Measuring the performance of coral phenotypes can link genotypes to their environment, potentially allowing practitioners to cultivate species and genotypes that are particularly well suited for restoration projects. Yet, performance depends on interactions between individuals and their local environment that are difficult to predict and trade-offs between desirable traits, such as growth and thermal tolerance, may be common. As a result, ensuring a diversity of corals are present in outplant populations that can thrive under future ocean conditions will provide resilience to restored populations. To that end, tracking key traits in nursery populations will not only help restoration practitioners optimize their nursery stock, but can ensure that such a diverse suite of potentially important traits is represented in outplanting designs. However, traits are not all equally relevant to success and measuring some traits can be technically challenging, time consuming, and expensive. Therefore, establishing consistent guidelines for collecting a minimum level of the most informative data is important for optimally managing nurseries. Here, we highlight several key phenotypic traits that correlate well with the performance and survival of corals on the reef. Specifically, we recommend tracking the rates of survival, wound healing, and skeletal growth, along with disease and bleaching susceptibility, and reproductive output for every genotype maintained in the nursery. We provide a standardized, low-cost protocol to measure each trait that will facilitate comparisons between genotypes, nurseries, and regions. By focusing on propagating corals with a high degree of phenotypic resilience to climate change, restoration practitioners can outplant genetically diverse populations with the greatest potential to survive, adapt, and acclimatize to changing environments.

Conventional coral reef conservation and management has been reliant on natural recovery processes following management actions to remove stressors. This approach is characterized by a laudable precautionary principle to ‘do no harm’ and to minimize intervention in natural processes. As active propagation and population enhancement measures have been deemed appropriate, this precautionary principle has been expressed in the ‘local is best’ approach for sourcing restoration stocks, or provenancing. However, in the current anthropocene era of rapid environmental change, adequate removal of stressors to allow recovery and persistence appears infeasible in most coral reef settings, attested to by observed drastic coral declines. Hence, increasing calls are heard to devise and implement restoration and management strategies that proactively maximize the adaptive capacities of species and communities, rather than conserving their historic state. Evolutionary theory identifies large effective population size, high connectedness and gene flow, and maximizing the standing genetic variation in populations (especially as relates to functionally adaptive traits) as key aspects to improve evolutionary resilience. Restoration, with some emphasis on sexual processes, can clearly play a key role in enhancing these population characteristics. However, exclusively local provenancing is not the way to maximize standing adaptive genetic variation in restored populations. This presentation will review alternative provenancing strategies that are expected to improve adaptive capacity of coral populations.

Nurseries are limited in the numbers of coral genets (fragments originating from the same colony) they can propagate, raising questions as to whether the genetic diversity of natural populations is adequately represented, and whether sexual propagation of these limited individuals will result in excessive inbreeding. Additional concerns arise when considering assisted gene flow: transplanting individuals from distant locations could lead to outbreeding depression, a decrease in fitness of the next generation due to the swamping of locally adaptive genetic variants with maladaptive foreign ones. Here, we present results suggesting that these issues are not as problematic as they seem. Based on existing population genetic data, we show that collecting as few as 3-4 individual corals is sufficient to capture the majority of common genetic diversity within a population. Such a low per-population effort also facilitates collections from multiple populations spanning a range of environments. For the long-term genetic success of restoration efforts, it is imperative for outplanted corals to breed with each other and with local corals. It is therefore essential to keep track of the genetic origin of nursery-propagated fragments to ensure outplanting of genetically diverse coral groups capable of cross-fertilization. For nurseries equipped to breed, another option would be to generate crosses within nurseries and outplant offspring. Given that coral populations are generally highly genetically diverse, the potential risk of inbreeding is low in these first-generation offspring. Finally, a simulation analysis indicates that introducing ~0.1-1% of foreign corals into a local population would ensure efficient transfer of adaptive genetic diversity while greatly lowering the risk of outbreeding depression.

As coral reefs continue to decline due to climate change and other stressors, scientists have proposed adopting genomic tools, such as biomarkers, to aid in conservation and restoration of these threatened ecosystems. Biomarkers are easily measured indicators of higher-order biological processes that can be used to predict or diagnose health, resilience, and other key performance metrics. The goal is to use biomarkers to determine the conservation value and utility of a given coral colony, including the host animal, its algal symbionts, and their microbial partners. However, we remain far from achieving this goal as most efforts have not yet moved beyond the initial discovery phase. Here, we review recent progress in the development of coral molecular biomarkers from a practical standpoint, considering the many challenges that remain as roadblocks to large-scale implementation. We caution practitioners that while biomarkers are a promising technology, they are unlikely to be available for field application in the near future barring a shift in research focus from discovery to the subsequent validation and field trial phases. To facilitate such a change, we propose a stepwise framework to guide additional study in this area, with the aim of accelerating practical molecular biomarker development to enhance coral restoration practice.

