Relationships Between Reef Fish Communities and Remotely Sensed Rugosity Measurements in Biscayne National Park,Florida, USA

The realization that coral reef ecosystem management must occur across multiple spatial scales and habitat types has led scientists and resource managers to seek variables that are easily measured over large areas and correlate well with reef resources. Here we investigate the utility of new technology in airborne laser surveying (NASA Experimental Advanced Airborne Research Lidar (EAARL)) in assessing topographical complexity (rugosity) to predict reef fish community structure on shallow (<10 m deep) patch reefs. Marine portions of Biscayne National Park, Florida, USA, were surveyed remotely using the EAARL, and reef fish populations were visually surveyed on 10 patch reefs at independent, randomly selected stations (n = 10–13 per reef). Rugosity at each station was assessed in situ by divers using the traditional chain-transect method (10-m scale), and remotely using the EAARL submarine topography data at multiple spatial scales (2, 5, and 10 m). The rugosity and biological datasets were analyzed together to elucidate the predictive power of EAARL rugosity in describing the variance in reef fish community variables and to assess the correlation between chain-transect and EAARL rugosity. EAARL rugosity was not well correlated with chain-transect rugosity, or with species richness of fishes (although statistically significant, the amount of variance explained by the model was very low). Variance in reef fish community attributes was better explained in reef-by-reef variability than by physical variables. However, once the reef-by-reef variability was taken into account in a two-way analysis of variance, the importance of rugosity could be seen on individual reefs. Fish species richness and abundance were statistically higher at high rugosity stations compared to medium and low rugosity stations, as predicted by prior ecological research. The EAARL shows promise as an important mapping tool for reef resource managers as they strive to inventory and protect coral reef resources.     

Patch-reef morphology as a proxy for Holocene sea-level variability,Northern Florida Keys,USA

A portion of the northern Florida Keys reef tract was mapped with the NASA Experimental Advanced Airborne Research Lidar (EAARL) and the morphology of patch reefs was related to variations in Holocene sea level. Following creation of a lidar digital elevation model (DEM), geospatial analyses delineated morphologic attributes of 1,034 patch reefs (reef depth, basal area, height, volume, and topographic complexity). Morphometric analysis revealed two morphologically different populations of patch reefs associated with two distinct depth intervals above and below a water depth of 7.7 m. Compared to shallow reefs, the deep reefs were smaller in area and volume and showed no trend in topographic complexity relative to water depth. Shallow reefs were more variable in area and volume and became flatter and less topographically complex with decreasing water depth. The knoll-like morphology of deep reefs was interpreted as consistent with steady and relatively rapidly rising early Holocene sea level that restricted the lateral growth of reefs. The morphology of shallow “pancake-shaped” reefs at the highest platform elevations was interpreted as consistent with fluctuating sea level during the late Holocene. Although the ultimate cause for the morphometric depth trends remains open to interpretation, these interpretations are compatible with a recent eustatic sea-level curve that hindcasts fluctuating late Holocene sea level. Thus it is suggested that the morphologic differences represent two stages of reef accretion that occurred during different sea-level conditions.     

A comparison of line transect versus linear percentage sampling for evaluating stony coral (Scleractinia andMilleporina) community similarity and area coverage on reefs of the central Bahamas

Three methods of evaluating stony coral communities were used on selected reefs in the Exuma Cays Land and Sea Park (24°22N, 77°30W) in the central Bahamas. Shallow reefs (< 4 meters depth) were selected from aerial surveys based on size, location, and physical setting, and grouped into three community types: (1) channel patch reefs, (2) soft-coral-sponge patch reefs and (3) fringing reefs. Three survey techniques used to evaluate the stony coral communities were a) species presence and absence lists, b) linear percentage and c) line transects using 1 mx1 m grids. Data collected from these survey methods was used to calculate coral colony density, species area coverage, and species diversity based on colony number and based on linear (cm) coral cover. The linear percentage sampling was considered too convervative in determining distribution patterns of a reef community; this technique takes into account the massive reef framework species such asM. annularis. The line transect technique can account for both colony number and area coverage, thus is a better method for characterizing reef communities. Sample size considerations are discussed for future applications of survey techniques for ground-truthing digital images of small, shallow reef communities.     

