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Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m(2)). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated.

Community structure and assembly are determined in part by environmental heterogeneity. While reef-building corals respond negatively to warming (i.e. bleaching events) and ocean acidification (OA), the extent of present-day natural variability in pH on shallow reefs and ecological consequences for benthic assemblages is unknown. We documented high resolution temporal patterns in temperature and pH from three reefs in the central Pacific and examined how these data relate to community development and net accretion rates of early successional benthic organisms. These reefs experienced substantial diel fluctuations in temperature (0.78°C) and pH (>0.2) similar to the magnitude of 'warming' and 'acidification' expected over the next century. Where daily pH within the benthic boundary layer failed to exceed pelagic climatological seasonal lows, net accretion was slower and fleshy, non-calcifying benthic organisms dominated space. Thus, key aspects of coral reef ecosystem structure and function are presently related to natural diurnal variability in pH.

Coral reefs around US- and US-affiliated Pacific islands and atolls span wide oceanographic gradients and levels of human impact. Here we examine the relative influence of these factors on coral reef fish biomass, using data from a consistent large-scale ecosystem monitoring program conducted by scientific divers over the course of >2,000 hours of underwater observation at 1,934 sites, across ~40 islands and atolls. Consistent with previous smaller-scale studies, our results show sharp declines in reef fish biomass at relatively low human population density, followed by more gradual declines as human population density increased further. Adjusting for other factors, the highest levels of oceanic productivity among our study locations were associated with more than double the biomass of reef fishes (including ~4 times the biomass of planktivores and piscivores) compared to islands with lowest oceanic productivity. Our results emphasize that coral reef areas do not all have equal ability to sustain large reef fish stocks, and that what is natural varies significantly amongst locations. Comparisons of biomass estimates derived from visual surveys with predicted biomass in the absence of humans indicated that total reef fish biomass was depleted by 61% to 69% at populated islands in the Mariana Archipelago; by 20% to 78% in the Main Hawaiian islands; and by 21% to 56% in American Samoa.

The 2014–2017 Global Coral Bleaching Event is the longest, most widespread, and impactful on record. Rapid ecological assessment surveys by NOAA’s Pacific Reef Assessment and Monitoring Program reported widespread coral mortality at Jarvis Island in the aftermath of the 2015–2016 super-El Niño warming event; hard coral cover declined from 18.7% in April 2015 (pre-bleaching) to 0.4% in May 2016 (post-bleaching), representing a catastrophic > 98% decline. Between 2015 and 2016, corals at Jarvis experienced maximum heat stress of 22.25 °C-weeks exceeding the bleaching threshold (28.72 °C) for 66 consecutive weeks. Mass coral bleaching was observed in November 2015, which resulted in mass mortality across all coral taxa, depths, and island sectors. The bleaching event altered the benthic community composition including the coral assemblage. In the 2 yrs post-bleaching, the benthic community has transitioned from a short-lived increase of encrusting macroalgae to a more recent near-recovery of crustose coralline algae. Coral cover had not recovered by 2017 and could be potentially delayed by fast-growing turf algae. Within the coral community, the pre-bleaching dominant genus Montipora exhibited extreme mortality and only a handful of colonies of this taxon were enumerated in the 2016 surveys and none in 2017. Some coral taxa have persisted in low densities, including the ESA-threatened Acropora retusa and colonies of encrusting Pavona, Psammocora, and the free living Fungia. As the frequency and intensity of these high-temperature events is projected to increase in coming years, it is essential to track how remote ecosystems normally undisturbed by human influence, such as Jarvis, respond to a climate change.