Caribbean coral populations are actively being restored via asexual fragmentation of adult populations and the production of sexual offspring. The goal of restoration is to increase population sizes while maximizing adaptive potential of restored populations. Because the total number of remaining wild coral genotypes far exceeds the capacity of nurseries to propagate them all, we provide guidelines for selecting species and genotypes for restoration projects. For each species selected, we suggest that collecting 3-4 genotypes per reef is sufficient to capture much of the allelic diversity. Because environmental conditions are rapidly changing, a mixed provenance strategy is preferred where genotypes are sourced both locally as well as from more distant sites within the management area, allowing for the inclusion of potentially adaptive genetic variants under a wider range of environmental gradients. We further recommend that nurseries concentrate on propagating genotypes with records of high relative growth, outplant survival, bleaching and infectious disease tolerance or resistance, and successful sexual propagation with other genotypes (“winners”). At the same time, some low-level propagation effort for genotypes not performing well in nurseries (“runts”) should be maintained to guard against unintended selection during captivity and to preserve genetic variants that could become adaptive in the future. Given current evidence, we do not think that outbreeding depression is a major problem. Likewise, we do not expect inbreeding depression to be an issue because currently only F1 and F2 larvae are raised. We stress that high rates of sexual reproductive success will be essential for adaptation. Hence, our recommendations outline tools to optimize coral fitness while providing adequate genetic diversity for restored coral populations to rapidly adapt to changing environmental conditions.

Coral reefs worldwide are threatened due to ocean warming and acidification, and their persistence hinges on corals capacity for adaptation. To maximize adaptive potential, coral genotypes with increased phenotypic resilience to climate change conditions should be selected for restoration. Corals from Kāne’ohe Bay (Oahu, HI) would be excellent candidates for this as they currently experience temperatures and pH levels not expected to occur on most Hawaiian reefs for another 30-50 years, and are likely locally adapted to their environment. We hypothesize that Kāne’ohe Bay corals (a) are phenotypically distinct from conspecific populations on other nearby reefs, and (b) possess certain phenotypic traits that facilitate their resilience. To investigate this, a variety of morphotypes (e.g. branching, mounding, encrusting) of eight species (constituting ~97% of the coral cover across the Hawaiian archipelago) were sampled from six sites around Oahu, which during the summer, span a natural range of temperature and pH profiles representative of today, through those predicted by 2050. Biomass, protein, and chlorophyll a concentration were quantified in each species from each site. Preliminary results suggest that phenotypic diversity is greatest among species and morphotypes, and contrary to hypothesis (a), differences due to environment are less pronounced. This suggests that morphotype variation may be more important than previously thought for yielding greater adaptive potential when selecting corals for restoration. Furthermore, no evidence was found to support hypothesis (b) as all variables influenced phenotypic variation equally. However, further research (including quantification of Symbiodinium density, carbohydrates, total lipids, lipid class analysis, and heterotrophic capacity) is being conducted to further investigate phenotypic resilience traits. Overall, this survey contributes to our understanding of source coral variability that can inform sampling practices for maximizing adaptive potential.

The contemporary distribution of Acropora cervicornis includes dispersed, isolated colonies and very dense interlocking assemblages called thickets that may cover hectares of the bottom. The density of thickets and sessile nature of corals creates the opportunity for ongoing interactions between genets which occur across a range of potential relatedness values. This type of interaction influences resistance, resilience and associated community function in other ecosystems. Using next generation sequencing data and field observations we document a positive relationship between genetic diversity and coral cover. This pattern does not appear to relate to growth, but may be due to changes in fragmentation mortality or disturbance response. In the Florida Keys, one thicket with observations during the 2015 bleaching event fared better than outplanted corals on the same reef and discrete colonies monitored as part of a region-wide survey (FRRP). Thickets (n=4) observed in Florida and The Dominican Republic contained between 13 and 30 genotypes, with clones distributed from 0-12m across the substrate, however some observed areas were nearly monoclonal. These data highlight the natural patterns of thickets which may be replicated during restoration in an attempt to gain added biomass or stress resistance from emergent properties of high-density assemblages.