Coral recruitment and juvenile mortality as structuring factors for reef benthic communities in Biscayne National Park, USA

Coral communities of Biscayne National Park (BNP) on offshore linear bank-barrier reefs are depauperate of reef corals and have little topographic relief, while those on lagoonal patch reefs have greater coral cover and species richness despite presumably more stressful environmental regimes closer to shore. We hypothesized that differences in rates of coral recruitment and/or of coral survivorship were responsible for these differences in community structure. These processes were investigated by measuring: (1) juvenile and adult coral densities, and (2) size-frequency distributions of smaller coral size classes, at three pairs of bank- and patch-reefs distributed along the north-south range of coral reefs within the Park. In addition, small quadrats (0.25 m²) were censused for colonies <2 cm in size on three reefs (one offshore and one patch reef in the central park, and one intermediate reef at the southern end), and re-surveyed after 1 year. Density and size frequency data confirmed that large coral colonies were virtually absent from the offshore reefs, but showed that juvenile corals were common and had similar densities to those of adjacent bank and patch reefs. Large coral colonies were more common on inshore patch reefs, suggesting lower survivorship (higher mortality) of small and intermediate sized colonies on the offshore reefs. The more limited small-quadrat data showed similar survivorship rates and initial and final juvenile densities at all three sites, but a higher influx of new recruits to the patch reef site during the single annual study period. We consider the size-frequency data to be a better indicator of juvenile coral dynamics, since it is a more time-integrated measurement and was replicated at more sites. We conclude that lack of recruitment does not appear to explain the impoverished coral communities on offshore bank reefs in BNP. Instead, higher juvenile coral mortality appears to be a dominant factor structuring these communities. Accepted: 9 September 1999     

The influence of habitat on the size distribution of groupers in the upper Florida Keys

Synopsis The influence of habitat on the size distribution of groupers was examined at sites in the middle and upper Florida Keys. Transects were used to quantify the size distribution of groupers at study sites. There were significant differences in the size distribution of groupers within and among reef community types related to differences in species composition and patch reef size. Groupers with a giant life-history style (Sullivan & de Garine 1994) were more abundant, but smaller, on inshore patch reefs than offshore reef community types. However, grouper species with a dwarf life-history style (Sullivan & de Garine 1994) showed an opposite pattern with a lower abundance, but larger size, inshore than offshore. The length category of groupers constituting the majority of individuals observed on patch reefs was inversely related to reef size. Graysby Epinephelus cruentatus were shown to recruit to deeper (15–20 m), low-relief habitats offshore. Several factors influenced the size distribution of groupers in the study sites including habitat type, spear-fishing, competition, predation, and recruitment.     

Using Agent-Based Models to Aid Reef Restoration: Enhancing Coral Cover and Topographic Complexity through the Spatial Arrangement of Coral Transplants

High coral cover and topographic complexity are favorable qualities of a healthy coral reef. Because coral reef restoration is expensive and coral growth is naturally slow, there is a need to strategically arrange coral transplants to maximize coral cover and topographic complexity. Similarly, it is important to understand how differences in the life history characteristics of coral transplants can influence changes in the structural attributes of coral reefs. This study utilizes agent‐based computer modeling to explore the different spatial scenarios of coral transplantation using corals with contrasting r‐ and K‐selected life histories. Spatial indexes are used to compare coral cover and topographic complexity at incremental time scales, within which disturbance events are of minor importance in spatial structuring. The outcomes of the model suggest that even‐spaced grided transplanting arrangements provide the fastest increase in coral cover and three‐dimensional habitat space (topographic complexity) across large temporal scales (<30 years) for corals with r‐selected life history strategies.     

The 1991–1992 rapid ecological assessment of Palau’s coral reefs

At the request of the Palau and US governments, a team of 30 scientists under the leadership of the Nature Conservancy completed a rapid ecological assessment (REA) of nearshore marine resources in Palau in 1992. The REA provided ecological input to Palau's ongoing master plan for economic development and identified 45 marine sites worthy of special protection. The REA relied on previous literature, 1992 aerial photography, interviews, and field observations. A combination of qualitative and quantitative techniques were used to assess stony corals, other reef invertebrates, reef and shore fishes, macroscopic algae, seagrasses, sea turtles and other marine organisms. The REA covered a variety of coral reef habitats including beaches, seagrass beds, fringing reefs, lagoons, passes, channels, reef holes, patch and pinnacle reefs, barrier reefs, atolls, submerged reefs, mangroves, and rock islands. Major stresses to Palau's coral reefs include sedimentation from soil erosion, overfishing, and damage from periodic storms and waves. Minor stresses include dredge-and fill activities, sewage pollution, anchor damage, tourism use, ship groundings, aquarium fish collecting, and minor crown-of-thorns (Acanthaster) infestations.     

