Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from 9 species were marked and sampled in 2017, and following hurricanes in September 2017, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes and the onset of stony coral tissue loss disease. While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.

The rapid loss of reef-building corals owing to ocean warming is driving the development of interventions such as coral propagation and restoration, selective breeding and assisted gene flow. Many of these interventions target naturally heat-tolerant individuals to boost climate resilience, but the challenges of quickly and reliably quantifying heat tolerance and identifying thermotolerant individuals have hampered implementation. Here, we used coral bleaching automated stress systems to perform rapid, standardized heat tolerance assays on 229 colonies of Acropora cervicornis across six coral nurseries spanning Florida's Coral Reef, USA. Analysis of heat stress dose–response curves for each colony revealed a broad range in thermal tolerance among individuals (approx. 2.5°C range in Fv/Fm ED50), with highly reproducible rankings across independent tests (r = 0.76). Most phenotypic variation occurred within nurseries rather than between them, pointing to a potentially dominant role of fixed genetic effects in setting thermal tolerance and widespread distribution of tolerant individuals throughout the population. The identification of tolerant individuals provides immediately actionable information to optimize nursery and restoration programs for Florida's threatened staghorn corals. This work further provides a blueprint for future efforts to identify and source thermally tolerant corals for conservation interventions worldwide.

This dataset contains in situ temperature data from August 2019 to May 2020 from one HOBO temperature logger deployed at Emerald Reef at 7.8 meters depth in southeast Florida. Coral cores were collected from this reef and underwent experimental heat stress. In situ temperature data were used to inform seasonal temperature variation on this reef. The publication based on these data is Buzzoni, et al. (2023) (DOI: 10.1007/s00338-023-02428-x).

This dataset contains results from assays to quantify the abundance and photochemical performance of Breviolum, Cladocopium, and Durusdinium symbionts relative to coral cells in Montastraea cavernosa, Orbicella faveolata, and Siderastrea siderea corals collected from colonies in southeast Florida in April 2019 and in October 2019, before, during and after aquarium-based experimental heat stress tests. Bulk genomic DNA was extracted from tissue scrapings taken from 2.5cm diameter cores of corals and was used as a template for symbiont genus-specific qPCR assays. The resulting CT values were used to calculate the relative abundance of each symbiont genus within each coral core over the course of the heat stress. The photochemical efficiency of each coral core was also measured periodically throughout heat stress tests using an imaging pulse amplitude modulated (I-PAM) fluorometer. The publication based on these data is Buzzoni, et al. (2023) (DOI: 10.1007/s00338-023-02428-x).

A global survey of coral reefs reveals that overfishing is driving resident shark species toward extinction, causing diversity deficits in reef elasmobranch (shark and ray) assemblages. Our species-level analysis revealed global declines of 60 to 73% for five common resident reef shark species and that individual shark species were not detected at 34 to 47% of surveyed reefs. As reefs become more shark-depleted, rays begin to dominate assemblages. Shark-dominated assemblages persist in wealthy nations with strong governance and in highly protected areas, whereas poverty, weak governance, and a lack of shark management are associated with depauperate assemblages mainly composed of rays. Without action to address these diversity deficits, loss of ecological function and ecosystem services will increasingly affect human communities.

This dataset contains results from genus-specific qPCR assays to quantify the abundance of Symbiodinium, Breviolum, Cladocopium, and Durusdinium symbionts relative to coral cells in Orbicella faveolata from Abaco, The Bahamas in January 2019. Bulk genomic DNA was extracted from tissue scrapings collected by SCUBA divers, and used as a template for qPCR assays. Resulting CT values were used to calculate symbiont to host cell ratios for each symbiont genus within each coral. The publication based on these data can be found here: http://dx.doi.org/10.1007/s00338-020-01948-0.

Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms (SNPs). We performed multiple matrix regression with randomization (MMRR) analyses on genetic distances for all species, as well as reconstructed scenarios for population sub-division in the species with signatures of isolation. We found that 1) widespread species displayed more genetic sub-division than regional endemics and 2) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.

This work describes impacts to coral reefs surrounding the 2013-2015 dredging of the Port of Miami based on data collected before, during, and after dredging by Dial Cordy and Associates (DCA) on behalf of Great Lakes Dredge and Dock Company, the dredging contractors for the U.S. Army Corps of Engineers (USACE) and for the Port of Miami (Miami-Dade County). A front page for this repository can be accessed at jrcunning.github.io/pom-dredge containing rendered R Markdown detailing all analyses conducted as part of this work.

This work describes impacts to coral reefs surrounding the 2013-2015 dredging of the Port of Miami based on data collected before, during, and after dredging by Dial Cordy and Associates (DCA) on behalf of Great Lakes Dredge and Dock Company, the dredging contractors for the U.S. Army Corps of Engineers (USACE) and for the Port of Miami (Miami-Dade County). A front page for this repository can be accessed at jrcunning.github.io/pom-dredge containing rendered R Markdown detailing all analyses conducted as part of this work.

Nutrients were analyzed from surface waters at 4 sites in Kanoehe Bay at time points from 2014-2016. Quantification of phosphate, silicate, nitrate and nitrite, ammonia and total nitrogen (all are in umol/L) were conducted by the SOEST Laboratory for Analytical Biochemistry.