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

Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef

The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here, we show that the reef-building coral, Acropora kenti, harbours at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein-coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.

Systematic review of the uncertainty of coral reef futures under climate change

Climate change impact syntheses, such as those by the Intergovernmental Panel on Climate Change, consistently assert that limiting global warming to 1.5 °C is unlikely to safeguard most of the world's coral reefs. This prognosis is primarily based on a small subset of available models that apply similar 'excess heat' threshold methodologies. Our systematic review of 79 articles projecting coral reef responses to climate change revealed five main methods. 'Excess heat' models constituted one third (32%) of all studies but attracted a disproportionate share (68%) of citations in the field. Most methods relied on deterministic cause-and-effect rules rather than probabilistic relationships, impeding the field's ability to estimate uncertainty. To synthesize the available projections, we aimed to identify models with comparable outputs. However, divergent choices in model outputs and scenarios limited the analysis to a fraction of available studies. We found substantial discrepancies in the projected impacts, indicating that the subset of articles serving as a basis for climate change syntheses may project more severe consequences than other studies and methodologies. Drawing on insights from other fields, we propose methods to incorporate uncertainty into deterministic modeling approaches and propose a multi-model ensemble approach to generating probabilistic projections for coral reef futures.

Diversification of refugia types needed to secure the future of coral reefs subject to climate change

Identifying locations of refugia from the thermal stresses of climate change for coral reefs and better managing them is one of the key recommendations for climate change adaptation. We review and summarize approximately 30 years of applied research focused on identifying climate refugia to prioritize the conservation actions for coral reefs under rapid climate change. We found that currently proposed climate refugia and the locations predicted to avoid future coral losses are highly reliant on  excess heat metrics, such as degree heating weeks. However, many existing alternative environmental, ecological, and life-history variables could be used to identify other types of refugia that lead to the desired diversified portfolio for coral reef conservation. To improve conservation priorities for coral reefs, there is a need to evaluate and validate the predictions of climate refugia with long-term field data on coral abundance, diversity, and functioning. There is also the need to identify and safeguard locations displaying resistance toprolonged exposure to heat waves and the ability to recover quickly after thermal exposure. We recommend using more metrics to identify a portfolio of potential refugia sites for coral reefs that can avoid, resist, and recover from exposure to high ocean temperatures and the consequences of climate change, thereby shifting past efforts focused on avoidance to a diversified risk-spreading portfolio that can be used to improve strategic coral reef conservation in a rapidly warming climate.

Larval precompetency and settlement behaviour in 25 Indo-Pacific coral species

Knowledge of coral larval precompetency periods and maximum competency windows is fundamental to understanding coral population dynamics, informing biogeography and connectivity patterns, and predicting reef recovery following disturbances. Yet for many species, estimates of these early-life history metrics are scarce and vary widely. Furthermore, settlement cues for many taxa are not known despite consequences to habitat selection. Here we performed a comprehensive experimental time-series investigation of larval settlement behaviour, for 25 Indo-Pacific broadcast-spawning species. To investigate the duration of precompetency, improve predictions of the competency windows, and compare settlement responses within and amongst species, we completed replicated and repeated 24-hour assays that exposed larvae to five common settlement cues. Our study revealed that larval competency in some broadcast-spawning species begins as early as two days post fertilization, but that the precompetency period varies within and between species from about two to six days, with consequences for local retention and population connectivity. We also found that larvae of some species are competent to settle beyond 70 days old and display complex temporal settlement behaviour, challenging the assumption that competency gradually wanes over time and adding to the evidence that larval longevity can support genetic connectivity and long-distance dispersal. Using these data, we grouped coral taxa by short, mid and long precompetency periods, and identified their preferred settlement cues. Taken together, these results inform our understanding of larval dynamics across a broad range of coral species and can be applied to investigations of population dynamics, connectivity, and reef recovery.

