Symbiodiniaceae diversity varies by host and environment across thermally distinct reefs.

Endosymbiotic dinoflagellates (Symbiodiniaceae) influence coral thermal tolerance at both local and regional scales. In isolation, the effects of host genetics, environment, and thermal disturbances on symbiont communities are well understood, yet their combined effects remain poorly resolved. Here, we investigate Symbiodiniaceae across 1300 km in Australia's Coral Sea Marine Park to disentangle these interactive effects. We identified Symbiodiniaceae to species-level resolution for three coral species (Acropora cf humilis, Pocillopora verrucosa, and Pocillopora meandrina) by sequencing two genetic markers of the symbiont (ITS2 and psbAncr), paired with genotype-by-sequencing of the coral host (DArT-seq). Our samples predominantly returned sequences from the genus Cladocopium, where Acropora cf humilis affiliated with C3k, Pocillopora verrucosa with C. pacificum, and Pocillopora meandrina with C. latusorum. Multivariate analyses revealed that Acropora symbionts were driven strongly by local environment and thermal disturbances. In contrast, Pocillopora symbiont communities were both partitioned 2.5-fold more by host genetic structure than by environmental structure. Among the two Pocillopora species, the effects of environment and host genetics explained four times more variation in symbionts for P. meandrina than P. verrucosa. The concurrent bleaching event in 2020 had variable impacts on symbiont communities, consistent with patterns in P. verrucosa and A. cf humilis, but not P. meandrina. Our findings demonstrate how symbiont macroscale community structure responses to environmental gradients depend on host species and their respective population structure. Integrating host, symbiont, and environmental data will help forecast the adaptive potential of corals and their symbionts amidst a rapidly changing environment.

Macroalgae exhibit diverse responses to human disturbances on coral reefs.

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human-driven disturbance. Using genus-level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats.

The effects of marine heatwaves on acute heat tolerance in corals.

Scleractinian coral populations are increasingly exposed to conditions above their upper thermal limits due to marine heatwaves, contributing to global declines of coral reef ecosystem health. However, historic mass bleaching events indicate there is considerable inter- and intra-specific variation in thermal tolerance whereby species, individual coral colonies and populations show differential susceptibility to exposure to elevated temperatures. Despite this, we lack a clear understanding of how heat tolerance varies across large contemporary and historical environmental gradients, or the selective pressures that underpin this variation. Here we conducted standardised acute heat stress experiments to identify variation in heat tolerance among species and isolated reefs spanning a large environmental gradient across the Coral Sea Marine Park. We quantified the photochemical yield (Fv /Fm ) of coral samples in three coral species, Acropora cf humilis, Pocillopora meandrina, and Pocillopora verrucosa, following exposure to four temperature treatments (local ambient temperatures, and + 3°C, +6°C and + 9°C above local maximum monthly mean). We quantified the temperature at which Fv /Fm decreased by 50% (termed ED50) and used derived values to directly compare acute heat tolerance across reefs and species. The ED50 for Acropora was 0.4-0.7°C lower than either Pocillopora species, with a 0.3°C difference between the two Pocillopora species. We also recorded 0.9°C to 1.9°C phenotypic variation in heat tolerance among reefs within species, indicating spatial heterogeneity in heat tolerance across broad environmental gradients. Acute heat tolerance had a strong positive relationship to mild heatwave exposure over the past 35 years (since 1986) but was negatively related to recent severe heatwaves (2016-2020). Phenotypic variation associated with mild thermal history in local environments provides supportive evidence that marine heatwaves are selecting for tolerant individuals and populations; however, this adaptive potential may be compromised by the exposure to recent severe heatwaves.

The El Niño Southern Oscillation drives multidirectional inter-reef larval connectivity in the Great Barrier Reef.

