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Timely detection of ecological regime shifts is a key problem for ecosystem managers, because changed ecosystem dynamics and function will usually necessitate a change in management strategies. However, currently available methods for detecting regime shifts depend on having multiple long time series data from both before and after the regime shift. This data requirement is prohibitive for many ecosystems. Here, we present a new approach for detecting regime shifts from one‐dimensional spatial (transect) data from just a single time step either side of the transition. Characteristic length scale (CLS) estimation is a method of attractor reconstruction combined with nonlinear prediction that enables identification of the emergent scale at which deterministic behavior of the system is best observed. Importantly, previous studies show that a fundamental change in ecosystem dynamics, from one domain of attraction to another, is reflected in a change in the CLS, i.e., the approach enables distinguishing regime shifts from variability in dynamics around a single attractor. Until now the method required highly resolved two‐dimensional spatial data, but here we adapted the approach so that the CLS can be estimated from one‐dimensional transect data. We demonstrate its successful application to both model and real ecosystem data. In our model test cases, we detected change in the CLS in cases where the shape (topology) of the interaction network had changed, leading to a shift in community composition. In an examination of benthic transect data from four Indonesian coral reefs, changes in the CLS for two of the reefs indicate a regime shift. This new development in estimating CLSs makes it possible to detect regime shifts in systems where data are limited, removing ambiguity in the interpretation of community change.

Coral disease is a major threat to the resilience of coral reefs; thus, understanding linkages between disease outbreaks and disturbances predicted to increase with climate change is becoming increasingly important. Coral disease surveys conducted twice yearly between 2008 and 2011 at a turbid inshore reef in the central Great Barrier Reef spanned two disturbance events, a coral bleaching event in 2009 and a severe cyclone (cyclone ‘Yasi’) in 2011. Surveys of coral cover, community structure and disease prevalence throughout this 4-yr study provide a unique opportunity to explore cumulative impacts of disturbance events and disease for inshore coral assemblages. The principal coral disease at the study site was atramentous necrosis (AtN), and it primarily affected the key inshore, reef-building coral Montipora aequituberculata. Other diseases detected were growth anomalies, white syndrome and brown band syndrome. Diseases affected eight coral genera, although Montipora was, by far, the genus mostly affected. The prevalence of AtN followed a clear seasonal pattern, with disease outbreaks occurring only in wet seasons. Mean prevalence of AtN on Montipora spp. (63.8 % ± 3.03) was three- to tenfold greater in the wet season of 2009, which coincided with the 2009 bleaching event, than in other years. Persistent wet season outbreaks of AtN combined with the impacts of bleaching and cyclone events resulted in a 50–80 % proportional decline in total coral cover. The greatest losses of branching and tabular acroporids occurred following the low-salinity-induced bleaching event of 2009, and the greatest losses of laminar montiporids occurred following AtN outbreaks in 2009 and in 2011 following cyclone Yasi. The shift to a less diverse coral assemblage and the concomitant loss of structural complexity are likely to have long-term consequences for associated vertebrate and invertebrate communities on Magnetic Island reefs.

We explored variations in polyp morphology of four ecologically important massive coral species, Porites lutea (Milne-Edwards and Haime, 1860), Diploastrea heliopora (Lamarck, 1816), Favia speciosa (Dana, 1846), and Favia matthaii (Vaughan, 1918), across a depth gradient and among sites of differing turbidity within the Wakatobi Marine National Park, Indonesia. Increased polyp area with decreased light availability was found in all target species except F. speciosa, whereas polyp density only varied across sites or depth in D. heliopora, P. lutea, and F. speciosa. Variability in polyp morphology may reflect both an optimization of light capture and an increase in heterotrophic efficiency of the host to compensate for decreased photosynthesis with depth. The morphological variability demonstrated in these key species, which acts to optimize environmental suitability, may be a crucial attribute that has contributed to the success and abundance of these species within the Wakatobi Marine National Park.

