, the Perfect project funded by the TOTAL Foundation, the Medchange project funded by the Agence Nationale pour la Recherche (ANR) and the European Union's Horizon 2020 research and innovation programme under grants agreements 689518 (MERCES) and SEP‐210597628 (FutureMARES). D.G.G. is supported by an FPU grant (FPU15/05457) from the Spanish Ministry of Education. CL gratefully acknowledges the financial support by ICREA under the ICREA Academia programme. VB is supported by the Templeton Foundation (grant #60501, ‘Putting the Extended Evolutionary Synthesis to the Test’). J‐B.L is supported by the strategic Funding UIDB/04423/2020 and UIDP/04423/2020. [...] D.G.G, C.L, J‐B.L, N.B, P.L.S & J.G are part of the Marine Conservation research group (www.medrecover.org) (2017 SGR 1521) from the Generalitat de Catalunya.

Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature‐adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter., Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation.

JSM and MM were supported by the National Science Foundation (NSF)1948946. MD is supported by the Warman Foundation, the Leverhulme Centre for Anthropocene Biodiversity (RC-2018-021) and NSF-NERC grant NE/V009338/1. MM is supported by a Leverhulme Trust Early Career Fellowship (ECF-2021-512). 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. Publisher PDF

The relative roles of top‐down (consumer‐driven) and bottom‐up (resource‐driven) forcing in exploited marine ecosystems have been much debated. Examples from a variety of marine systems of exploitation‐induced, top‐down trophic forcing have led to a general view that human‐induced predator perturbations can disrupt entire marine food webs, yet other studies that have found no such evidence provide a counterpoint. Though evidence continues to emerge, an unresolved debate exists regarding both the relative roles of top‐down versus bottom‐up forcing and the capacity of human exploitation to instigate top‐down, community‐level effects. Using time‐series data for 104 reef communities spanning tropical to temperate Australia from 1992 to 2013, we aimed to quantify relationships among long‐term trophic group population density trends, latitude, and exploitation status over a continental‐scale biogeographic range. Specifically, we amalgamated two long‐term monitoring databases of marine community dynamics to test for significant positive or negative trends in density of each of three key trophic levels (predators, herbivores, and algae) across the entire time series at each of the 104 locations. We found that trophic control tended toward bottom‐up driven in tropical systems and top‐down driven in temperate systems. Further, alternating long‐term population trends across multiple trophic levels (a method of identifying trophic cascades), presumably due to top‐down trophic forcing, occurred in roughly fifteen percent of locations where the prerequisite significant predator trends occurred. Such alternating trophic trends were significantly more likely to occur at locations with increasing predator densities over time. Within these locations, we found a marked latitudinal gradient in the prevalence of long‐term, alternating trophic group trends, from rare in the tropics (, Using time‐series data for 104 reef communities spanning tropical to temperate Australia from 1992 to 2013, we quantified relationships among long‐term trophic group population density trends, latitude, and exploitation status over a continental‐scale biogeographic range. These data suggest that the type and degree of trophic forcing in this system are likely related to one or more covariates of latitude, and that ecosystem resiliency to top‐down control does not universally vary in this system based on exploitation level.

Many life history traits relate to trade-offs among an organism’s energy investments in growth, reproduction, and maintenance, as well as to fundamental physiological processes or body size. Other traits reflect affordances, or possibilities enabled by an investment strategy. In scleractinian corals, growth and reproduction have been studied to a much greater extent than maintenance. Species traits likely to correlate or trade off with maintenance investments include those relating to colony growth, reproduction, and susceptibility to bleaching. Here, we measure tissue biomass per cm2 for 29 Caribbean reef corals and evaluate whether the more easily measured corallite diameter is a proxy for tissue biomass as is often assumed. We examine hypotheses concerning corallite size and tissue biomass on the one hand, and growth rate, reproduction, competitive ability, and bleaching susceptibility on the other. Our results indicate that biomass per unit area ranges from one to two orders of magnitude across species, that corallite size is a weak predictor of tissue biomass per cm2, and that tissue biomass is strongly correlated with growth rate and competitive ability. Relationships between biomass or module size and reproductive characteristics or bleaching susceptibility are not evident in this set of Caribbean corals. These findings expand our understanding about energy investment strategies in colonial corals and suggest that biomass may be an important metric to consider in cross-species comparisons, especially among corals from different families. Finally, this work can help inform predictions of reef response to continued threats.