The El Niño Southern Oscillation (ENSO) is the strongest source of interannual global climate variability, and extreme ENSO events are projected to increase in frequency under climate change. Interannual variability in the Coral Sea circulation has been associated with ENSO, although uncertainty remains regarding ENSO's influence on hydrodynamics and larval dispersal in the adjacent Great Barrier Reef (GBR). We investigated larval connectivity during ENSO events from 2010 to 2017 throughout the GBR, based on biophysical modelling of a widespread predatory reef fish, Lutjanus carponotatus. Our results indicate a well-connected system over the study period with high interannual variability in inter-reef connectivity associated with ENSO. Larval connectivity patterns were highly correlated to variations in the Southern Oscillation Index (SOI). During El Niño conditions and periods of weak SOI, larval dispersal patterns were predominantly poleward in the central and southern regions, reversing to a predominant equatorward flow during very strong SOI and extreme La Niña conditions. These ENSO-linked connectivity patterns were associated with positive connectivity anomalies among reefs. Our findings identify ENSO as an important source of variation in larval dispersal and connectivity patterns in the GBR, which can influence the stability of population dynamics and patterns of biodiversity in the region.

Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus).

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here, we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50% smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~10-120 kya) and may be vulnerable to localized disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of the Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

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.

Influence of offshore oil and gas structures on seascape ecological connectivity.

Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure.

Regional versus latitudinal variation in the life-history traits and demographic rates of a reef fish, Centropyge bispinosa, in the Coral Sea and Great Barrier Reef Marine Parks, Australia.

Environmental temperature is an important determinant of physiological processes and life histories in ectotherms. Over latitudinal scales, variation in temperature has been linked to changes in life-history traits and demographic rates, with growth and mortality rates generally being greatest at low latitudes, and longevity and maximum length being greater at higher latitudes. Using the two-spined angelfish, Centropyge bispinosa, as our focal species, we compared growth patterns, growth rates, longevity, mortality, asymptotic length and maximum length across 22 reefs that span 13° of latitude within the Great Barrier Reef Marine Park (GBRMP) and the Coral Sea Marine Park (CSMP), Australia. We found no predictable latitudinal variation in mortality rates, growth patterns, growth rates, asymptotic or maximum length of C. bispinosa at regional to biogeographic scales. However, C. bispinosa consistently exhibited reduced longevity at lower, warmer latitudes within the CSMP. The greatest differences in mean maximum length of C. bispinosa were between continental (GBRMP) and oceanic (central CSMP) reefs of similar latitude, with individuals being larger on average on continental versus oceanic reefs. The lack of predictable life-history and demographic variation in C. bispinosa across a 13° latitudinal gradient within the CSMP, coupled with differences in mean maximum length between continental and oceanic reefs at similar latitudes, suggest that local environmental conditions have a greater influence than environmental temperature on the demographic rates and life-history traits of C. bispinosa.

Stochastic nature of larval dispersal at sea.

The movement of individuals across landscapes remains a fundamental process in population and community ecology. All species have developed a capacity to disperse but this process remains elusive in organisms with complex life-cycles, and none more so than in the marine environment. Here, most organisms have developed a two-phased life-cycle, leaving the risky business of dispersing through the open ocean to their very small and intractable larval offspring. To this day, quantifying dispersal patterns in marine seascapes remains a significant challenge, and yet it is critical to the way we preserve marine ecosystems and the services they provide. In this issue of Molecular Ecology, Catalano et al. (2021) present one of the first longitudinal studies to demonstrate the stochastic nature of larval dispersal. Their work challenges some of our current ideas about marine population connectivity and provides new methodological insights to study its temporal dimension.

Minimum size limits and the reproductive value of numerous, young, mature female fish.

Fisheries management relies on various catch and effort controls to preserve spawning stock biomass and maximize sustainable yields while limiting fishery impacts on marine ecosystems. These include species-specific minimum or maximum size limits to protect either small non-reproductive subadults, a portion of reproductively mature adults, or large highly fecund individuals. Protecting size classes of mature fish is expected to yield a viable source of larvae for replenishing populations and reduce the risk of recruitment overfishing, yet size-specific recruitment contributions have rarely been assessed empirically. Here, we apply genetic parentage analysis to measure the reproductive success of a size-structured population of a commercially important species of coral grouper (Plectropomus maculatus-Serranidae) in no-take marine reserves (NTMRs) in the Great Barrier Reef Marine Park, Australia. Although the per capita reproductive success of individual fish increases rapidly with body length, the numerous young mature female fish, below the minimum size limit (MSL) (38 cm total length), were responsible for generating disproportionately large contributions (36%) towards larval replenishment of both fished and reserve reefs. Our findings indicate that MSLs are an effective harvest control measure to safeguard a portion of the spawning stock biomass for coral grouper and supplement recruitment subsidies assured from NTMRs.