Once largely abundant throughout the Florida Keys and Caribbean, Acropora cervicornis and A. palmata populations have drastically declined (>98% at some locations) due to multiple, compounding natural and anthropogenic stressors. As these threats continue, there is a clear need for innovative methods to reinforce remaining coral populations. Incorporating conservation genetics for the recovery of a species is not a novel concept, and its implications for the continued persistence of the species is quintessential, especially in the era of accelerating climate change. Guided by NOAA’s Acropora Recovery Plan, Coral Restoration Foundation (CRF) has developed a large-scale restoration program that encourages coral diversity for two reasons: 1) to promote resiliency at restoration sites in the context of a changing world, and 2) to better understand the influence of genetics on success at restoration sites. In 2016, CRF launched a restoration plan that emphasizes genetic diversity through outplanting nearly 50 genotypes of both A. cervicornis and A. palmata onto eight reef sites along the Florida Reef Tract. Genotypes of each species were sequenced and selected to ensure the largest range of genetic diversity possible. Here, we present preliminary findings from initial surveys of the outplanted Acroporids from all eight restoration sites. This information can help provide insight not only into survivorship of different genotypes, but also the role that genetic makeup plays in restoration strategies. Variable responses to the environment have been recorded at restoration sites and in nurseries, yet the role of genetics is still unclear in its contribution to the long-term success of local and regionally restored Acropora populations, warranting further investigation into the role of genetics and recovery of the species. This restoration strategy, coupled with subsequent tracking of coral health post-outplanting, can provide insights as to what factors promote survivorship and resilience of restored coral populations in the face of a changing ocean environment.

In the Caribbean, corals are commonly cultured in ocean-based nurseries and outplanted back to reefs for population enhancement. Intraspecific diversity in host and symbiont is an important consideration for nursery and resource managers. We built upon a previous study that quantified Acropora cervicornis growth phenotypes in a nursery by outplanting the same genets across two reef sites and tracking their performance for 1 yr. Further, we identified the Symbiodinium ‘fitti’ strains present in each of the A. cervicornis genets during the restoration process from the initial wild collection as early as 2008 to 24 months post-outplant in 2017. Survival to 1 yr post-outplant was consistent with regional averages and did not differ significantly among A. cervicornis genets or between outplant sites. Outplant site and host genet had significant effects on coral growth. However, genet growth response did not depend on outplant site, providing no evidence for site-genet matching. Conversely, growth rates measured for each genet in the nursery were not predictive of performance following outplanting. Instead, A. cervicornis genets appear to exhibit differences in relative growth through the restoration process. Despite this variability, relative differences in growth among genets were consistent within a given timeframe, even across varying environments. Most colonies sampled were infected by one of five unique strains of S. ‘fitti’. Host-symbiont specificity varied among coral genets, but four out of five genets exhibited spatial and/or temporal differences in symbiont strain composition throughout the restoration process. The ability for A. cervicornis to associate with more than one S. ‘fitti’ strain and the lack of correlation between nursery and outplant growth performance contribute to a growing understanding of the A. cervicornis population enhancement process.

Acropora cervicornis is a key Caribbean species, both in structural and functional terms. It has suffered an important population loss since the 1980s and exhibited no signs of recovery in the following three generations. Hence, it is classified as a Critically Endangered Species. Its fast growth rate compared to other species makes it a perfect candidate for use in active coral restoration programs. In 2011 Fundación Dominicana de Estudios Marinos (Dominican Marine Studies Foundation, FUNDEMAR) started the A. cervicornis restoration program at Bayahibe in the southeastern part of the island. In this study we present the methodology and results of the program's assessment since its beginning until year 2017, as well as a preliminary analysis after the strong cyclonic seasons in 2016 and 2017 in the greater Caribbean, and the genetic characterization of the "mother nursery". Mean survival of the fragments for 12 months was 87.45 ± 4.85% and mean productivity value was 4.01 ± 1.88 for the eight nurseries. Mean survival of transplanted colonies during 12 months for six outplanting sites was 71.55 ± 10.4% and mean productivity value was 3.03 ± 1.30. The most common cause of mortality during the first 12 months, both from the nurseries and the outplanting sites, was predation by Hermodice carunculata fireworm. We identified 111 multilocus genes from the 145 analyzed individuals, 54 clonal individuals distributed in 20 genets, which indicates there is high genotype richness in the germplasm bank. Finally, only three nurseries and two outplanting sites were considerably damaged after the cyclonic seasons of 2016 and 2017. The results and techniques described here will help to continue developing current and future restoration programs in nurseries and outplanting sites.