Despite increasing research effort on coral diseases, little is known about factors driving disease dynamics on the Great Barrier Reef (GBR). This is the first study to investigate the temporal patterns of coral disease prevalence and potential drivers of disease around Heron Island, in the southern Capricorn Bunker sector of the GBR. Surveys were conducted in two austral summers and three winters between November 2007 and August 2009 on six sites around the island. Six diseases were detected: brown band syndrome (BrB), growth anomalies (GA), ulcerative white spots (UWS), white syndrome (WS), skeletal eroding band disease (SEB) and black band disease (BBD). The lowest overall mean disease prevalence was 1.87 ± 0.75% (mean ± SE) in November 2007 and the highest 4.22 ± 1.72% in August 2008. There was evidence of seasonality for two diseases: BrB and UWS. This is the first study to report a higher prevalence of BrB in the winter. BrB had a prevalence of 3.29 ± 0.58% in August 2008 and 1.53 ± 0.28% in August 2009, while UWS was the most common syndrome in the summer with a prevalence of 1.12 ± 0.31% in November 2007 and 2.67 ± 0.52% prevalence in January 2008. The prevalence of GAs and SEB did not depend on the season, although the prevalence of GAs increased throughout the study period. WS had a slightly higher prevalence in the summer, but its overall prevalence was low (

Coral health data are poorly documented in New Caledonia, particularly from reefs chronically subject to anthropogenic and natural runoff. We investigated patterns of coral disease and non-disease conditions on reefs situated downstream of mining sites off the coast of New Caledonia. Surveys were conducted in March 2013 at 2 locations along the west coast and 2 locations along the east coast of the main island. Only 2 coral diseases were detected: growth anomalies and white syndrome. The most prevalent signs of compromised health at each location were sediment damage and algal overgrowth. These results support earlier findings that sedimentation and turbidity are major threats to in-shore reefs in New Caledonia. The Poritidae-dominated west coast locations were more subject to sediment damage, algal overgrowth and growth anomalies compared to the Acroporidae-dominated east coast locations. If growth form and resistance of coral hosts influence these results, differences in environmental conditions including hydro-dynamism between locations may also contribute to these outputs. Our results highlight the importance of combining coral health surveys with measurements of coral cover when assessing the health status of a reef, as reefs with high coral cover may have a high prevalence of corals demonstrating signs of compromised health.

The ecological consequences of coral mining can be severe, with immediate reduction in reef-associated biodiversity and longer term implications for linked habitats such as mangrove forests and seagrass meadows. However, research into the effects of coral mining must take into account other environmental processes which may affect reef communities and the socio-economic context within which coral mining takes place if appropriate and proportionate management responses are to be identified. This article builds upon recently published research detailing the adverse effects of coral mining in Indonesia to illustrate the significance of these points. We use the previous paper to demonstrate that accurate identification of the ecological impacts of coral mining requires the use of appropriate control sites and recognizing natural stresses which may account for short-term variability in ecological parameters. We also underline the need to appreciate that government institutions can directly or indirectly facilitate coral mining, whilst proposed alternative income-generating activities intended to reduce coral mining should be tailored to the local economic, cultural and environmental context if they are to gain community support. This demonstrates the value of an integrated approach to analyzing marine resource usage which combines information from the natural and social sciences to address environmental problems such as coral mining.

This is the first quantitative study on the prevalence of epizoic Waminoa sp. acoel worms and their association with corals in the Wakatobi Marine National Park (WMNP), South-East Sulawesi, Indonesia. Three replicate transects were laid on the reef crest, flat and slope at six sites in 2006 and eight sites in 2007. Four of the sites were common in both years. In total 69 transects were surveyed in 2006, and 87 transects in 2007. A total of 4.8% of all observed hard corals were associated with acoel worms in 2006 and 2.6% of hard and soft corals in 2007. Acoels were present on 16 and 21 of the coral taxa studied in 2006 and 2007 respectively. The worms were strongly associated with the azooxanthellate coral Tubastrea spp. and were rare or absent on the most abundant coral genera Montipora and Porites. The mean number of corals having acoels was highest on reef slopes, whereas acoels were virtually absent on reef flats. Corals that had a high and a medium cover of worms were more common in 2007 than in 2006. No significant trend in the adaptation of the zooxanthellae of Waminoa sp. to different depths at different sites was revealed. The impact of the worm on the coral is unknown, but high numbers may have a shading effect and a negative impact on the coral's photophysiology. This acoel merits more study of its life cycle, its photophysiology, and its impact on its host corals. © 2009 Springer-Verlag.