A connectivity portfolio effect stabilizes marine reserve performance.

Well-managed and enforced no-take marine reserves generate important larval subsidies to neighboring habitats and thereby contribute to the long-term sustainability of fisheries. However, larval dispersal patterns are variable, which leads to temporal fluctuations in the contribution of a single reserve to the replenishment of local populations. Identifying management strategies that mitigate the uncertainty in larval supply will help ensure the stability of recruitment dynamics and minimize the volatility in fishery catches. Here, we use genetic parentage analysis to show extreme variability in both the dispersal patterns and recruitment contribution of four individual marine reserves across six discrete recruitment cohorts for coral grouper (Plectropomus maculatus) on the Great Barrier Reef. Together, however, the asynchronous contributions from multiple reserves create temporal stability in recruitment via a connectivity portfolio effect. This dampening effect reduces the variability in larval supply from individual reserves by a factor of 1.8, which effectively halves the uncertainty in the recruitment contribution of individual reserves. Thus, not only does the network of four marine reserves generate valuable larval subsidies to neighboring habitats, the aggregate effect of individual reserves mitigates temporal fluctuations in dispersal patterns and the replenishment of local populations. Our results indicate that small networks of marine reserves yield previously unrecognized stabilizing benefits that ensure a consistent larval supply to replenish exploited fish stocks.

Comparative demography of commercially important species of coral grouper, Plectropomus leopardus and P. laevis, from Australia's great barrier reef and Coral Sea marine parks.

Understanding the spatial and environmental variation in demographic processes of fisheries target species, such as coral grouper (Genus: Plectropomus), is important for establishing effective management and conservation strategies. Herein we compare the demography of Plectropomus leopardus and P. laevis between Australia's Great Barrier Reef Marine Park (GBRMP), which has been subject to sustained and extensive fishing pressure, and the oceanic atolls of Australia's Coral Sea Marine Park (CSMP), where there is very limited fishing for reef fishes. Coral grouper length-at-age data from contemporary and historical otolith collections across 9.4 degrees of latitude showed little difference in lifetime growth between GBRMP and CSMP regions. Plectropomus laevis populations in GBRMP reefs had significantly higher rates of total mortality than populations in the CSMP. Mean maximum lengths and mean maximum ages of P. laevis were also smaller in the GBRMP than in the CSMP, even when considering populations sampled within GBRMP no-take marine reserves (NTMRs). Plectropomus leopardus, individuals were on average smaller on fished reefs than NTMRs in the GBRMP, but all other aspects of demography were broadly similar between regions despite the negligible levels of fishing pressure in the CSMP. Similarities between regions in growth profiles and length-at-age comparisons of P. laevis and P. leopardus suggest that the environmental differences between the CSMP and the GBRMP may not have significant impacts on lifetime growth. Our results show that fishing may have influenced the demography of coral grouper on the GBR, particularly for the slower growing and longer lived species, P. laevis.

Natal philopatry increases relatedness within groups of coral reef cardinalfish.

A central issue in evolutionary ecology is how patterns of dispersal influence patterns of relatedness in populations. In terrestrial organisms, limited dispersal of offspring leads to groups of related individuals. By contrast, for most marine organisms, larval dispersal in open waters is thought to minimize kin associations within populations. However, recent molecular evidence and theoretical approaches have shown that limited dispersal, sibling cohesion and/or differential reproductive success can lead to kin association and elevated relatedness. Here, we tested the hypothesis that limited dispersal explains small-scale patterns of relatedness in the pajama cardinalfish Sphaeramia nematoptera. We used 19 microsatellite markers to assess parentage of 233 juveniles and pairwise relatedness among 527 individuals from 41 groups in Kimbe Bay, Papua New Guinea. Our findings support three predictions of the limited dispersal hypothesis: (i) elevated relatedness within groups, compared with among groups and elevated relatedness within reefs compared with among reefs; (ii) a weak negative correlation of relatedness with distance; (iii) more juveniles than would be expected by chance in the same group and the same reef as their parents. We provide the first example for natal philopatry at the group level causing small-scale patterns of genetic relatedness in a marine fish.