The staghorn coral, Acropora cervicornis, was previously a major reef-building scleractinian coral throughout Florida and the Caribbean, but since in the 1980s the species has experienced unprecedented population declines primarily due to disease and bleaching. As a result, the species was listed as “Threatened” under the US Endangered Species Act in 2006. To help restore population numbers, Acropora coral nurseries grow large numbers of colonies to outplant to depauperate reefs. Nurseries allow corals to grow in a more protected environment, but managers still face the challenges of disease and other stressors. Previous research in Panama documented three disease-resistant A. cervicornis genotypes, but it was unknown if disease-resistant genotypes exist in the Florida Keys. This study conducted pathogen transmission assays to investigate disease resistance among 39 A. cervicornis genotypes from a Florida Keys nursery. Corals were exposed in situ to rapid tissue loss (RTL) through direct contact assays. Tissue degradation was documented visually based on presence or absence of RTL, and confirmed using histological analysis. In a pathogen transmission pilot study, 7 out of 39 genotypes developed signs of RTL. Of the 32 resistant genotypes, 12 genotypes were selected for a replicated (n=5 fragments per colony) transmission study. All genotypes developed signs of RTL and no statistical difference (p>0.05) in pathogen transmission was found among genotypes. However, susceptibility was variable among fragments from a single colony, ranging from 40–100% transmission. This study provides evidence that disease resistance is present within colonies of Florida A. cervicornis. The variability of disease resistance found here suggests that genotype is not the only factor influencing pathogen transmission. Caribbean Acropora restoration managers could potentially improve restoration success by propagating and outplanting larger quantities of colonies with disease resistant characteristics, while continuing to maintain a genetically diverse population. These results also provide insights into the persistence of wild A. cervicornis populations in Florida and elsewhere.

Signatures of disease resistance for the threatened Caribbean branching coral, Acropora palmata. Ben Young1*, Xaymara Serrano2, Margaret Miller3, Stephanie Rosales4,5, and Nikki Traylor-Knowles1 1 Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, USA 2 Environmental Branch, Planning and Policy Division, USACE, Jacksonville, USA 3 SECORE International, Miami, USA 4 Atlantic Oceanographic and Meteorological Laboratory, Miami, USA 5 Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, USA Coral reefs are important ocean ecosystems that provide biodiversity and economic stability. Despite this value, they are under threat from anthropogenic stressors that have caused drastic decreases in global coral cover. In the Caribbean, White Band Disease has caused tremendous declines in the critical ecosystem building coral, Acropora palmata. With disease incidence and virulence rising, an in-depth knowledge of disease resistance dynamics is needed by restoration institutions for all coral species. To maintain the critical ecosystem functions Acropora palmata provides, disease resistance dynamics for the already decimated wild populations are invaluable in ensuring its survival. Previous observational work with Acropora palmata genotypes has shown large differences in disease tolerance, with percent disease transmission ranging from 0% to 100%. In this study RNA-seq was used to look at the differential gene expression of 12 Acropora palmata genotypes, with different disease tolerances, in 2016 and 2017. Fragments were sampled before disease exposure, and after a 7-day disease exposure. We hypothesise that differential gene expression will elucidate the expression of important immune genes and identify signatures of disease resistance. Preliminary results indicate significant gene expression differences among genotypes of varied disease susceptibility within each year. Large differences between genotype gene expression in year is also apparent, indicating that virulence of disease or environmental conditions are strong drivers of disease resistance. This work will contribute to scientifically driven restoration work by informing out-planting efforts of disease resistant individuals, while also providing the benchmark for a field monitoring experiment of Acropora palmata on the Florida Reef Tract.

Rapid developments in coral restoration represent a glimmer of hope for globally declining reefs. Despite these advancements, the world's oceans are becoming increasingly hostile to reef building corals. Considering only climate change amongst numerous stressors, a complete collapse of coral reefs may occur within a human lifetime- even in the absence of further CO2 emissions. Clearly, lasting restoration will depend not only on production and outplanting effort, but also alteration of coral physiological limits.
Numerous approaches have been proposed to facilitate physiological "enhancement" of restoration corals including Symbiodiniaceae community change, thermal priming, and selective breeding. The utility, feasibility, and sustainability of these approaches have been debated, but rarely measured. In order to compare the relative potential for each of these approaches to increase disease and bleaching resistance, we assessed the relative efficacy of host genetic identity, Symbiodiniaceae community, and bleaching experience of Acropora cervicornis during consecutive mass bleaching years. Resistance conveyed by host genetic identity strongly explained both disease and bleaching resistance through the consecutive thermal stress events, suggesting that approaches leveraging host genetic identity are the most promising avenues for propagating resistant phenotypes.
Despite the symbiont specialist nature of Caribbean Acropora, we justify our expectation that coral host genetics will be the most tractable tool for restoration across numerous coral taxa and ecological scenarios with exceptions. Finally, we suggest avenues of synergy with approaches focuses on other mechanisms to increase holobiont resistance.