A macroplastic vulnerability index for marine mammals, seabirds, and sea turtles in Hawai'i

Plastic pollution is having devastating consequences for marine organisms across the planet. However, the population level effects of macroplastic pollution remain difficult and costly to quantify. As a result, there is a need for alternative approaches to evaluate species risk to plastic pollution and inform management needs. We apply a trait-based framework for macroplastic pollution to develop a relative vulnerability index-informed by three dimensions: likelihood of exposure, species' sensitivity, and population resilience-for marine mammals, seabirds, and sea turtles found in Hawai'i. This index ranks 63 study species based on their population level vulnerability to macroplastic pollution, with the highest scoring species being the most vulnerable. Our results indicate that ducks, waders, and noddies with large populations were the least vulnerable to macroplastics, while the most vulnerable were the Hawaiian monk seal, sea turtles, baleen whales, and some albatross and petrel species. This index can inform species in need of population monitoring in Hawai'i, and direct other management priorities (e.g., locations for clean-ups or booms). More broadly, this work exemplifies the value of qualitative risk assessment approaches for better understanding the population level effects of macroplastic pollution and showcases how vulnerability indices can be used to inform management priorities.

Coral Reef Population Genomics in an Age of Global Change

Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.

Emergent increase in coral thermal tolerance reduces mass bleaching under climate change

Recurrent mass bleaching events threaten the future of coral reefs. To persist under climate change, corals will need to endure progressively more intense and frequent marine heatwaves, yet it remains unknown whether their thermal tolerance can keep pace with warming. Here, we reveal an emergent increase in the thermal tolerance of coral assemblages at a rate of 0.1 °C/decade for a remote Pacific coral reef system. This led to less severe bleaching impacts than would have been predicted otherwise, indicating adaptation, acclimatisation or shifts in community structure. Using future climate projections, we show that if thermal tolerance continues to rise over the coming century at the most-likely historic rate, substantial reductions in bleaching trajectories are possible. High-frequency bleaching can be fully mitigated at some reefs under low-to-middle emissions scenarios, yet can only be delayed under high emissions scenarios. Collectively, our results indicate a potential ecological resilience to climate change, but still highlight the need for reducing carbon emissions in line with Paris Agreement commitments to preserve coral reefs.

Demographic resilience may sustain significant coral populations in a 2°C-warmer world

Projections of coral reefs under climate change have important policy implications, but most analyses have focused on the intensification of climate-related physical stress rather than explicitly modelling how coral populations respond to stressors. Here, we analyse the future of the Great Barrier Reef (GBR) under multiple, spatially realistic drivers which allows less impacted sites to facilitate recovery. Under a Representative Concentration Pathway (RCP) 2.6 CMIP5 climate ensemble, where warming is capped at ~2°C, GBR mean coral cover declined mid-century but approached present-day levels towards 2100. This is considerably more optimistic than most analyses. However, under RCP4.5, mean coral cover declined by >80% by late-century, and reached near zero under RCP ≥6.0. While these models do not allow for adaptation, they significantly extend past studies by revealing demographic resilience of coral populations to low levels of additional warming, though more pessimistic outcomes might be expected under CMIP6. Substantive coral populations under RCP2.6 would facilitate long-term genetic adaptation, adding value to ambitious greenhouse emissions mitigation.

Moving beyond heritability in the search for coral adaptive potential

Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change. For wild populations to persist, they must adapt. Knowledge shortfalls about corals' complex ecological and evolutionary dynamics, however, stymie predictions about potential adaptation to future conditions. Here, we review adaptation through the lens of quantitative genetics. We argue that coral adaptation studies can benefit greatly from "wild" quantitative genetic methods, where traits are studied in wild populations undergoing natural selection, genomic relationship matrices can replace breeding experiments, and analyses can be extended to examine genetic constraints among traits. In addition, individuals with advantageous genotypes for anticipated future conditions can be identified. Finally, genomic genotyping supports simultaneous consideration of how genetic diversity is arrayed across geographic and environmental distances, providing greater context for predictions of phenotypic evolution at a metapopulation scale.