Digital photography is widely used by coral reef monitoring programs to assess benthic status and trends. In addition to creating a permanent archive, photographic surveys can be rapidly conducted, which is important in environments where bottom-time is frequently limiting. However, substantial effort is required to manually analyze benthic images; which is expensive and leads to lags before data are available. Using previously analyzed imagery from NOAA’s Pacific Reef Assessment and Monitoring Program, we assessed the capacity of a trained and widely used machine-learning image analysis tool – CoralNet (coralnet.ucsd.edu) - to generate fully-automated benthic cover estimates for the main Hawaiian Islands (MHI) and American Samoa. CoralNet was able to generate estimates of site-level coral cover for both regions that were highly comparable to those generated by human analysts (Pearson’s r > 0.97, and with bias of 1% or less). CoralNet was generally effective at estimating cover of common coral genera (Pearson’s r > 0.92 and with bias of 2% or less in 6 of 7 cases), but performance was mixed for other groups including algal categories, although generally better for American Samoa than MHI. CoralNet performance was improved by simplifying the classification scheme from genus to functional group and by training within habitat types, i.e., separately for coral-rich, pavement, boulder, or ‘other’ habitats. The close match between human-generated and CoralNet-generated estimates of coral cover pooled to the scale of island and year demonstrates that CoralNet is capable of generating data suitable for assessing spatial and temporal patterns. The imagery we used was gathered from sites randomly located in <30 m hard-bottom at multiple islands and habitat-types per region, suggesting our results are likely to be widely applicable. As image acquisition is relatively straightforward, the capacity of fully-automated image analysis tools to minimize the need for resource intensive human analysts opens possibilities for enormous increases in the quantity and consistency of coral reef benthic data that could become available to researchers and managers.

Ecosystem modelling is increasingly used to explore ecosystem-level effects of changing environmental conditions and management actions. For coral reefs there has been increasing interest in recent decades in the use of ecosystem models for evaluating the effects of fishing and the efficacy of marine protected areas. However, ecosystem models that integrate physical forcings, biogeochemical and ecological dynamics, and human induced perturbations are still underdeveloped. We applied an ecosystem model (Atlantis) to the coral reef ecosystem of Guam using a suite of management scenarios prioritized in consultation with local resource managers to review the effects of each scenario on performance measures related to the ecosystem, the reef-fish fishery (e.g., fish landings) and coral habitat. Comparing tradeoffs across the selected scenarios showed that each scenario performed best for at least one of the selected performance indicators. The integrated 'full regulation' scenario outperformed other scenarios with four out of the six performance metrics at the cost of reef-fish landings. This model application quantifies the socio-ecological costs and benefits of alternative management scenarios. When the effects of climate change were taken into account, several scenarios performed equally well, but none prevented a collapse in coral biomass over the next few decades assuming a business-as-usual greenhouse gas emissions scenario.

Coral reefs are exceptionally biodiverse, and human dependence on their ecosystem services is high. Reefs experience significant direct and indirect anthropogenic pressures, and provide a sensitive indicator of coastal ocean health, climate change and ocean acidification, with associated implications for society. Monitoring coral reef status and trends is essential to better inform science, management and policy, but the projected collapse of reef systems within a few decades makes the provision of accurate and actionable monitoring data urgent. The Global Coral Reef Monitoring Network has been the foundation for global reporting on coral reefs for two decades, and is entering into a new phase with improved operational and data standards incorporating the Essential Ocean Variables (EOVs) (www.goosocean.org/eov) and Framework for Ocean Observing developed by the Global Ocean Observing System. Three EOVs provide a robust description of reef health: hard coral cover and composition, macro-algal canopy cover, and fish diversity and abundance. A data quality model based on comprehensive metadata is designed to facilitate maximum global coverage of coral reef data, and tangible steps to track capacity building. Improved monitoring of events such as mass bleaching and disease outbreaks, citizen science and socio-economic monitoring have the potential to greatly improve the relevance of monitoring to managers and stakeholders, and to address the complex and multi- dimensional interactions between reefs and people. XX THERE IS SOMETHING WRONG IN THE ABSTRACT WORD LIMIT, ONE MORE PARAGRAPH WAS INCLUDED IN THE ORIGINAL TEXT!!

The resilience of coral reefs depends on the balance between reef growth and reef breakdown, and their responses to changing environmental conditions. Across the 2500-km Hawaiian Archipelago, we quantified rates of carbonate production, bioerosion, and net accretion at regional, island, site, and within-site spatial scales and tested how these rates respond to environmental conditions across different spatial scales. Overall, there were four major outcomes from this study: (1) bioerosion rates were generally higher in the populated Main Hawaiian Islands (MHI) than the remote, protected Northwestern Hawaiian Islands (NWHI), while carbonate production rates did not vary significantly between the two regions; (2) variability in carbonate production, bioerosion, and net accretion rates was greatest at the smallest within-reef spatial scale; (3) carbonate production and bioerosion rates were associated with distinct sets of environmental parameters; and (4) the strongest correlates of carbonate production, bioerosion, and net accretion rates were different between the MHI region and the NWHI region: in the MHI, the dominant correlates were percent cover of macroalgae and herbivorous fish biomass for carbonate production and bioerosion, respectively, whereas in the NWHI, the top correlates were total alkalinity and benthic cover. This study highlights the need to understand accretion and erosion processes as well as local environmental conditions to predict net coral reef responses to future environmental changes.