An enigmatic decoupling between heat stress and coral bleaching on the Great Barrier Reef.

Ocean warming threatens the functioning of coral reef ecosystems by inducing mass coral bleaching and mortality events. The link between temperature and coral bleaching is now well-established based on observations that mass bleaching events usually occur when seawater temperatures are anomalously high. However, times of high heat stress but without coral bleaching are equally important because they can inform an understanding of factors that regulate temperature-induced bleaching. Here, we investigate the absence of mass coral bleaching on the Great Barrier Reef (GBR) during austral summer 2004. Using four gridded sea surface temperature data products, validated with in situ temperature loggers, we demonstrate that the summer of 2004 was among the warmest summers of the satellite era (1982-2017) on the GBR. At least half of the GBR experienced temperatures that were high enough to initiate bleaching in other years, yet mass bleaching was not reported during 2004. The absence of bleaching is not fully explained by wind speed or cloud cover. Rather, 2004 is clearly differentiated from bleaching years by the slow speed of the East Australian Current (EAC) offshore of the GBR. An anomalously slow EAC during summer 2004 may have dampened the upwelling of nutrient-rich waters onto the GBR shelf, potentially mitigating bleaching due to the lower susceptibility of corals to heat stress in low-nutrient conditions. Although other factors such as irradiance or acclimatization may have played a role in the absence of mass bleaching, 2004 remains a key case study for demonstrating the dynamic nature of coral responses to marine heatwaves.

Successful validation of a larval dispersal model using genetic parentage data.

Larval dispersal is a critically important yet enigmatic process in marine ecology, evolution, and conservation. Determining the distance and direction that tiny larvae travel in the open ocean continues to be a challenge. Our current understanding of larval dispersal patterns at management-relevant scales is principally and separately informed by genetic parentage data and biological-oceanographic (biophysical) models. Parentage datasets provide clear evidence of individual larval dispersal events, but their findings are spatially and temporally limited. Biophysical models offer a more complete picture of dispersal patterns at regional scales but are of uncertain accuracy. Here, we develop statistical techniques that integrate these two important sources of information on larval dispersal. We then apply these methods to an extensive genetic parentage dataset to successfully validate a high-resolution biophysical model for the economically important reef fish species Plectropomus maculatus in the southern Great Barrier Reef. Our results demonstrate that biophysical models can provide accurate descriptions of larval dispersal at spatial and temporal scales that are relevant to management. They also show that genetic parentage datasets provide enough statistical power to exclude poor biophysical models. Biophysical models that included species-specific larval behaviour provided markedly better fits to the parentage data than assuming passive behaviour, but incorrect behavioural assumptions led to worse predictions than ignoring behaviour altogether. Our approach capitalises on the complementary strengths of genetic parentage datasets and high-resolution biophysical models to produce an accurate picture of larval dispersal patterns at regional scales. The results provide essential empirical support for the use of accurately parameterised biophysical larval dispersal models in marine spatial planning and management.

Extra-pair mating in a socially monogamous and paternal mouth-brooding cardinalfish.

Many vertebrates form monogamous pairs to mate and care for their offspring. However, genetic tools have increasingly shown that offspring often arise from matings outside of the monogamous pair bond. Social monogamy is relatively common in coral reef fishes, but there have been few studies that have confirmed monogamy or extra-pair reproduction, either for males or for females. Here, long-term observations and genetic tools were applied to examine the parentage of embryos in a paternally mouth-brooding cardinalfish, Sphaeramia nematoptera. Paternal care in fishes, such as mouth-brooding, is thought to be associated with a high degree of confidence in paternity. Two years of observations confirmed that S. nematoptera form long-term pair bonds within larger groups. However, genetic parentage revealed extra-pair mating by both sexes. Of 105 broods analysed from 64 males, 30.1% were mothered by a female that was not the partner and 11.5% of broods included eggs from two females. Despite the high paternal investment associated with mouth-brooding, 7.6% of broods were fertilized by two males. Extra-pair matings appeared to be opportunistic encounters with individuals from outside the immediate group. We argue that while pair formation contributes to group cohesion, both males and females can maximize lifetime reproductive success by taking advantage of extra-pair mating opportunities.

