Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases.

Emerging diseases can have devastating consequences for wildlife and require a rapid response. A critical first step towards developing appropriate management is identifying the etiology of the disease, which can be difficult to determine, particularly early in emergence. Gathering and synthesizing existing information about potential disease causes, by leveraging expert knowledge or relevant existing studies, provides a principled approach to quickly inform decision-making and management efforts. Additionally, updating the current state of knowledge as more information becomes available over time can reduce scientific uncertainty and lead to substantial improvement in the decision-making process and the application of management actions that incorporate and adapt to newly acquired scientific understanding. Here we present a rapid prototyping method for quantifying belief weights for competing hypotheses about the etiology of disease using a combination of formal expert elicitation and Bayesian hierarchical modeling. We illustrate the application of this approach for investigating the etiology of stony coral tissue loss disease (SCTLD) and discuss the opportunities and challenges of this approach for addressing emergent diseases. Lastly, we detail how our work may apply to other pressing management or conservation problems that require quick responses. We found the rapid prototyping methods to be an efficient and rapid means to narrow down the number of potential hypotheses, synthesize current understanding, and help prioritize future studies and experiments. This approach is rapid by providing a snapshot assessment of the current state of knowledge. It can also be updated periodically (e.g., annually) to assess changes in belief weights over time as scientific understanding increases. Synthesis and applications: The rapid prototyping approaches demonstrated here can be used to combine knowledge from multiple experts and/or studies to help with fast decision-making needed for urgent conservation issues including emerging diseases and other management problems that require rapid responses. These approaches can also be used to adjust belief weights over time as studies and expert knowledge accumulate and can be a helpful tool for adapting management decisions.

Tight coupling between coral reef morphology and mapped resilience in the Red Sea.

Lack of knowledge on the conservation value of different reef types can stymie decision making, and result in less optimal management solutions. Addressing the information gap of coral reef resilience, we produce a map-based Remote Sensed Resilience Index (RSRI) from data describing the spatial distribution of stressors, and properties of reef habitats on the Farasan Banks, Saudi Arabia. We contrast the distribution of this index among fourteen reef types, categorized on a scale of maturity that includes juvenile (poorly aggraded), mature (partially aggraded), and senile (fully aggraded) reefs. Sites with high reef resilience can be found in most detached reef types; however they are most common in mature reefs. We aim to stimulate debate on the coupling that exists between geomorphology and conservation biology, and consider how such information can be used to inform management decisions.

The status of coral reefs and associated fishes and invertebrates of commercial importance in Pedro Bank, Jamaica / Estado de los arrecifes de coral y comunidades de peces e invertebrados con interés comercial asociadas al Banco de Pedro, Jamaica

The coral reefs located off the north coast of the Jamaican mainland are some of the best and most studied reefs in the world. Coral reefs of Pedro Bank, Jamaica were assessed in March, 2012 as part of the KSLOF Global Reef Expedition using a modified Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol. The main objectives were to: 1) characterize the distribution, structure and health of coral reefs; and 2) evaluate the population status of commercially important reef fishes and invertebrates. This work was conducted to assist in characterizing coral reef habitats within and outside a proposed fishery reserve, and identify other possible conservation zones. Within 20 reefs, live coral cover ranged from 4.9% to 19.2%. Coral communities were dominated by small corals (esp. Agaricia, Porites and Siderastrea) although many sites had high abundances of large colonies of Montastraea annularis and M. faveolata, and these were generally in good condition. A single area, within the proposed fishery reserve, had extensive Acropora cervicornis thickets, and several shallow locations had small, but recovering A. palmata stands. Macroalgal cover at all sites was relatively low, with only three sites having greater than 30% cover; crustose coralline algae (CCA) was high, with eight sites exceeding 20% cover. Fish biomass at all sites near the Cays was low, with a dominance of herbivores (parrotfish and surgeonfish) and a near absence of groupers, snappers and other commercially important species. While parrotfish were the most abundant fish, these were all extremely small (mean size= 12cm; <4% over 29cm), and they were dominated by red band parrotfish (Sparisoma aurofrenatum) followed by striped parrotfish (Scarus iseri). While coral communities remain in better condition than most coastal reefs in Jamaica, intense fishing pressure using fish traps (main target species: surgeonfish) and hookah/spear fishing (main target: parrotfish) is of grave concern to the future persistence of these reefs. The proposed fishery reserve encompasses some of the best coral reef habitat near the Cays, but this MPA should be expanded to encompass other habitats and MPAs should be considered for bank reefs at the northwestern end, as well as Banner Reef and Blowers Rock.