Humans have long sought to restore species, but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests that are increasingly threatened by environmental change.We propose a two-part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that biodiversity supports ecosystem functions and services, and so it takes precaution against loss by ensuring an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—e.g., abundance, species range and tolerance to environmental change.Using existing phenotypic trait and ecological characteristic data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world’s southern-most coral reef which naturally harbors low coral diversity to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and may be improved by including species with different traits.Synthesis and applications. While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved.

The process of coral recruitment is crucial to the functioning of coral reef ecosystems, as well as recovery of coral assemblages following disturbances. Fishes can be key mediators of this process by removing benthic competitors like algae, but their foraging impacts are capable of being facilitative or harmful to coral recruits depending on species traits. Reef fish assemblages are highly diverse in foraging strategies and the relationship between this diversity with coral settlement and recruitment success remains poorly understood. Here, we investigate how foraging trait diversity of reef fish assemblages covaries with coral settlement and recruitment success across multiple sites at Lizard Island, Great Barrier Reef. Using a multi-model inference approach incorporating six metrics of fish assemblage foraging diversity (foraging rates, trait richness, trait evenness, trait divergence, herbivore abundance, and sessile invertivore abundance), we found that herbivore abundance was positively related to both coral settlement and recruitment success. However, the correlation with herbivore abundance was not as strong in comparison with foraging trait diversity metrics. Coral settlement and recruitment exhibited a negative relationship with foraging trait diversity, especially with trait divergence and richness in settlement. Our findings provide further evidence that fish play a role in making benthic habitats more conducive for coral settlement and recruitment. Because of their ability to shape the reef benthos, the variation of fish biodiversity is likely to contribute to spatially uneven patterns of coral recruitment and reef recovery.

Niche construction is the process through which organisms modify environmental states in ways favourable to their own fitness. Here, we test experimentally whether scleractinian corals can be considered niche constructors. In particular, we demonstrate a positive feedback involved in corals building structures which facilitate recruitment. Coral larval recruitment is a key process for coral reef persistence. Larvae require low flow conditions to settle from the plankton, and hence the presence of colony structures that can break the flow is expected to facilitate coral recruitment. Here, we show an increase in settler presence on artificial tiles deployed in the field along a gradient of coral-built structural complexity. Structural complexity had a positive effect on settlement, with an increase of 15,71% of settler presence probability along the range of structural complexity considered. This result provides evidence that coral built structural complexity creates conditions that facilitate coral settlement, while demonstrating that corals meet the criteria for ecological niche construction.

Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.

Spatial genetic structure (SGS) is important to a population’s ability to adapt to environmental change. For species that reproduce both sexually and asexually, the relative contribution of each reproductive mode has important ecological and evolutionary implications because asexual reproduction can have a strong effect on SGS. Reef building corals reproduce sexually, but many species also propagate asexually under certain conditions. In order to understand SGS and the relative importance of reproductive mode across environmental gradients, we evaluated genetic relatedness in almost 600 colonies of Montipora capitata across 30 environmentally characterized sites in Kāne’ohe Bay, O’ahu, Hawai’i using low-depth restriction digest associated sequencing. Clonal colonies were relatively rare overall but influenced SGS. Clones were located significantly closer to one another spatially than average colonies and were more frequent on sites where wave energy was relatively high, suggesting a strong role of mechanical breakage in their formation. Excluding clones, we found no evidence of isolation by distance within sites or across the bay. Several environmental characteristics were significant predictors of the underlying genetic variation (including degree heating weeks, time spent above 30°C, depth, sedimentation rate and wave height); however, they only explained 5% of this genetic variation. Our results show that colony fragmentation contributes to the ecology of M. capitata at local scales and that genetic diversity is maintained despite strong environmental gradients in a highly impacted ecosystem, suggesting potential for broad adaptation or acclimatization in this population.

