Are coral reefs victims of their own past success?

Evolution and environment of Caribbean coastal ecosystems

Isolation of the Caribbean Sea from the tropical Eastern Pacific by uplift of the Isthmus of Panama in the late Pliocene was associated with major, taxonomically variable, shifts in Caribbean biotic composition, and extinction, but inferred causes of these biological changes have remained elusive. We addressed this through falsifiable hypotheses about how independently determined historical changes in oceanographic conditions may have been responsible. The most striking environmental change was a sharp decline in upwelling intensity as measured from decreases in intra-annual fluctuations in temperature and consequently in planktonic productivity. We then hypothesized three general categories of biological response based upon observed differences in natural history between the oceans today. These include changes in feeding ecology, life histories, and habitats. As expected, suspension feeders and predators became rarer as upwelling declined. However, predicted increases in benthic productivity by reef corals, and benthic algae were drawn out over more than 1 Myr as seagrass and coral reef habitats proliferated; a shift that was itself driven by declining upwelling. Similar time lags occurred for predicted shifts in reproductive life history characteristics of bivalves, gastropods, and bryozoans. Examination of the spatial variability of biotic change helps to understand the time lags. Many older species characteristic of times before environmental conditions had changed tended to hang on in progressively smaller proportions of locations until they became extinct as expected from metapopulation theory and the concept of extinction debt. Faunal turnover may not occur until a million or more years after the environmental changes ultimately responsible.

9000 years of change in coral community structure and accretion in Belize reefs, western Atlantic

Tropical coral reefs, as prominent marine diversity hotspots, are in decline, and long-term studies help to improve understanding of the effects of global warming, sea-level rise, ocean acidification, deterioration of water quality, and disease. Here, we evaluated relative coral abundance and reef accretion rates over the past 9000 years in Belize barrier and atoll reefs, the largest reef system in the Atlantic Ocean. Acropora palmata and Orbicella spp. have been the most common corals. The abundance of competitive, fast-growing acroporids was constant over multi-millennial timescales. A decline in A. cervicornis abundance, however, and three centennial-scale gaps in A. palmata occurrence, suggest that the modern decline in acroporids was not unprecedented. Stress-tolerant corals predominate at the beginning of Holocene successions. Following the improvement of environmental conditions after inundation of the reef pedestal, their abundance has decreased. The abundance of weedy corals has increased during the Holocene underlining the importance of fecundity for the coral community. Reef-accretion rate, as calculated based on 76 new U-series age dates, has decreased over the Holocene and the mean value of 3.36 m kyr-1 is at the lower end of global reef growth compilations and predicted future rates of rise in sea level.

The evolution of fast-growing coral reef fishes

Individual growth is a fundamental life history trait^1-4, yet its macroevolutionary trajectories have rarely been investigated for entire animal assemblages. Here we analyse the evolution of growth in a highly diverse vertebrate assemblage-coral reef fishes. We combine state-of-the-art extreme gradient boosted regression trees with phylogenetic comparative methods to detect the timing, number, location and magnitude of shifts in the adaptive regime of somatic growth. We also explored the evolution of the allometric relationship between body size and growth. Our results show that the evolution of fast growth trajectories in reef fishes has been considerably more common than the evolution of slow growth trajectories. Many reef fish lineages shifted towards faster growth and smaller body size evolutionary optima in the Eocene (56-33.9 million years ago), pointing to a major expansion of life history strategies in this Epoch. Of all lineages examined, the small-bodied, high-turnover cryptobenthic fishes shifted most towards extremely high growth optima, even after accounting for body size allometry. These results suggest that the high global temperatures of the Eocene⁵ and subsequent habitat reconfigurations⁶ might have been critical for the rise and retention of the highly productive, high-turnover fish faunas that characterize modern coral reef ecosystems.