Coral adaptive capacity insufficient to halt global transition of coral reefs into net erosion under climate change

Projecting the effects of climate change on net reef calcium carbonate production is critical to understanding the future impacts on ecosystem function, but prior estimates have not included corals' natural adaptive capacity to such change. Here we estimate how the ability of symbionts to evolve tolerance to heat stress, or for coral hosts to shuffle to favourable symbionts, and their combination, may influence responses to the combined impacts of ocean warming and acidification under three representative concentration pathway (RCP) emissions scenarios (RCP2.6, RCP4.5 and RCP8.5). We show that symbiont evolution and shuffling, both individually and when combined, favours persistent positive net reef calcium carbonate production. However, our projections of future net calcium carbonate production (NCCP) under climate change vary both spatially and by RCP. For example, 19%-35% of modelled coral reefs are still projected to have net positive NCCP by 2050 if symbionts can evolve increased thermal tolerance, depending on the RCP. Without symbiont adaptive capacity, the number of coral reefs with positive NCCP drops to 9%-13% by 2050. Accounting for both symbiont evolution and shuffling, we project median positive NCPP of coral reefs will still occur under low greenhouse emissions (RCP2.6) in the Indian Ocean, and even under moderate emissions (RCP4.5) in the Pacific Ocean. However, adaptive capacity will be insufficient to halt the transition of coral reefs globally into erosion by 2050 under severe emissions scenarios (RCP8.5).

Assessing the potential for demographic restoration and assisted evolution to build climate resilience in coral reefs

Interest is growing in developing conservation strategies to restore and maintain coral reef ecosystems in the face of mounting anthropogenic stressors, particularly climate warming and associated mass bleaching events. One such approach is to propagate coral colonies ex situ and transplant them to degraded reef areas to augment habitat for reef-dependent fauna, prevent colonization from spatial competitors, and enhance coral reproductive output. In addition to such "demographic restoration" efforts, manipulating the thermal tolerance of outplanted colonies through assisted relocation, selective breeding, or genetic engineering is being considered for enhancing rates of evolutionary adaptation to warming. Although research into such "assisted evolution" strategies has been growing, their expected performance remains unclear. We evaluated the potential outcomes of demographic restoration and assisted evolution in climate change scenarios using an eco-evolutionary simulation model. We found that supplementing reefs with pre-existing genotypes (demographic restoration) offers little climate resilience benefits unless input levels are large and maintained for centuries. Supplementation with thermally resistant colonies was successful at improving coral cover at lower input levels, but only if maintained for at least a century. Overall, we found that, although demographic restoration and assisted evolution have the potential to improve long-term coral cover, both approaches had a limited impact in preventing severe declines under climate change scenarios. Conversely, with sufficient natural genetic variance and time, corals could readily adapt to warming temperatures, suggesting that restoration approaches focused on building genetic variance may outperform those based solely on introducing heat-tolerant genotypes.

Climate refugia on the Great Barrier Reef fail when global warming exceeds 3°C

Increases in the magnitude, frequency, and duration of warm seawater temperatures are causing mass coral mortality events across the globe. Although, even during the most extensive bleaching events, some reefs escape exposure to severe stress, constituting potential refugia. Here, we identify present-day climate refugia on the Great Barrier Reef (GBR) and project their persistence into the future. To do this, we apply semi-dynamic downscaling to an ensemble of climate projections released for the IPCC's recent sixth Assessment Report. We find that GBR locations experiencing the least thermal stress over the past 20 years have done so because of their oceanographic circumstance, which implies that longer-term persistence of climate refugia is feasible. Specifically, tidal and wind mixing of warm water away from the sea surface appears to provide relief from warming. However, on average this relative advantage only persists until global warming exceeds ~3°C.

From coral reefs to Joshua trees: What ecological interactions teach us about the adaptive capacity of biodiversity in the Anthropocene

The pervasive loss of biodiversity in the Anthropocene necessitates rapid assessments of ecosystems to understand how they will respond to anthropogenic environmental change. Many studies have sought to describe the adaptive capacity (AC) of individual species, a measure that encompasses a species’ ability to respond and adapt to change. Only those adaptive mechanisms that can be used over the next few decades (e.g. via novel interactions, behavioural changes, hybridization, migration, etc.) are relevant to the timescale set by the rapid changes of the Anthropocene. The impacts of species loss cascade through ecosystems, yet few studies integrate the capacity of ecological networks to adapt to change with the ACs of its species. Here, we discuss three ecosystems and how their ecological networks impact the AC of species and vice versa. A more holistic perspective that considers the AC of species with respect to their ecological interactions and functions will provide more predictive power and a deeper understanding of what factors are most important to a species’ survival. We contend that the AC of a species, combined with its role in ecosystem function and stability, must guide decisions in assigning ‘risk’ and triaging biodiversity loss in the Anthropocene.