Los arrecifes de coral ubicados en la costa norte de Jamaica son los mejores y mas estudiados corales del mundo. Los corales de arrecife del Banco de Pedro, Jamaica, fueron evaluados en marzo 2012 como parte de la expedición global KSLOF utilizando una modificación del protocolo de estimación rápida de arrecifes para el Atlántico y el Caribe (AGRRA). Los objetivos principales fueron: 1) caracterizar la distribución, estructura y salud de los arrecifes de coral; y 2) evaluar la condición de las poblaciones de peces arrecifales e invertebrados de interés comercial. Este trabajo fue realizado con el propósito de colaborar en la caracterización de hábitats arrecifales, tanto dentro como fuera de un área sugerida como reserva marina, e identificar otras áreas de conservación. Para los 20 arrecifes, la cobertura de coral vivo varió entre 4.9% y 19.2%. Las comunidades de corales son dominadas por corales pequeños (Agaricia, Porites y Siderastrea), aunque en varias localidades se presentó una mayor abundancia de colonias grandes de M. annularis y M. faveolata, y estos se encontraban por lo general en buenas condiciones. Dentro de la reserva pesquera propuesta, una sola área presentó fragmentos de A. cervicornis, y varias localidades someras presentaron pequeños fragmentos de A. palmata, pero en proceso de recuperación. La cobertura de macroalgas en todas las áreas fue relativamente baja, solo tres lugares presentaron más de un 30%; la cobertura de algas coralinas calcárea (CCA) fue alta, ocho lugares excedieron el 20%. La biomasa de peces fue baja en todos los sitios cercanos a los cayos, y hubo dominancia de herbívoros (pez loro y cirujanos), y en general ausencia de chernas, pargos y otras especies de peces de interés comercial. Aunque los peces loro fueron los más abundantes, estos presentaron tamaños extremadamente pequeños (tamaño promedio = 12cm; <4% por encima de 29cm), y estuvieron dominados por el pez loro de banda roja (Sparisoma aurofrenatum), y por el pez loro de rayas (Scarus iseri). Mientras que las comunidades de coral permanecen en mejor condición que muchos de los arrecifes costeros de Jamaica, existe una intensa presión pesquera usando trampas de pesca (principal objetivo: cirujanos) y de compresores de aire (hookah)/ pesca con arpón (principal objetivo: pez loro) es preocupante, y compromete la persistencia y el futuro de estos arrecifes. La reserva marina (MPA) que se sugiere incluye algunos de los mejores hábitats de arrecife coralino cerca de los cayos, pero es recomendable que se amplíe para incluir otros hábitats y que se consideren áreas marinas protegidas en los bancos de arrecife del extremo noroeste, así como el arrecife Banner y Blowers Rock.

Coral population trajectories, increased disturbance and management intervention: a sensitivity analysis.

Coral reefs distant from human population were sampled in the Red Sea and one-third showed degradation by predator outbreaks (crown-of-thorns-starfish = COTS observed in all regions in all years) or bleaching (1998, 2010). Models were built to assess future trajectories. They assumed variable coral types (slow/fast growing), disturbance frequencies (5,10,20 years), mortality (equal or not), and connectivity (un/connected to un/disturbed community). Known disturbances were used to parameterize models. Present and future disturbances were estimated from remote-sensing chlorophyll and temperature data. Simulations and sensitivity analysis suggest community resilience at >20-year disturbance frequency, but degradation at higher frequency. Trajectories move from fast-grower to slow-grower dominance at intermediate disturbance frequency, then again to fast-grower dominance. A similar succession was observed in the field: Acropora to Porites to Stylophora/Pocillopora dominance on shallow reefs, and a transition from large poritids to small faviids on deep reefs. Synthesis and application: Even distant reefs are impacted by global changes. COTS impacts and bleaching were key driver of coral degradation, coral population decline could be reduced if these outbreaks and bleaching susceptibility were managed by maintaining water quality and by other interventions. Just leaving reefs alone, seems no longer a satisfactory option.

Red Sea coral reef trajectories over 2 decades suggest increasing community homogenization and decline in coral size.