Reef fishes weaken dietary preferences after coral mortality, altering resource overlap

The direct and indirect effects of climate change can affect, and are mediated by, changes in animal behaviour. However, we often lack sufficient empirical data to assess how large-scale disturbances affect the behaviour of individuals, which scales up to influence communities. Here, we investigate these patterns by focusing on the foraging behaviour of butterflyfishes, prominent coral-feeding fishes on coral reefs, before and after a mass coral bleaching event in Iriomote, Japan. In response to 65% coral mortality, coral-feeding fishes broadened their diets, showing a significant weakening of dietary preferences across species. Multiple species reduced their consumption of bleaching-sensitive Acropora corals, while expanding their diets to consume a variety of other coral genera. This resulted in decreased dietary overlap among butterflyfishes. Behavioural changes in response to bleaching may increase resilience of coral reef fishes in the short term. However, coral mortality has reduced populations of coral-feeders world-wide, indicating the changes in feeding behaviour we document here may not be sufficient to ensure long-term resilience of butterflyfishes on coral reefs.

Rising from the Ashes: The Biogeographic Origins of Modern Coral Reef Fishes

During the excavation of Mayan tombs, little did the archaeologists know that the fossils they discovered in the tomb stones would fundamentally alter our understanding of the earliest origins of coral reef fishes. Located just 500 kilometers from the point where an asteroid impact reconfigured the world's biological systems 66 million years ago, we find the earliest origins of three typical reef fish groups. Their presence in Mexico just 3 million years after this impact finally reconciles the conflict between the fossil and phylogenetic evidence for the earliest origins of reef fishes. The incorporation of these fossils into a global reconstruction of fish evolutionary history reveals a new picture of the early biogeography of reef fishes, with strong Atlantic links. From locations associated with biological destruction and societal collapse, we see evidence of the origins of one of the world's most diverse and spectacular marine ecosystems: coral reefs.

Fast-growing species shape the evolution of reef corals

Ecological interactions are ubiquitous on tropical coral reefs, where sessile organisms coexist in limited space. Within these high-diversity systems, reef-building scleractinian corals form an intricate interaction network. The role of biotic interactions among reef corals is well established on ecological timescales. However, its potential effect on macroevolutionary patterns remains unclear. By analysing the rich fossil record of Scleractinia, we show that reef coral biodiversity experienced marked evolutionary rate shifts in the last 3 million years, possibly driven by biotic interactions. Our models suggest that there was an overwhelming effect of staghorn corals (family Acroporidae) on the fossil diversity trajectories of other coral groups. Staghorn corals showed an unparalleled spike in diversification during the Pleistocene. But surprisingly, their expansion was linked with increases in both extinction and speciation rates in other coral families, driving a nine-fold increase in lineage turnover. These results reveal a double-edged effect of diversity dependency on reef evolution. Given their fast growth, staghorn corals may have increased extinction rates via competitive interactions, while promoting speciation through their role as ecosystem engineers. This suggests that recent widespread human-mediated reductions in staghorn coral cover, may be disrupting the key macroevolutionary processes that established modern coral reef ecosystems.

The effect of biotic interactions among reef corals on macroevolutionary patterns is unclear. Here, the authors study the rich coral fossil record, finding that reef coral diversity experienced potentially biotic interaction-driven evolutionary rate changes, and that Staghorn corals affected fossil diversity trajectories of other coral groups.

Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts

Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef-building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata, A. cervicornis and their F₁ hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium 'fitti'. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S. 'fitti' populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S. 'fitti' strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600-Mb draft assembly of the S. 'fitti' genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S. 'fitti' strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S. 'fitti' strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S. 'fitti' strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.

Ecomorphological divergence and trophic resource partitioning in 15 syntopic Indo-Pacific parrotfishes (Labridae: Scarini)

Adaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.