The dynamics of architectural complexity on coral reefs under climate change

One striking feature of coral reef ecosystems is the complex benthic architecture which supports diverse and abundant fauna, particularly of reef fish. Reef‐building corals are in decline worldwide, with a corresponding loss of live coral cover resulting in a loss of architectural complexity. Understanding the dynamics of the reef architecture is therefore important to envision the ability of corals to maintain functional habitats in an era of climate change. Here, we develop a mechanistic model of reef topographical complexity for contemporary Caribbean reefs. The model describes the dynamics of corals and other benthic taxa under climate‐driven disturbances (hurricanes and coral bleaching). Corals have a simplified shape with explicit diameter and height, allowing species‐specific calculation of their colony surface and volume. Growth and the mechanical (hurricanes) and biological erosion (parrotfish) of carbonate skeletons are important in driving the pace of extension/reduction in the upper reef surface, the net outcome being quantified by a simple surface roughness index (reef rugosity). The model accurately simulated the decadal changes of coral cover observed in Cozumel (Mexico) between 1984 and 2008, and provided a realistic hindcast of coral colony‐scale (1–10 m) changing rugosity over the same period. We then projected future changes of Caribbean reef rugosity in response to global warming. Under severe and frequent thermal stress, the model predicted a dramatic loss of rugosity over the next two or three decades. Critically, reefs with managed parrotfish populations were able to delay the general loss of architectural complexity, as the benefits of grazing in maintaining living coral outweighed the bioerosion of dead coral skeletons. Overall, this model provides the first explicit projections of reef rugosity in a warming climate, and highlights the need of combining local (protecting and restoring high grazing) to global (mitigation of greenhouse gas emissions) interventions for the persistence of functional reef habitats.     

Habitat complexity and fish size affect the detection of Indo-Pacific lionfish on invaded coral reefs

A standard approach to improving the accuracy of reef fish population estimates derived from underwater visual censuses (UVCs) is the application of species-specific correction factors, which assumes that a species’ detectability is constant under all conditions. To test this assumption, we quantified detection rates for invasive Indo-Pacific lionfish (Pterois volitans and P. miles), which are now a primary threat to coral reef conservation throughout the Caribbean. Estimates of lionfish population density and distribution, which are essential for managing the invasion, are currently obtained through standard UVCs. Using two conventional UVC methods, the belt transect and stationary visual census (SVC), we assessed how lionfish detection rates vary with lionfish body size and habitat complexity (measured as rugosity) on invaded continuous and patch reefs off Cape Eleuthera, the Bahamas. Belt transect and SVC surveys performed equally poorly, with both methods failing to detect the presence of lionfish in >50 % of surveys where thorough, lionfish-focussed searches yielded one or more individuals. Conventional methods underestimated lionfish biomass by ~200 %. Crucially, detection rate varied significantly with both lionfish size and reef rugosity, indicating that the application of a single correction factor across habitats and stages of invasion is unlikely to accurately characterize local populations. Applying variable correction factors that account for site-specific lionfish size and rugosity to conventional survey data increased estimates of lionfish biomass, but these remained significantly lower than actual biomass. To increase the accuracy and reliability of estimates of lionfish density and distribution, monitoring programs should use detailed area searches rather than standard visual survey methods. Our study highlights the importance of accounting for sources of spatial and temporal variation in detection to increase the accuracy of survey data from coral reef systems.     

The oldest labechiid stromatoporoids from intraskeletal crypts in lithistid sponge–Calathium reefs

Early Ordovician (early Floian) reefs of South China include lithistid sponge–Calathium reefs with a three‐dimensional skeletal framework. These structures are among the first post‐Cambrian skeletal‐dominated reef structures and provides an opportunity to test how the novel metazoan builders changed the environments and increased topographic complexity within benthic communities. We document the oldest labechiid stromatoporoid (Cystostroma) in a lithistid sponge–Calathium reef of the Hunghuayuan Formation in southeastern Guizhou, South China. These earliest stromatoporoids may have originated in reefs, and we argue that the complex topography created by the hypercalcified sponge Calathium facilitated the emergence of stromatoporoids. Beyond Cystostroma, keratose sponges, Pulchrilamina (hypercalcified sponge) and bryozoans have also inhabited in the micro‐habitats (cavities and hard substrates) provided by Calathium. These findings suggest that ecosystem engineering by Calathium played an important role in the further diversification of reefs during the Ordovician.     