Acclimatization of massive reef-building corals to consecutive heatwaves.

Reef-building corals typically live close to the upper limits of their thermal tolerance and even small increases in summer water temperatures can lead to bleaching and mortality. Projections of coral reef futures based on forecasts of ocean temperatures indicate that by the end of this century, corals will experience their current thermal thresholds annually, which would lead to the widespread devastation of coral reef ecosystems. Here, we use skeletal cores of long-lived Porites corals collected from 14 reefs across the northern Great Barrier Reef, the Coral Sea, and New Caledonia to evaluate changes in their sensitivity to heat stress since 1815. High-density 'stress bands'-indicative of past bleaching-first appear during a strong pre-industrial El Niño event in 1877 but become significantly more frequent in the late twentieth and early twenty-first centuries in accordance with rising temperatures from anthropogenic global warming. However, the proportion of cores with stress bands declines following successive bleaching events in the twenty-first century despite increasing exposure to heat stress. Our findings demonstrate an increase in the thermal tolerance of reef-building corals and offer a glimmer of hope that at least some coral species can acclimatize fast enough to keep pace with global warming.

Harvesting changes mating behaviour in European lobster.

Removing individuals from a wild population can affect the availability of prospective mates and the outcome of competitive interactions, with subsequent effects on mating patterns and sexual selection. Consequently, the rate of harvest-induced evolution is predicted to be strongly dependent on the strength and dynamics of sexual selection, yet there is limited empirical knowledge on the interplay between selective harvesting and the mating systems of exploited species. In this study, we used genetic parentage assignment to compare mating patterns of the highly valued and overexploited European lobster (Homarus gammarus) in a designated lobster reserve and nearby fished area in southern Norway. In the area open to fishing, the fishery is regulated by a closed season, a minimum legal size and a ban on the harvest of egg-bearing females. Due to the differences in size and sex-specific fishing mortality between the two areas, males and females are of approximately equal average size in the fished area, whereas males tend to be larger in the reserve. Our results show that females would mate with males larger than their own body size, but the relative size difference was significantly larger in the reserve. Sexual selection acted positively on both body size and claw size in males in the reserve, while it was nonsignificant in fished areas. This strongly suggests that size truncation of males by fishing reduces the variability of traits that sexual selection acts upon. If fisheries continue to target large individuals (particularly males) with higher relative reproductive success, the weakening of sexual selection will likely accelerate fisheries-induced evolution towards smaller body size.

Spatial and temporal patterns of mass bleaching of corals in the Anthropocene.

Tropical reef systems are transitioning to a new era in which the interval between recurrent bouts of coral bleaching is too short for a full recovery of mature assemblages. We analyzed bleaching records at 100 globally distributed reef locations from 1980 to 2016. The median return time between pairs of severe bleaching events has diminished steadily since 1980 and is now only 6 years. As global warming has progressed, tropical sea surface temperatures are warmer now during current La Niña conditions than they were during El Niño events three decades ago. Consequently, as we transition to the Anthropocene, coral bleaching is occurring more frequently in all El Niño-Southern Oscillation phases, increasing the likelihood of annual bleaching in the coming decades.

Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish.

Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus leopardus) and the bar-cheek coral trout (Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first- and later-generation hybrids, identifying 124 interspecific hybrids from a collection of 2,991 coral trout sampled in inshore and mid-shelf reefs of the southern Great Barrier Reef. Hybrids were ubiquitous among reefs, fertile and spanned multiple generations suggesting both ecological and evolutionary processes are acting to maintain species barriers. We elaborate on these finding to investigate the extent of genomic introgression and admixture from 2,271 SNP loci recovered from a ddRAD library of pure and hybrid individuals. An analysis of genomic clines on recovered loci indicates that 261 SNP loci deviate from a model of neutral introgression, of which 132 indicate a pattern of introgression consistent with selection favouring both hybrid and parental genotypes. Our findings indicate genome-wide, bidirectional introgression between two sympatric species of coral reef fishes and provide further support to a growing body of evidence for the role of hybridization in the evolution of coral reef fishes.