Evolutionary History Drives Biogeographic Patterns of Coral Reef Resilience

Modern-day Indo-Pacific coral reefs are characterized by rapid recovery driven by pulses of coral recruitment, but Caribbean reefs exhibit low rates of recruitment and poor recovery following a wide range of disturbance events. The contrasting evolutionary history of coral taxa offers key insight into biogeographic patterns of coral resilience. Following the closure of the Isthmus of Panama approximately 2.8 million years ago, widespread extinction of Caribbean corals led to an evolutionary bottleneck that favored large and long-lived species with a relatively high reliance on asexual versus sexual reproduction. In contrast, adaptive radiation led to the evolution of superrecruiting tabular, digitate, and corymbose corals that drive the rapid recovery of modern-day Indo-Pacific reefs following disturbance. The dominance of branching growth forms and evolutionary absence of superrecruiting growth forms throughout the entire evolutionary history of the Caribbean (approximately 38 million years ago to present) may explain the exceptionally high recruitment rates on modern-day Indo-Pacific reefs and low historical recruitment on Caribbean reefs. The evolutionary history of the Caribbean coral reef-building taxa implies that, even with a reversal of ecosystem state, widespread recovery of Caribbean reefs may be limited.

A possible link between coral reef success, crustose coralline algae and the evolution of herbivory

Crustose coralline red algae (CCA) play a key role in the consolidation of many modern tropical coral reefs. It is unclear, however, if their function as reef consolidators was equally pronounced in the geological past. Using a comprehensive database on ancient reefs, we show a strong correlation between the presence of CCA and the formation of true coral reefs throughout the last 150 Ma. We investigated if repeated breakdowns in the potential capacity of CCA to spur reef development were associated with sea level, ocean temperature, CO₂ concentration, CCA species diversity, and/or the evolution of major herbivore groups. Model results show that the correlation between the occurrence of CCA and the development of true coral reefs increased with CCA diversity and cooler ocean temperatures while the diversification of herbivores had a transient negative effect. The evolution of novel herbivore groups compromised the interaction between CCA and true reef growth at least three times in the investigated time interval. These crises have been overcome by morphological adaptations of CCA.

Coral reef diversity losses in China's Greater Bay Area were driven by regional stressors

Observations of coral reef losses to climate change far exceed our understanding of historical degradation before anthropogenic warming. This is a critical gap to fill as conservation efforts simultaneously work to reverse climate change while restoring coral reef diversity and function. Here, we focused on southern China's Greater Bay Area, where coral communities persist despite centuries of coral mining, fishing, dredging, development, and pollution. We compared subfossil assemblages with modern-day communities and revealed a 40% decrease in generic diversity, concomitant to a shift from competitive to stress-tolerant species dominance since the mid-Holocene. Regions with characteristically poor water quality-high chl-a, dissolved inorganic nitrogen, and turbidity-had lower contemporary diversity and the greatest community composition shift observed in the past, driven by the near extirpation of Acropora These observations highlight the urgent need to mitigate local stressors from development in concert with curbing greenhouse gas emissions.

Long-term imaging of the photosensitive, reef-building coral Acropora muricata using light-sheet illumination

Coral reefs are in alarming decline due to climate emergency, pollution and other man-made disturbances. The numerous ecosystem services derived from coral reefs are underpinned by the growth and physical complexity of reef-forming corals. Our knowledge of their fundamental biology is limited by available technology. We need a better understanding of larval settlement and development, skeletogenesis, interactions with pathogens and symbionts, and how this biology interacts with environmental factors such as light exposure, temperature, and ocean acidification. We here focus on a fast-growing key coloniser, Acropora muricata (Linnaeus, 1758). To enable dynamic imaging of this photosensitive organism at different scales, we developed light-sheet illumination for fluorescence microscopy of small coral colonies. Our approach reveals live polyps in previously unseen detail. An imaging range for Acropora muricata with no measurable photodamage is defined based upon polyp expansion, coral tissue reaction, and photobleaching. We quantify polyp retraction as a photosensitive behavioural response and show coral tissue rupture at higher irradiance with blue light. The simple and flexible technique enables non-invasive continuous dynamic imaging of highly photosensitive organisms with sizes between 1 mm³ and 5 cm³, for eight hours, at high temporal resolution, on a scale from multiple polyps down to cellular resolution. This live imaging tool opens a new window into the dynamics of reef-building corals.