Inventory of the Maldives’ coral reefs using morphometrics generated from Landsat ETM+ imagery

In this study, we present exact measures of the number, area, and basic morphometric statistics for every single reef of the Maldivian archipelago, as derived from the interpretation of remotely sensed data collected by the Landsat-7 ETM+ earth-observing satellite sensor. We classified and mapped seven morphological attributes of reefs (six marine habitats and reef-top islands) to 30-m depth at 30×30 m spatial resolution (pixel size) for the entire archipelago. The total archipelagic area (all coral reef and lagoon habitats) of the 16 atolls, five oceanic faros, and four oceanic platform reefs which comprise the Maldives is 21,372.72±1,068.64 km² (approx. 20% of the Maldives Territorial Sea). A total of 2,041±10 distinct coral reef structures larger than 0.01 km² occur in the Maldives, covering an area of 4,493.85 km² (including enclosed reef lagoons and islands) to 30-m depth. Smaller areas of coral reef substratum cover another 19.29 km², bringing the total area of Maldivian coral reefs to 4,513.14±225.65 km². Shallow coral platforms thus occupy 21.1% of the total area of the archipelago (0.0052% of the EEZ area of the Maldives). Of these reefs, 538 are rim and oceanic reefs, covering 3,701.93 km² (82.5% of the total reef area), and 1,503 are patch reefs within the atoll lagoons, covering 791.92 km² (17.5% of the total reef area). Islands occupy only 5.1% of the total reef area. Mapping the Maldives coral reefs at high spatial resolution is only possible with remote sensing and spatial analysis technologies. These greatly reduce the large uncertainty around current estimates of reef area. Our accurate measure of total reef area is only 50.6% of the current best estimate, a result having significant implications for predictions of the Maldives reef productivity and response to global climate change. Here we present current best practice and compare the methods and measures with previous approaches.     

Carbon isotope ratios of soil organic matter and their use in assessing community composition changes in Curlew Valley,Utah

Summary Stable carbon isotope ratios of roots and soil organic matter were measured in Curlew Valley, Utah to determine if changes in the relative dominance of two shrub species had occurred in this salt-desert community. Measurements were made on soil cores along transects stretching from monospecific stands of Ceratoides lanata, a C₃ shrub, to monospecific stands of Atriplex confertifolia, a C₄ shrub. ¹³C values of roots and soil organic matter under Ceratoides cover appeared to be in equilibrium with the current plant community. By contrast, ¹³C values of roots and soils under Atriplex portions of the transects were more negative than would be expected for a C₄-dominated community. These results indicate that a change in relative C₃/C₄ dominance has occurred, and suggest that the C₄ shrub Atriplex confertifolia is increasing in importance in this salt-desert community.     

Configuration of small patch reefs and population abundance of a resident reef fish in a complex coral reef landscape

Habitat use by the resident coral reef anemonefish, Amphiprion frenatus, was examined in the complex coral reef landscape of Shiraho Reef, Ishigaki Island, Okinawa, Japan, using an enlarged color aerial photograph processed using image analysis software as an accurate field map. The anemonefish inhabit assemblages of the host sea anemone, Entacmaea quadricolor (clonal type), which inhabit various patch reefs in the back reef moat. We located all patch reefs inhabited by the host in the map based on snorkel observations: 297 anemonefish were found in 93 host assemblages in the study site of 2.9 ha. These patch reefs could be recognized by the reef colors, including the shadows (blackish color) in the photograph. Using image analysis software, the colors of the patch reefs were chosen and pixels with the same color values were regarded as potential habitat patches for the fish (PHPs). PHPs were 3D patch reefs (>0.5 m in height). Total areas (TA) and total perimeters (TP) of PHPs were measured in nine quadrats in the digitized aerial photograph. Host abundance and anemonefish abundance in a quadrat showed stronger correlations with the product of TA and TP of PHPs than TA alone. A site with numerous large 3D patch reefs (≥0.75 m² in situ) can be a better habitat for the fish than other sites consisting of several huge 3D patch reefs of the same total area. The methodology applied here may be useful for assessing the quality of habitats for small resident animals in shallow subtidal reefs.     