This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

Present and future bright and dark spots for coral reefs through climate change

Marine heatwaves can cause coral bleaching and reduce coral cover on reefs, yet few studies have identified "bright spots," where corals have recently shown a capacity to survive such pressures. We analyzed 7714 worldwide surveys from 1997 to 2018 along with 14 environmental and temperature metrics in a hierarchical Bayesian model to identify conditions that contribute to present-day coral cover. We also identified locations with significantly higher (i.e., "bright spots") and lower coral cover (i.e., "dark spots") than regionally expected. In addition, using 4-km downscaled data of Representative Concentration Pathways (RCPs) 4.5 and 8.5, we projected coral cover on reefs for the years 2050 and 2100. Coral cover on modern reefs was positively associated with historically high maximum sea-surface temperatures (SSTs), and negatively associated with high contemporary SSTs, tropical-cyclone frequencies, and human-population densities. By 2100, under RCP8.5, we projected relative decreases in coral cover of >40% on most reefs globally but projected less decline on reefs in Indonesia, Malaysia, the central Philippines, New Caledonia, Fiji, and French Polynesia, which should be focal localities for multinational networks of protected areas.

Coral-bleaching responses to climate change across biological scales

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.

Planning for resilience: Incorporating scenario and model uncertainty and trade-offs when prioritizing management of climate refugia

Climate change has become the greatest threat to the world's ecosystems. Locating and managing areas that contribute to the survival of key species under climate change is critical for the persistence of ecosystems in the future. Here, we identify 'Climate Priority' sites as coral reefs exposed to relatively low levels of climate stress that will be more likely to persist in the future. We present the first analysis of uncertainty in climate change scenarios and models, along with multiple objectives, in a marine spatial planning exercise and offer a comprehensive approach to incorporating uncertainty and trade-offs in any ecosystem. We first described each site using environmental characteristics that are associated with a higher chance of persistence (larval connectivity, hurricane influence, and acute and chronic temperature conditions in the past and the future). Future temperature increases were assessed using downscaled data under four different climate scenarios (SSP1 2.6, SSP2 4.5, SSP3 7.0 and SSP5 8.5) and 57 model runs. We then prioritized sites for intervention (conservation, improved management or restoration) using robust decision-making approaches that select sites that will have a benign climate under most climate scenarios and models. The modelling work is novel because it solves two important issues. (1) It considers trade-offs between multiple planning objectives explicitly through Pareto analyses and (2) It makes use of all the uncertainty around future climate change. Priority intervention sites identified by the model were verified and refined through local stakeholder engagement including assessments of local threats, ecological conditions and government priorities. The workflow is presented for the Insular Caribbean and Florida, and at the national level for Cuba, Jamaica, Dominican Republic and Haiti. Our approach allows managers to consider uncertainty and multiple objectives for climate-smart spatial management in coral reefs or any ecosystem across the globe.

Unifying climate change biology across realms and taxa

A major challenge in modern biology is to understand extinction risk from climate change across all realms. Recent research has revealed that physiological tolerance, behavioral thermoregulation, and small elevation shifts are dominant coping strategies on land, whereas large-scale latitudinal shifts are more important in the ocean. Freshwater taxa may face the highest global extinction risks. Nevertheless, some species in each realm face similar risks because of shared adaptive, dispersal, or physiological tolerances and abilities. Taking a cross-realm perspective offers unique research opportunities because confounding physical factors in one realm are often disaggregated in another realm. Cross-realm, across taxa, and other forms of climate change biology synthesis are needed to advance our understanding of emergent patterns of risk across all life.

Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecast future genetic offset in gradient forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming scenario (RCP 2.6), we predicted a general pattern of increasing genetic offset with latitude. Under the extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch between current allele frequencies and those required to cope with local environmental change, compared to populations in the inshore Kimberley region. The study suggests complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.