Defining variation in pre-human ecosystems can guide conservation: An example from a Caribbean coral reef

Many Caribbean coral reefs are heavily degraded, yet their pre-human, natural states are often assumed or estimated using space-for-time substitution approaches. Here we use an 11-hectare suite of fossilised mid-Holocene (7.2-5.6 ka) fringing reefs in Caribbean Panama to define natural variation in hard coral community structure before human-impact to provide context to the states of the same reefs today. We collected bulk samples from four trenches dug into the mid-Holocene fossil reef and surficial bulk samples from 2-10 m depths on five adjacent modern reefs extending over 5 km. Analysis of the abundances of coral taxa in fossil bulk samples define the Historical Range of Variation (HRV) in community structure of the reefs. When compared to the community structure of adjacent modern reefs, we find that most coral communities today fall outside the HRV, identifying them as novel ecosystems and corroborating the well-documented transition from acroporid-dominated Caribbean reefs to reefs dominated by stress-tolerant taxa (Porites and Agaricia). We find one modern reef, however, whose community composition remains within the HRV showing that it has not transitioned to a novel state. Reef-matrix cores extracted from this reef reveal that the coral community has remained in this state for over 800 years, suggesting long-term stability and resistance to the region-wide shift to novel states. Without these data to provide historical context, this potentially robust and stable reef would be overlooked since it does not fulfil expectations of what a Caribbean coral reef should look like in the absence of humans. This example illustrates how defining past variation using the fossil record can improve our understanding of modern degradation and guide conservation.

Young fishes persist despite coral loss on the Great Barrier Reef

Unprecedented global bleaching events have led to extensive loss of corals. This is expected to lead to extensive losses of obligate coral-dependent fishes. Here, we use a novel, spatially-matched census approach to examine the nature of fish-coral dependency across two mass coral bleaching events. Despite a >40% loss of coral cover, and the ecological extinction of functionally important habitat-providing Acropora corals, we show that populations of obligate coral-dependent fishes, including Pomacentrus moluccensis, persisted and - critically - recruitment was maintained. Fishes used a wide range of alternate reef habitats, including other coral genera and dead coral substrata. Labile habitat associations of 'obligate' coral-dependent fishes suggest that recruitment may be sustained on future reefs that lack Acropora, following devastating climatic disturbances. This persistence without Acropora corals offers grounds for cautious optimism; for coral-dwelling fishes, corals may be a preferred habitat, not an obligate requirement.

Adapting to extreme environments: can coral reefs adapt to climate change?

Reef-building corals throughout the world have an annual value of tens of billions of dollars, yet they are being degraded at an increasing rate by many anthropogenic and environmental factors. Despite this, some reefs show resilience to such extreme environmental changes. This review shows how techniques in computational modelling, genetics, and transcriptomics are being used to unravel the complexity of coral reef ecosystems, to try and understand if they can adapt to new and extreme environments. Considering the ambitious climate targets of the Paris Agreement to limit global warming to 2°C, with aspirations of even 1.5°C, questions arise on how to achieve this. Geoengineering may be necessary if other avenues fail, although global governance issues need to play a key role. Development of large and effective coral refugia and marine protected areas is necessary if we are not to lose this vital resource for us all.

A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora, concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora.

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An ancient genome duplication occurred in the most recent common ancestor of Acropora

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This WGD event likely occurred between 28 and 36 mya in Acropora

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The WGD event potentially contributes to the origin and diversification of Acropora

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Duplications of toxic proteins were found in Acropora following the WGD

Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (<1.75 Ma). Even though deep reef environments were drastically reduced during the extreme low sea level stands of glacial ages, shallow reefs persisted, and as such there was no evidence supporting mass extirpation of fauna in this region.