Toxicity of carbofuran to soil isolates of Chlorella vulgaris,Nostoc linckia and N. muscorum

A microalga, Chlorella vulgaris, and two diazotrophic cyanobacteria, Nostoc linckia and N. muscorum, all isolated from a rice soil, were compared for their response in terms of growth and metabolic activities to the application of carbofuran. The toxicity criteria included cell constituents (chlorophyll a, total protein, carbohydrate), ¹⁴CO₂ uptake and nitrate reductase, besides nitrogenase activity (acetylene reduction) in the cyanobacteria. C. vulgaris and N. muscorum were more sensitive to carbofuran than was N. linckia. The significant toxicity of the insecticide, observed with higher concentrations of 20 and 50 g ml^–1, to nitrogenase activity in N. linckia was reversed by the addition of ATP at 10 M. Transmission electron microscopy of the cultures, exposed to 50 g carbofuran ml^–1 showed certain cellular abnormalities, indicating interference of the insecticide with membrane properties. Correspondence to: K. Venkateswarlu     

The Cassian patch reefs (lower Carnian,southern Alps)

The fauna of the upper Cassian Formation is composed mainly of reef-building and reef-dwelling organisms which occur as reeeposited material in basinal sediments, but have not been found as original reef bodies. Such bodies have now been discovered in the uppermost Cassian Formation of the central Dolomites from the Sella Group in the west to the Monti Cadini in the east. Generally they are small-scale patch reefs, not exceeding a few metres in thickness and lateral extent, which are intercalated in well-bedded detrital and micritic limestones. locally, larger biostromes spread out from the margins of the Cassian Dolomite buildups. Four types of faunal communities have been encountered in these reefs:

1. The thrombolite-calcareous algae community, composed of small patchy cryptalgal structures binding poorly sorted debris and associated with other Cyanophyta, sessile formainifera and scattered calcareous sponges and corals. This type is the most common within the calcareous and marly-tuffaceous facies of the Cassian Formation.
2. The calcareous sponge-coral community, composed mostly of calcareous sponges (stromatoporoids, some pharetronids) and, to a lesser extent, colonial corals and thrombolites. This community corre-sponds well to the Cassian reef fauna, best known from erratic blocks at Alpe di Specie, but has been found in situ only at one locality.
3. The Spongiomorpha-Solenopora community, associated with scattered calcareous sponges and colonial corals, forming a thin biostrome at one locality.
4. Coral communities, composed predominantly of colonial Scleractinia; found only in small or stratigraphically illdefined outcrops and in erratic blocks.

The Cassian patch reefs and biostromes mark the end of a basinal evolution which began in the Lower Ladinian, and the onset of newly expanding carbonate buildups of Cassian Dolomite. These buildups and the sponge-coral patch reefs might have been the source for the allochthonous reef fauna of the Cassian Formation which interfingers with both shallow water environments.     

Triassic reefs in Slovenia

The paper deals with the distribution, paleogeography, age and biota of Triassic reefs in Slovenia. Most of these reefs have not been studied in detail up to now, but the paleographical distributional pattern can be outlined (Figs. 1 and 2). Triassic reefs are known from Central and Northern Slovenia, predominantly occurring at the margins of the “Slovenian trough” (which separates the northern Julian Platform and the southern Dinaric Platform) and at the margins of an intraplatform trough within the Julian platform. Reef growth started in the Ladinian and Cordevolian and continued (with interruptions during the Upper Carnian ?) to the Norian and Rhaetian. Anisian environments are characterized by the predominance of algal mats and dasycladacean algae. Cordevolian patch reefs as well as Norian and Rhaetian reefs were built during the Late Triassic by calcareous sponges and corals, which belong to different species (Tab. 1 and 2). Some smaller Cordevolian patch reefs may have been formed within deeper-water sediments. An interesting facies sequence is developed in the Norian Dachstein Limestone reef of Pokljuka (Julian Alps), starting with deeper-marine cherty limestones, which gradually succeeded by crinoidal limestones followed by reef limestones and lagoonal Dachstein Limestones.     

Coral and sea urchin assemblage structure and interrelationships in Kenyan reef lagoons