The structure of ecosystems is usually determined by the shape of the organisms that build it, commonly known as ecosystem engineers. Understanding to what extent plasticity and environmental filtering determine variation in ecosystem engineer physical structure is necessary to predict how ecosystem structure may change. Here, we explored coral survival and the plasticity of morphological traits that are critical for habitat provision in coral reefs. We conducted a reciprocal clonal transplant experiment in which branching corals from the genus Porites and Acropora were moved to and from a deep and a shallow site within a lagoon in the Maldives. Survival and trait analyses showed that transplant destination consistently induced the strongest changes, particularly among Acropora spp. The origin of the corals only marginally affected some of the traits. We also detected variation in the way individuals from the same species and site differentiate their shape, showing that traits linked to habitat provision are phenotypically plastic. The results suggest coral phenotypic plasticity plays a stronger role than environmental filtering, in determining zonation of coral morphologies, and consequently the habitats they provide for other taxa.

Comparative lists of species’ extinction risk are increasingly being used to prioritise conservation resources. Extinction risk is most rigorously assessed using quantitative data on species’ population trajectories, but in the absence of such data, assessments often rely on qualitative estimates based on expert opinion of species abundances, distributions and threats. For example, one-third of coral species are classified as threatened and another third as near threatened on the IUCN Red List, despite a lack of data at the population level for the vast majority of species. Since many taxa show a strong correlation between species traits and extinction risk, an alternate approach is to identify traits associated with extinction in other groups and apply them to the taxon of interest. Here, we examine whether life-history traits associated with stress tolerance, fecundity and habitat specialisation are correlated with Red List conservation status in reef corals. We found no relationship between conservation status and life-history traits, suggesting that either traits identified as important predictors of extinction risk in other taxa are not important in corals, or that conservation status does not accurately reflect species’ relative extinction risk. Therefore, using global-scale extinction risk assessments to inform conservation of coral reefs presents a high risk of ‘silent extinctions’ of undescribed species. We argue that the conservation status for the vast majority of coral species should be ‘data deficient’ and is likely to remain so for the foreseeable future, and that the status and trends of coral populations can only be reliably assessed at relatively small scales.

M.D. is grateful for support from the Templeton Foundation (grant #60501, “Putting the Extended Evolutionary Synthesis to the Test”) and from a Leverhulme Trust Fellowship. The problem Earth‐based observations of the biosphere are spatially biased in ways that can limit our ability to detect macroecological patterns and changes in biodiversity. To resolve this problem, we need to supplement the ad hoc data currently collected with planned biodiversity monitoring, in order to approximate global stratified random sampling of the planet. We call this all‐encompassing observational system ‘the macroscope’. The solution With a focus on the marine realm, we identify seven main biosphere observation tools that compose the macroscope: satellites, drones, camera traps, passive acoustic samplers, biologgers, environmental DNA and human observations. By deploying a nested array of these tools that fills current gaps in monitoring, we can achieve a macroscope fit for purpose and turn these existing powerful tools into more than the sum of their parts. An appeal Building a macroscope requires commitment from many fields, together with coordinated actions to attract the level of funding required for such a venture. We call on macroecologists to become advocates for the macroscope and to engage with existing global observation networks. Postprint

The morphology of coral colonies has important implications for their biological and ecological performance, including their role as ecosystem engineers. However, given that morphology is difficult to quantify across many taxa, morphological variation is typically shoehorned into coarse growth form categories (e.g., arborescent and digitate). In this study, we develop a quantitative schema for morphology by identifying three-dimensional shape variables that can describe coral morphology. We contrast six variables estimated from 152 laser scans of coral colonies that ranged across seven growth form categories and three orders of magnitude of size. We found that 88% of the variation in shape was captured by two axes of variation and three shape variables. The main axis was variation in volume compactness (cf. sphericity) and the second axis was the trade-off between surface complexity and the vertical distribution of volume (i.e., top heaviness). Variation in volume compactness also limited variation along the second axis, where surface complexity and vertical volume distribution ranged more freely when compactness was low. Traditional growth form categories occupied distinct regions within this morpho-space. However, these regions overlapped due to shape changes with colony size. Nonetheless, four of the shape variables were able to predict traditional growth form categories with 70 to 95% accuracy, suggesting that the continuous variables captured much of the qualitative variation inherently implied by these growth forms. Distilling coral morphology into geometric variables that capture shape variation will allow for better tests of the mechanisms that govern coral biology, ecology and ecosystem services such as reef building and provision of habitat.