Three independent line intercept transect surveys on northern Red Sea reef slopes conducted in 1988/9 and 1997/8 in Egypt and from 2006-9 in Saudi Arabia were used to compare community patterns and coral size. Coral communities showed scale-dependent variability, highest at fine spatial and taxonomic scale (species-specific within and among reef patterns). At coarser scale (generic pattern across regions), patterns were more uniform (regionally consistent generic dominance on differently exposed reef slopes and at different depths). Neither fine- nor coarse-scale patterns aligned along the sampled 1700 km latitudinal gradient. Thus, a latitudinal gradient that had been described earlier from comparable datasets, separating the Red Sea into three faunistic zones, was no longer apparent. This may indicate subtle changes in species distributions. Coral size, measured as corrected average intercept of corals in transects, had decreased from 1997 to 2009, after having remained constant from 1988 to 1997. Recruitment had remained stable (∼12 juvenile corals per m(2)). Size distributions had not changed significantly but large corals had declined over 20 years. Thus, data from a wide range of sites taken over two decades support claims by others that climate change is indeed beginning to show clear effects on Red Sea reefs.

Revealing the appetite of the marine aquarium fish trade: the volume and biodiversity of fish imported into the United States.

The aquarium trade and other wildlife consumers are at a crossroads forced by threats from global climate change and other anthropogenic stressors that have weakened coastal ecosystems. While the wildlife trade may put additional stress on coral reefs, it brings income into impoverished parts of the world and may stimulate interest in marine conservation. To better understand the influence of the trade, we must first be able to quantify coral reef fauna moving through it. Herein, we discuss the lack of a data system for monitoring the wildlife aquarium trade and analyze problems that arise when trying to monitor the trade using a system not specifically designed for this purpose. To do this, we examined an entire year of import records of marine tropical fish entering the United States in detail, and discuss the relationship between trade volume, biodiversity and introduction of non-native marine fishes. Our analyses showed that biodiversity levels are higher than previous estimates. Additionally, more than half of government importation forms have numerical or other reporting discrepancies resulting in the overestimation of trade volumes by 27%. While some commonly imported species have been introduced into the coastal waters of the USA (as expected), we also found that some uncommon species in the trade have also been introduced. This is the first study of aquarium trade imports to compare commercial invoices to government forms and provides a means to, routinely and in real time, examine the biodiversity of the trade in coral reef wildlife species.

Satellite imaging coral reef resilience at regional scale. A case-study from Saudi Arabia.

We propose a framework for spatially estimating a proxy for coral reef resilience using remote sensing. Data spanning large areas of coral reef habitat were obtained using the commercial QuickBird satellite, and freely available imagery (NASA, Google Earth). Principles of coral reef ecology, field observation, and remote observations, were combined to devise mapped indices. These capture important and accessible components of coral reef resilience. Indices are divided between factors known to stress corals, and factors incorporating properties of the reef landscape that resist stress or promote coral growth. The first-basis for a remote sensed resilience index (RSRI), an estimate of expected reef resilience, is proposed. Developed for the Red Sea, the framework of our analysis is flexible and with minimal adaptation, could be extended to other reef regions. We aim to stimulate discussion as to use of remote sensing to do more than simply deliver habitat maps of coral reefs.

Static measurements of the resilience of Caribbean coral populations / Mediciones estáticas de la resiliencia de las poblaciones de coral del Caribe

The progressive downward shift in dominance of key reef building corals, coupled with dramatic increases in macroalgae and other nuisance species, fields of unstable coral rubble ,loss of structural relief, and declines of major functional groups of fishes is a common occurrence throughout the Caribbean today. The incorporation of resilience principles into management is a proposed strategy to reverse this trend and ensure proper functioning of coral reefs under predicted scenarios of climate change, yet ecosystem processes and functions that underlie reef resilience are not fully understood. Rapid assessments using the Atlantic and Gulf Rapid Reef Assessment (AGRRA) and the IUCN Resilience Assessment protocol can provide baseline information on reef resilience. A key aspect of these surveys focuses on coral population dynamics, including measures of coral cover, size, partial and whole-colony mortality, condition, and recruitment. One challenge is that these represent static measures involving a single assessment. Without following individual corals over time, it is difficult to determine rates of survival and growth of recruits and adult colonies, and differentiation of juveniles from small remnants of older colonies may not be possible, especially when macroalgal cover is high. To address this limitation, corals assessed in Bonaire in July 2010 were subdivided into two categories: 1) colonies on the reef substrate; and 2) colonies colonizing dead corals and exposed skeletal surfaces of living corals. Coral populations in Bonaire exhibited many features indicative of high resilience, including high coral cover (often 30-50%), high levels of recruitment, and a large number of corals that settled on dead corals and survived to larger size-classes. Overall, the skeletal surfaces of 12 species of corals were colonized by 16 species of corals, with up to 12 settlers on each colony, most (67%) on M. annularis (complex) skeletons. Nevertheless, completely dead M. annularis colonies were common, survivors were frequently reduced in size and subdivided into smaller tissue remnants, and these species exhibited higher amounts of partial mortality than all other species. A notable absence of sexual recruits and juveniles of M. annularis illustrates a progressive shift away from a Montastraea dominated system. This shift, characterized by an increasing dominance of smaller, short-lived species such as Agaricia and Porites and a reduction in size of longer-lived massive corals, is occurring throughout the Caribbean. Monitoring of the survival of recruits is necessary to determine whether Caribbean reefs will retain the same function, structure, identity and feedbacks (key signs of resilience) if the losses of M. annularis (complex) continue at present levels. The rapid assessment protocol utilized here allows characterization of colony size structure, partial mortality, recruitment, and whether small corals represent surviving recruits that increased in size or larger (older) colonies that continue to shrink in size. This approach can help determine the history of a site and its resilience.