Patterns of hard coral and sea urchin assemblage structure (species richness, diversity, and abundance) were studied in Kenyan coral reef lagoons which experienced different types of human resource use. Two protected reefs (Malindi and Watamu Marine National Parks) were protected from fishing and coral collection, but exposed to heavy tourist use. One reef (Mombasa MNP) received protection from fishermen for one year and was exploited for fish and corals prior to protection and was defined as a transitional reef. Three reefs (Vipingo, Kanamai, and Diani) were unprotected and experienced heavy fishing and some coral collection. Protected and unprotected reefs were distinct in terms of their assemblage structure with the transitional reef grouping with unprotected reefs based on relative and absolute abundance of coral genera. Protected reefs had slightly higher (p<0.01) coral cover (23.6 ± 8.3 % ± S.D.) than unprotected reefs (16.7 ± 8.5), but the transitional reef had the highest coral cover (30.8 ± 6.4) which increased by 250% since measured in 1987: largely attributable to a large increase inPorites nigrescens cover. Protected reefs had higher coral species richness and diversity and a greater relative abundance ofAcropora, Montipora andGalaxea than unprotected reefs. The transitional reef had high species richness, but lower diversity due to the high dominance ofPorites. Sea urchins showed the opposite pattern with highest diversity in most unprotected reefs. Coral cover, species richness, and diversity were negatively associated with sea urchin abundance, but the relative abundance ofPorites increased with sea urchin abundance to the point wherePorites composed >90% of the coral cover at sites with the highest sea urchin abundance. Effects of coral overcollection was only likely for the genusAcropora (staghorn corals). A combination of direct and indirect effects of human resource use may reduce diversity, species richness, and abundance of corals while increasing the absolute abundance of sea urchins and the relative cover ofPorites.     

Behavioural and developmental responses of predatory coral reef fish to variation in the abundance of prey

Ecological theory suggests that the behaviour, growth and abundance of predators will be strongly influenced by the abundance of prey. Predators may in turn play an important role in structuring prey populations and communities. Responses of predators to variation in prey abundance have most commonly been demonstrated in low-diversity communities where food webs are relatively simple. How predators respond in highly diverse assemblages such as in coral reef habitats is largely unknown. This study describes an experiment that examined how the movement, diet and growth of the coral reef piscivore, Cephalopholis boenak (Serranidae) responded to variation in the abundance of its prey. Predator densities were standardised on small patch reefs made from the lagoonal reef-building coral, Porites cylindrica. These patch reefs exhibited natural variation in the abundance and community structure of multiple species of prey. However, our experiment generated a relatively simple predator–prey relationship, with C. boenak primarily responding to the most abundant species of prey. Three responses of predators were observed: aggregative, functional and developmental. Thirty-one per cent of individuals moved between patch reefs during the experiment, all from areas of relatively low to high prey density. Feeding rates were higher on patch reefs of high prey density, while growth rates of fish that remained on low prey density reefs throughout the experiment were lower. Growth rates of C. boenak on the experimental reefs were also much higher than for those living on natural patch reefs over the same time period, corresponding with overall differences in prey abundance. These results suggest that local abundance, feeding rate and growth of C. boenak were closely linked to the abundance of their main prey. This combination of predatory responses is a potential mechanism behind recent observations of density-dependent mortality and population regulation of prey in coral reef fish communities.     

Millennial-scale change in the structure of a Caribbean reef ecosystem and the role of human and natural disturbance

Caribbean coral reefs have transformed into algal-dominated habitats over the past half-century, but the role of specific anthropogenic drivers is unresolved due to the lack of ecosystem-level data predating human disturbance. To better understand the extent and causes of long-term Caribbean reef declines, we produced a continuous 3000-yr record of the ecosystem state of three reefs in Bocas del Toro, Caribbean Panama. From fossils and sediments obtained from reef matrix cores, we tracked changes in reef accretion rates and the taxonomic and functional group composition of fish, coral, urchin, bivalve and benthic foraminifera. This dataset provided a comprehensive picture of reef community and environmental change. At all sites, reefs shifted from systems with greater relative abundance of herbivorous fish, epifaunal suspension feeding bivalves and Diadema urchins to systems with greater relative abundance of micropredator fish, infaunal bivalves and Echinometra urchins. These transitions were initiated a millennium ago at two less-degraded reefs fringing offshore islands and ~250 yr ago at a degraded patch reef near the continental coast. Ecosystem shifts were accompanied by a decline in reef accretion rates, and at the patch reef, a decline in water quality since the 18th century. Within all cores, synchronous increases in infaunal bivalves and declines in herbivorous fish regardless of water quality suggest a loss of hard substrate and increasingly hypoxic sediment conditions related to herbivore loss. While the early timing of ecosystem transitions at the fringing reefs implicates large-scale hydrological change, the more recent timing of change and loss of water quality at the patch reef implicates terrigenous runoff from land-clearing. Our whole-ecosystem reconstruction reveals that reef ecosystem deterioration appears to follow a predictable trajectory whether driven by natural or anthropogenic disturbances and that historical local human activities have quickly unraveled reefs at a scale similar to longer-term natural environmental change.