Susceptibility to human-driven environmental changes is mediated by species traits. Therefore, identifying traits that predict organism performance, ecosystem function and response to changes in environmental conditions can help forecast how ecosystems are responding to the Anthropocene. Morphology dictates how organisms interact with their environment and other organisms, partially determining the environmental and biological contexts in which they are successful. Morphology is important for autogenic ecosystem engineering organisms, such as reef-building corals, because it determines the shape of the structures they create and by extension the communities they support. Here, we present six morphological traits that capture variation in volume compactness, surface complexity and top-heaviness. With support from the literature, we propose causal links between morphology and a performance–function–response framework. To illustrate these concepts, we combine 3D scanning and coral survey data to predict morphological traits from in situ colonies. We present a case study that examines how assemblage-scale morphological traits have responded to two cyclones and the 2016 mass bleaching event—two phenomena predicted to increase in severity in the Anthropocene—and discuss how these changes may impact ecosystem function. The morphological traits outlined here offer a generalised and hypothesis-driven approach to tracking how reefs respond to the Anthropocene. The ability to predict these traits from field data and the increasing use of photogrammetry makes them readily applicable across broad spatiotemporal scales. A plain language summary is available for this article.

Changes in disturbance regimes due to climate change are increasingly challenging the capacity of ecosystems to absorb recurrent shocks and reassemble afterwards, escalating the risk of widespread ecological collapse of current ecosystems and the emergence of novel assemblages1–3. In marine systems, the production of larvae and recruitment of functionally important species are fundamental processes for rebuilding depleted adult populations, maintaining resilience and avoiding regime shifts in the face of rising environmental pressures4,5. Here we document a regional-scale shift in stock–recruitment relationships of corals along the Great Barrier Reef—the world’s largest coral reef system—following unprecedented back-to-back mass bleaching events caused by global warming. As a consequence of mass mortality of adult brood stock in 2016 and 2017 owing to heat stress6, the amount of larval recruitment declined in 2018 by 89% compared to historical levels. For the first time, brooding pocilloporids replaced spawning acroporids as the dominant taxon in the depleted recruitment pool. The collapse in stock–recruitment relationships indicates that the low resistance of adult brood stocks to repeated episodes of coral bleaching is inexorably tied to an impaired capacity for recovery, which highlights the multifaceted processes that underlie the global decline of coral reefs. The extent to which the Great Barrier Reef will be able to recover from the collapse in stock–recruitment relationships remains uncertain, given the projected increased frequency of extreme climate events over the next two decades7. A regional-scale shift in the relationships between adult stock and recruitment of corals occurred along the Great Barrier Reef, following mass bleaching events in 2016 and 2017 caused by global warming.

Structure-from-motion (SfM) photogrammetry is a technique used to generate three-dimensional (3D) reconstructions from a sequence of two-dimensional (2D) images. SfM methods are becoming increasingly popular as a noninvasive way to monitor many systems, including anthropogenic and natural landscapes, geologic structures, and both terrestrial and aquatic ecosystems. Here, a detailed protocol is provided for collecting SfM imagery to generate 3D models of benthic habitats. Additionally, the cost, time efficiency, and output quality of employing a Digital Single Lens Reflex (DSLR) camera versus a less expensive action camera have been compared. A tradeoff between computational time and resolution was observed, with the DSLR camera producing models with more than twice the resolution, but taking approximately 1.4-times longer to produce than the action camera. This primer aims to provide a thorough description of the steps necessary to collect SfM data in benthic habitats for those who are unfamiliar with the technique as well as for those already using similar methods.

A recent compilation of traits across culturable species of bacteria and archaea allows relationships to be quantified between genome size and other traits and habitat. Cell morphology, size, motility, sporulation and doubling time were not strongly correlated with genome size. Aerobic species averaged ca 35% larger genomes than anaerobic, adjusted for growth temperature. Aerobes had a similar mix of gene functions compared to anaerobes of the same genome size. Shifting proportions of aerobes to anaerobes accounted for about half of previously-known differences in mean genome size between habitats. One possible factor in these results could be if effective population sizes are larger for aerobes, reducing the potential for gene loss via genetic drift. Larger genomes also confer versatility. They can transport and metabolise a wider range of substrates. More of their genome is engaged in signal detection and response, indicating they benefit from different resources at different times or under different condition. Aerobic habitats might well present opportunities and challenges that vary through time more than anaerobic habitats. The genome size trait-dimension contributes a useful quantitative descriptor for ecological strategies.

Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology., info:eu-repo/semantics/published