En la actualidad se está viendo en el Caribe un cambio en la composición de los corales constructores de arrecifes, aumento en la cobertura de macroalgas y otras especies, un aumento en áreas cubiertas por escombros de corales, y una pérdida de relieve. La incorporación de principios de resiliencia en el manejo es una estrategia propuesta para revertir esta tendencia y asegurar la sobrevivencia y el adecuado funcionamiento de los arrecifes de coral bajo escenarios previstos de cambio climático. Sin embargo, todavía quedan grandes vacíos en la comprensión de los factores que promueven la resiliencia. Evaluaciones rápidas realizadas con la metodología AGRRA (Atlantic and Gulf Rapid Reef Assessment) y con el protocolo de Evaluación de Resiliencia para arrecifes coralinos de la IUCN brindan información de línea base sobre la resiliencia de los arrecifes del Caribe. Un aspecto clave de estos estudios se centra en la dinámica de las poblaciones de los corales, incluyendo medidas de cobertura de coral, estructura de tallas, la extensión de la mortalidad parcial y total de toda la comunidad, condición de los corales y reclutamiento. Un reto es que esto representa una medida estática que involucra una única evaluación. Sin seguir las colonias individuales y el reclutamiento en el tiempo, es difícil determinar las tasas de sobrevivencia y crecimiento de los reclutas, y podría no ser posible la diferenciación de los juveniles de los restos pequeños de colonias más viejas, especialmente cuando la cobertura algal es alta. Para abordar esta limitación, los corales monitoreados en Bonaire en julio del 2010 fueron subdivididos en dos categorías: 1) colonias sobre la estructura arrecifal; y 2) colonias creciendo sobre coral muerto o sobre las superficies expuestas del esqueleto de los corales vivos. Los arrecifes en Bonaire exhiben muchas características indicativas de alta resiliencia, incluyendo una alta cobertura de coral (frecuentemente 30-50%), altos niveles de reclutamiento, y un gran número de corales que se asentaron sobre los corales muertos y crecieron. En general, las superficies del esqueleto de 12 especies de corales fueron colonizadas por 16 especies de corales, con un máximo de 12 colonizadores en cada colonia, la mayoría (67%) sobre esqueletos de Montastraea annularis (complejo). Colonias completamente muertas de M. annularis fueron comunes y los sobrevivientes con frecuencia son más pequeños o subdivididos en pequeños restos de tejido. Montastraea annularis es la especie que exhibe una mayor mortalidad parcial en relación con los demás corales. Una notable ausencia de reclutamiento sexual y juveniles de M. annularis ilustra el cambio progresivo de cambio de un sistema dominado por Montastraea. Este cambio, que se está produciendo en todo el Caribe, se caracteriza por un dominio cada vez mayor de especies más pequeñas y de vida corta como Agaricia y Porites, y una reducción en el tamaño de los corales masivos longevos. El seguimiento de la sobrevivencia de los reclutas es necesario para determinar si los arrecifes del Caribe mantendrán la misma función, estructura, identidad y retroalimentación (signos clave de la resiliencia), y si las pérdidas de M. annularis (complejo) continuarán a los niveles actuales. La evaluación rápida presentada aquí posibilita caracterizar la estructura de tamaño de las colonias, los niveles de reclutamiento y determinar si los corales pequeños representan sobrevivientes de colonias que incrementan su tamaño o colonias grandes (más viejas) que siguen disminuyendo de tamaño. Este enfoque puede ayudar a determinar la historia de un sitio y su capacidad de recuperación.