In the present study we investigated inter-annual coral disease dynamics, in situ disease progression rates, and disease-associated coral tissue mortality in the Wakatobi Marine National Park (WMNP) situated in the coral triangle in South-East Sulawesi, Indonesia. In 2005, only 2 known syndromes were recorded within the sampling area transect surveys: white syndrome (WS; 0.42% prevalence) and growth anomalies (GA; 0.15% prevalence), whilst 4 diseases were recorded in 2007: WS (0.19%), Porites ulcerative white spot disease (PUWS; 0.08%), GA (0.05%) and black band disease (BBD; 0.02%). Total disease prevalence decreased from 0.57% in 2005 to 0.33% in 2007. In addition to prevalence surveys, in situ progression rates of 4 diseases were investigated in 2007: BBD on Pachyseris foliosa, P. rugosa and Diploastrea heliopora, WS on Acropora clathrata, and brown band (BrB) and skeletal eroding band (SEB) diseases on Acropora pulchra. BrB and WS had the highest progression rates, 1.2 +/- 0.36 and 1.1 +/- 0.07 cm d(-1), respectively, indicating that diseases may have a significant impact on local Acropora populations. BBD had the lowest progression rate (0.39 +/- 0.14 cm d(-1)). WS caused the most severe recorded total tissue mortality: 53 923 cm2 over a period of 36 d. Sedimentation and coral cover were studied and a highly significant drop in coral cover was observed. This study provides the first documentation of spatio-temporal coral disease dynamics from Indonesia. Despite low total disease prevalence, progression rates comparable to the ones observed in the Caribbean and Australia indicate that diseases may threaten the reef framework in some locations and add to the degradation of coral reefs in a region already at high risk from anthropogenic impacts.

The relationship between coral community structure and disease prevalence is poorly understood, particularly in the Coral Triangle. Improved understanding of this relationship will assist in identifying assemblages that might be particularly vulnerable to disease, and in predicting possible future impacts. Here, we report results from the last 2 years (2010 and 2011) of a 4-year coral disease-monitoring program (2005, 2007, 2010, 2011) in the Wakatobi Marine National Park (Indonesia), and evaluate changes in total disease prevalence and coral cover since 2005. A comparison with previously published results from 2005 and 2007 indicates that the number of coral diseases increased from two to eight and total disease prevalence tripled between 2005 and 2011. We observed a dramatic decline in coral cover and an increase in disease prevalence at a site with a unique community of foliose corals. However, because of the 3-year period between surveys (2007, 2010), it is likely that the peak of the disease event was not observed. While multi-year studies provide useful insights into the relationships between community structure and disease, our results emphasise how determining the drivers of change in remote reef locations is especially challenging if events such as disease outbreaks are missed.

[Extract] Focal bleached spots are commonly recorded on Porites, Montipora and Acropora (Beeden et al. 2008). During a diving expedition in April 2010 to the pinnacle of Hin Daeng ('Red Rock') (7°9'1"N; 98°49'20"E), in the Andaman Sea off Western Thailand, we discovered a new type of focal white spots on a massive colony of Porites lobata Dana, 1846.

Growth anomalies (GAs) are common, tumor-like diseases that can cause significant morbidity and decreased fecundity in the major Indo-Pacific reef-building coral genera, Acropora and Porites. GAs are unusually tractable for testing hypotheses about drivers of coral disease because of their pan-Pacific distributions, relatively high occurrence, and unambiguous ease of identification. We modeled multiple disease-environment associations that may underlie the prevalence of Acropora growth anomalies (AGA) (n = 304 surveys) and Porites growth anomalies (PGA) (n = 602 surveys) from across the Indo-Pacific. Nine predictor variables were modeled, including coral host abundance, human population size, and sea surface temperature and ultra-violet radiation anomalies. Prevalence of both AGAs and PGAs were strongly host density-dependent. PGAs additionally showed strong positive associations with human population size. Although this association has been widely posited, this is one of the first broad-scale studies unambiguously linking a coral disease with human population size. These results emphasize that individual coral diseases can show relatively distinct patterns of association with environmental predictors, even in similar diseases (growth anomalies) found on different host genera (Acropora vs. Porites). As human densities and environmental degradation increase globally, the prevalence of coral diseases like PGAs could increase accordingly, halted only perhaps by declines in host density below thresholds required for disease establishment.