The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals

Reef-building corals provide the structural basis for one of Earth's most spectacular and diverse-but increasingly threatened-ecosystems. Modern Indo-Pacific reefs are dominated by species of the staghorn coral genus Acropora, but the evolutionary and ecological factors associated with their diversification and rise to dominance are unclear. Recent work on evolutionary radiations has demonstrated the importance of introgression and ecological opportunity in promoting diversification and ecological success. Here, we analyze the genomes of five staghorn coral species to examine the roles of introgression and ecological opportunity in the rise to dominance of Acropora. We found evidence for a history marked by a major introgression event as well as recurrent gene flow across species. In addition, we found that genes with topologies mismatching the species tree are evolving faster, which is suggestive of a role for introgression in spreading adaptive genetic variation. Demographic analysis showed that Acropora lineages profited from climate-driven mass extinctions in the Plio-Pleistocene, indicating that Acropora exploited ecological opportunity opened by a new climatic regime favoring species that could cope with rapid sea-level changes. Collectively, the genomes of reef-building corals have recorded an evolutionary history shaped by introgression and climate change, suggesting that Acropora-among most vulnerable corals to stressors-may be critical for understanding how reefs track the impending rapid sea-level changes of the Anthropocene.

Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia)

Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as ‘homing’. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians. However, the central role of LAGLIDADG motifs in intron mobility mechanisms remains poorly understood. To resolve questions regarding the evolutionary origin and distribution of group I introns and HEGs in Scleractinia and Corallimorpharia, we examined intron/HEGs sequences within a comprehensive phylogenetic framework. Analyses of LAGLIDADG motif conservation showed a high degree of degradation in complex Scleractinia and Corallimorpharia. Moreover, the two motifs lack the respective acidic residues necessary for metal-ion binding and catalysis, potentially impairing horizontal intron mobility. In contrast, both motifs are highly conserved within robust Scleractinia, indicating a fully functional endonuclease capable of promoting horizontal intron transference. A higher rate of non-synonymous substitutions (K_a) detected in the HEGs of complex Scleractinia and Corallimorpharia suggests degradation of the HEG, whereas lower K_a rates in robust Scleractinia are consistent with a scenario of purifying selection. Molecular-clock analyses and ancestral inference of intron type indicated an earlier intron insertion in complex Scleractinia and Corallimorpharia in comparison to robust Scleractinia. These findings suggest that the lack of horizontal intron transfers in the former two groups is related to an age-dependent degradation of the endonuclease activity. Moreover, they also explain the peculiar geographical patterns of introns in stony and mushroom corals.

Empty Niches after Extinctions Increase Population Sizes of Modern Corals

Large environmental fluctuations often cause mass extinctions, extirpating species and transforming communities [1, 2]. While the effects on community structure are evident in the fossil record, demographic consequences for populations of individual species are harder to evaluate because fossils reveal relative, but not absolute, abundances. However, genomic analyses of living species that have survived a mass extinction event offer the potential for understanding the demographic effects of such environmental fluctuations on extant species. Here, we show how environmental variation since the Pliocene has shaped demographic changes in extant corals of the genus Orbicella, major extant reef builders in the Caribbean that today are endangered. We use genomic approaches to estimate previously unknown current and past population sizes over the last 3 million years. Populations of all three Orbicella declined around 2-1 million years ago, coincident with the extinction of at least 50% of Caribbean coral species. The estimated changes in population size are consistent across the three species despite their ecological differences. Subsequently, two shallow-water specialists expanded their population sizes at least 2-fold, over a time that overlaps with the disappearance of their sister competitor species O. nancyi (the organ-pipe Orbicella). Our study suggests that populations of Orbicella species are capable of rebounding from reductions in population size under suitable conditions and that the effective population size of modern corals provides rich standing genetic variation for corals to adapt to climate change. For conservation genetics, our study suggests the need to evaluate genetic variation under appropriate demographic models.