Caribbean corals in crisis: record thermal stress, bleaching, and mortality in 2005.

BACKGROUND: The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS: Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE: Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.

Implications of coral harvest and transplantation on reefs in northwestern Dominica

In June, 2002, the government of Dominica requested assistance in evaluating the coral culture and transplantation activities being undertaken by Oceanographic Institute of Dominica (OID), a coral farm culturing both western Atlantic and Indo-Pacific corals for restoration and commercial sales. We assessed the culture facilities of OID, the condition of reefs, potential impacts of coral collection and benefits of coral transplantation. Coral reefs (9 reefs, 3-20m depth) were characterized by 35 species of scleractinian corals and a live coral cover of 8-35%. Early colonizing, brooders such as Porites astreoides (14.8% of all corals), P. porites (14.8%), Meandrina meandrites (14.7%) and Agaricia agaricites (9.1%) were the most abundant corals, but colonies were mostly small (mean=25cm diameter). Montastraea annularis (complex) was the other dominant taxa (20.8% of all corals) and colonies were larger (mean=70cm). Corals (pooled species) were missing an average of 20% of their tissue, with a mean of 1.4% recent mortality. Coral diseases affected 6.4% of all colonies, with the highest prevalence at Cabrits West (11.0%), Douglas Bay (12.2%) and Coconut Outer reef (20.7%). White plague and yellow band disease were causing the greatest loss of tissue, especially among M. annularis (complex), with localized impacts from corallivores, overgrowth by macroalgae, storm damage and sedimentation. While the reefs appeared to be undergoing substantial decline, restoration efforts by OID were unlikely to promote recovery. No Pacific species were identified at OID restoration sites, yet species chosen for transplantation with highest survival included short-lived brooders (Agaricia and Porites) that were abundant in restoration sites, as well as non-reef builders (Palythoa and Erythropodium) that monopolize substrates and overgrow corals. The species of highest value for restoration (massive broadcast spawners) showed low survivorship and unrestored populations of these species were most affected by biotic stressors and human impacts, all of which need to be addressed to enhance survival of outplants. Problems with culture practices at OID, such as high water temperature, adequate light levels and persistent overgrowth by macroalgae could be addressed through simple modifications. Nevertheless, coral disease and other stressors are of major concern to the most important reef builders, as these species are less amenable to restoration, collection could threaten their survival and losses require decades to centuries to replace. Rev. Biol. Trop. 58 (Suppl. 3): 111-127. Epub 2010 October 01.

En junio del año 2002 el gobierno de Dominica solicitó asistencia para evaluar el Instituto Oceanográfico de Dominica (OID), una operación de cultivo de corales del océano Atlántico y del Indo Pacifico para propósitos de restauración y comercio. Evaluamos las facilidades de cultivo del OID, la condición de los arrecifes y el impacto potencial de la recolección de corales y los posibles beneficios del transplante de colonias. Los arrecifes de coral (9 arrecifes de profundidades entre 3 y 20m se caracterizaban por 35 especies escleractíneos y una cobertura viva de coral entre 8 y 35%. Las especies que liberan larvas tales como Porites astreoides (14.8 % de todos los corales), P. porites (14.8%), Meandrina meandrites (14.7%) y Agaricia agaricites (9.1%) fueron los más abundantes, pero sus colonias eran pequeñas (promedio de 25cm de diámetro). El complejo de Montastraea annularis fue otro grupo dominante (20.8% de todos los corales) y sus colonias eran mayores (promedio de 70cm de diámetro). Entre todas las especies los corales habían perdido el 20% de sus tejidos, con un promedio de 1.4% por mortandad reciente. Las enfermedades de coral afectaron 6.4% de todas las colonias, con la incidencia mayor en Cabrits Oeste (11%), Bahía Douglas (12.2%) y el arrecife de Coconut Afuera (20.7%). Plaga blanca y la enfermedad de la banda amarilla causaron la mayoría de la pérdida de tejido vivo, especialmente en el complejo de M. annularis, con impactos localizados por caracoles coralívoros, sobre crecimiento por macroalgas, impactos de tormentas y sedimentación. Mientras los arrecifes parecen estar declinando substancialmente, los esfuerzos de restauración de OID no parecen entablar su recuperación debido a que las especies escogidas para transplantar con las mayores tasas de sobrevivencia incluyen especies que liberan larvas (Agaricia y Porites) que fueron abundantes en las restauraciones, al igual que los organismos potencialmente parasíticos (Palythoa ...