The decline of living coral throughout much of the Florida Reef Tract, with no sign of community recovery over the last several decades, has resulted in a substantial need for active coral restoration. However, much of the threats associated with coral mortality, such as high water temperatures and disease outbreaks, continue to occur unabated. Therefore, the preference to select and outplant corals resilient to these threats is a primary goal among many restoration practitioners. Our objective was to screen genotypes of Acropora cervicornis used for restoration for heat tolerance, disease resistance, and resilience to ocean acidification, and determine whether there were tradeoffs among these resilient traits. We conducted a series of wetlab experiments exposing five replicates of 12 - 20 different genotypes of A. cervicornis to high water temperature, ocean acidification conditions, and white band disease. We measured the physiological responses of the corals under these different environmental scenarios including their photosynthetic efficiency using Imaging Pulse-Amplitude-Modulation Fluorometry, buoyant weight, net photosynthesis and respiration using oxygen evolution measurements, and calcification using alkalinity anomaly techniques. Additionally, we quantified the microbiome of the corals to determine whether the Symbiodinium strain or the bacterial community influenced resilience to these threats. Our results indicate that the resilient traits tested were independent of each other and few genotypes may exist that are resilient to all three threats. Disease resistant genotypes had a significantly different bacterial community compared with disease susceptible genotypes, indicating that the microbiome plays a key role in host immunity. However, the Symbiodinium strain did not appear to influence either heat tolerance or resilience to ocean acidification. These results suggest that maintaining a high genetic diversity, while also thoughtfully incorporating genotypes that are heat tolerant, resistant to disease, and/or resilient to ocean acidification, should be a primary practice incorporated into coral restoration initiatives.

Over the last four decades the biota of the Florida Reef Tract has suffered from a number of disturbances and stresses, including disease outbreaks, warm-water bleaching events, storms and hurricanes, outbreaks of coral predators, winter cold spells, and a host of direct and indirect anthropogenic impacts. Of these perturbations, disease outbreaks have had the greatest impact in reducing coral cover. Disease outbreaks continue to present a significant threat to coral populations in the western Atlantic region. Recent studies have forged a clear link between rising ocean temperatures and the increased incidence and virulence of these diseases, suggesting that the impact of coral diseases will increase with continued global warming. Controlling disease outbreaks will, therefore, be critical to conserving coral reefs. Under scenarios of increasing frequency and duration of coral-disease outbreaks, coral genotypes with high disease resistance and resilience should have an ecological and evolutionary advantage over low-resistance genotypes, provided their ability to cope with disease does not incur unworkable tradeoffs in fitness. Understanding the coral immune system, and in particular its heritable components, as well as the links between host genetics and beneficial microbes, will be crucial to the search for the host and symbiont genotypes best suited to large-scale restoration efforts. Thus, the increasing prevalence and incidence of marine diseases and their link to climate change, make genetically-based applied research imperative to fostering the recovery of reef ecosystems.

The coral reefs of Florida and the Caribbean have seen upwards of 95% decline in hard coral cover over the last several decades. This decline has been attributed to multiple, compounding, anthropogenic factors including but not limited to climate change, water pollution, and overfishing. This unprecedented decline has created a need for active intervention. The Coral Restoration Foundation has been working to develop and implement best practices for coral restoration efforts. Within the greater Caribbean and Florida, restoration organizations have focused on restoring the two dominant reef-building species: Acropora cervicornis and A. palmata. As such, the asexual fragmentation and nursery propagation of both species, for subsequent restoration outplanting, has been well examined. This cannot be said for other Caribbean coral species, especially regarding slower growing massive boulder corals. As stressors continue to impact coral reefs, boulder coral species are becoming even more at risk, and will require similar efforts to protect and restore. In 2014 the three Caribbean Orbicella sp. (annularis, faveolata, and franksi) have been classified as threatened on the ESA and on the IUCN redlist, highlighting the need for conservation actions. In an effort to broaden and expand its ecological impact and species diversity, CRF has begun to develop in-situ fragmentation and growth techniques for O. annularis and O. faveolata. Utilizing existing nursery infrastructure and available restoration materials we have developed an effective and low-cost methodology for the asexually propagation of these two species in the field; that can be extrapolated to any nursery setting or any boulder coral species. Following initial collection and fragmentation of wild genotypes, all work is done on site in the nursery, thus eliminating the possibility of transport stress/shock and allowing for efficient use of time and resources. CRF plans to incorporate these nursery-grown corals into future outplanting efforts.