Sharks and other large predators are scarce on most coral reefs, but studies of their historical ecology provide qualitative evidence that predators were once numerous in these ecosystems. Quantifying density of sharks in the absence of humans (baseline) is, however, hindered by a paucity of pertinent time-series data. Recently researchers have used underwater visual surveys, primarily of limited spatial extent or nonstandard design, to infer negative associations between reef shark abundance and human populations. We analyzed data from 1607 towed-diver surveys (>1 ha transects surveyed by observers towed behind a boat) conducted at 46 reefs in the central-western Pacific Ocean, reefs that included some of the world's most pristine coral reefs. Estimates of shark density from towed-diver surveys were substantially lower (<10%) than published estimates from surveys along small transects (<0.02 ha), which is not consistent with inverted biomass pyramids (predator biomass greater than prey biomass) reported by other researchers for pristine reefs. We examined the relation between the density of reef sharks observed in towed-diver surveys and human population in models that accounted for the influence of oceanic primary productivity, sea surface temperature, reef area, and reef physical complexity. We used these models to estimate the density of sharks in the absence of humans. Densities of gray reef sharks (Carcharhinus amblyrhynchos), whitetip reef sharks (Triaenodon obesus), and the group \"all reef sharks\" increased substantially as human population decreased and as primary productivity and minimum sea surface temperature (or reef area, which was highly correlated with temperature) increased. Simulated baseline densities of reef sharks under the absence of humans were 1.1-2.4/ha for the main Hawaiian Islands, 1.2-2.4/ha for inhabited islands of American Samoa, and 0.9-2.1/ha for inhabited islands in the Mariana Archipelago, which suggests that density of reef sharks has declined to 3-10% of baseline levels in these areas. Los tiburones y otros depredadores mayores son escasos en la mayoría de los arrecifes de coral, pero estudios de su ecología histórica proporcionan evidencia cualitativa de que los depredadores una vez fueron numerosos en estos ecosistemas. Sin embargo, la cuantificación de la densidad de tiburones en ausencia de humanos (línea de base) es obstaculizada por la falta de datos de series de tiempo pertinentes. Recientemente, los investigadores han utilizado muestreos visuales submarinos, de extensión espacial limitada o de diseño no estándar, para inferir asociaciones negativas entre la abundancia de tiburones de arrecife y las poblaciones humanas. Analizamos datos de 1607 muestreos por remolque de buzos (transectos > muestreados por observadores remolcados por una lancha) realizados en 46 arrecifes en el Océano Pacífico centro-occidental, arrecifes que incluyeron algunos de los más prístinos del mundo. Las estimaciones de densidad de tiburones fue sustancialmente menor (<10%) que estimaciones publicadas a partir de muestreos a lo largo de transectos pequeños (<0.02 ha), lo cual no es consistente con las pirámides de biomasa invertidas (la biomasa de depredadores es mayor que la biomasa de presas) reportadas para arrecifes prístinos por otros autores. Examinamos la relación entre la densidad de tiburones de arrecife observados en los muestreos por remolque de buzos y la población humana en modelos y consideramos la influencia de la productividad oceánica primaria, la temperatura de la superficie del mar, la superficie del arrecife y su complejidad física. Utilizamos estos modelos para estimar la densidad de tiburones en ausencia de humanos. Las densidades de Carcharhinus amblyrhynchos, Triaenodon obesus y el grupo de \"tiburones estrictamente arrecifales\" incrementó sustancialmente a medida que disminuyó la población humana y que incrementó la productividad primaria y la temperatura de la superficie del mar (o superficie del arrecife, que estaba altamente correlacionada con la temperatura. Las densidades basales simuladas de tiburones arrecifales en ausencia de humanos fueron 1.1-2.4/ha para las Islas Hawaianas, 1.2-2.4/ha en islas deshabitadas de Samoa Americana y 0.9-2.1/ha e islas deshabitadas del Archipiélago Mariana, lo que sugiere que la densidad de tiburones arrecifales ha declinado entre 3 -10% en relación con los niveles basales en esas áreas.