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opencc-zeroJul 2020View details →

Data from: Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments particularly for vertebrates in species-rich regions. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species, which is never met. As an alternative, a diversity of Operational Taxonomic Units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1,531 fish OTUs while 1,611 fish species are recorded in the region. Besides, we also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

opencc-by-4.0Jan 2021View details →

Data from 'Planktivores as trophic drivers of global coral reef fish diversity patterns'

Datasets and scripts generated in the paper 'Planktivores as trophic drivers of global coral reef fish diversity patterns', published in PNAS. More details can be found in the README file.

opencc-by-nc-4.0Feb 2016View details →

Bermuda Reef Ecosystem Assessment and Mapping Programme: Baseline Coral Reef and Fish data

BREAM: Bermuda Reef Ecosystem Analysis and Mapping Programme, mapped all coral reefs across the Bermuda platform in 2003. We then surveyed over 200 sites for benthic and fish assemblages using the AGRRA.org v4 methods, with local modifications.  See www.bermudaBREAM.org for more information about the baseline monitoring work, or to contact us for additional data and information. Contributors: Research Associates: Jessie Murdoch MSc; Robert Fisher, BFA; Gretchen Goodbody-Gringley, PhD, Matthew Strong BSc; Struan R. Smith PhD Undergraduate Interns Taylor Gorham, Anke Moesinger, Molly Sinnott, D’mitri Williams Graduate Interns Gerardo Toro-Farmer, Mike Colella, Brittany Huntington, Katherine Yates Volunteers Ian Murdoch; Judie Clee; Teddy Gosling; Gil Nolan; Lynn Wolfe RV Endurance Captain: Tim Hasselbring

opencc-zeroDec 2023View details →

Western Indian Ocean coral and fish normalized site richness collected between 1991 to 2000

Aim: Strong social-ecological trade-offs between resource extraction and protection have created challenges for large, protected area management in natural-resource-dependent countries. Therefore, local governments and community conservation activities are becoming common and need information about low environmental exposure and high biodiversity for planning localized conservation activities. Location: the western Indian Ocean Methods: Coral reef sites were evaluated for local scale environmental and species richness to elucidate local patterns in spatial heterogeneity. Local coral and fish taxonomic richness were normalized to partially account for common and heterogeneous disturbances to coral cover and fish biomass. Residuals were evaluated for patterns of local diversity with geography, environmental stress, and by machine learning to evaluate the relationship with 21 specific environmental variables. Results: High variability in richness was found at similar latitudes where richness was high. Relationships with specific environmental and human influences variables were complex and spatially heterogeneous. Expected large-scale biogeographic variables influenced richness but variability and environmental influences were highly specific and localized. Among the environmental and human influence variables examined, ~ 8 variables contributed 8 to 25% of the variance to the richness of both coral and fishes. Main conclusions: Decisions to focus small-scale conservation on locally biodiverse locations could contribute to species persistence by planning for local heterogeneity in richness and stress. From this specific data set, sites in the Pemba Channel between the Tanzanian mainland and Pemba Island, and northern Mozambique and Madagascar fit these characteristics.

opencc-by-4.0Feb 2024View details →

Data from 'The rise of dietary diversity in coral reef fishes'

Open the record for dataset details and reuse information.

Figure 1 in First report of two gobiid fishes from the coral reefs of Gulf of Mannar, Tamil Nadu, India

Figure 1. Map of the Mandapam group of Islands in GoM showing the collection sites.

Figure 3. Silhouettea indica Visweswara Rao, 1971 in First report of two gobiid fishes from the coral reefs of Gulf of Mannar, Tamil Nadu, India

Figure 3. Silhouettea indica Visweswara Rao, 1971.

Figure 2 in First report of two gobiid fishes from the coral reefs of Gulf of Mannar, Tamil Nadu, India

Figure 2. Istigobius ornatus (Rüppell, 1830).

opencc-zeroApr 2024View details →

Data From: Shortened food chain length in a fished versus unfished coral reef

Direct exploitation through fishing is driving dramatic declines in wildlife populations in ocean environments, particularly for predatory and large-bodied taxa. Despite wide recognition of this pattern and well-established consequences of such trophic downgrading on ecosystem function, there have been few empirical studies examining the effects of fishing on whole system trophic architecture. Understanding these kinds of structural impacts is especially important in coral reef ecosystems - often heavily fished and facing multiple stressors. Given often high dietary flexibility and numerous functional redundancies, especially in diverse ecosystems such as coral reefs, it is important to establish if web architecture is strongly impacted by fishing pressure, or if it might be resilient, at least to moderate intensity pressure. To examine this question, we used a combination of bulk and compound-specific stable isotope analyses measured across a range of predatory and low trophic level consumers between two coral reef ecosystems that differed with respect to fishing pressure but otherwise remained largely similar. We find that even in a high diversity system with relatively modest fishing pressure, there are strong reductions in the trophic position of the three highest trophic position consumers examined in the fished system but no effects on the trophic position of lower-level consumers. We see no evidence that this shortening of these affected food webs is being driven by changes in basal resource consumption, e.g., through changes in spatial location of foraging by consumers. Instead, this likely reflects internal changes in food web architecture suggesting that even in diverse systems, and with relatively modest pressure, human harvest causes significant compressions in food chain length. This observed shortening of these food webs may have many important emergent ecological consequences for the functioning of ecosystems impacted by fishing or hunting. Such important structural shifts may be widespread but unnoticed by traditional surveys. This insight may also be useful for applied ecosystems managers grappling with choices about the relative importance of protection for remote and pristine areas and the value of strict no-take areas to protect not just the raw constituents of systems affected by fishing and hunting but also the health and functionality of whole systems.

opencc-by-4.0Dec 2021View details →

Traits, landmarks and outlines: Three congruent sides of a tale on coral reef fish morphology

Quantifying the morphology of organisms remains fundamental in ecology given the form-function relationship. Morphology is quantifiable in traits, landmarks, and outlines, and the choice of approach may influence ecological conclusions to an unknown extent. Here, we apply these three approaches to 111 individual coral reef fish of 40 species common in Micronesia. We investigate the major dimensions of morphological variability among individuals, families, and predefined feeding functional groups. We find that although the approaches are complementary, they coincide in capturing elongation as the main dimension of variability. Further, the choice of approach led to different interpretations regarding the degree of morphological differentiation among taxonomic and feeding functional groups. We also use each morphology dataset to compute community-scale morphological diversity on Palauan reefs and investigate how the choice of dataset affects the detection of differences among sites and wave exposure levels. The exact ranking of sites from highest to lowest morphological diversity was sensitive to the approach used, but not the broad spatial pattern of morphological diversity. Conclusions regarding the effect of wave exposure on morphological diversity were robust to the approach used. Biodiversity hotspots (e.g. areas of exceptionally high diversity and/or endemism) are considered important conservation targets but their location may depend on the biodiversity metric used. In the same vein, our results caution against labelling particular sites as morphological diversity hotspots when metrics consider only a single aspect of morphology.

opencc-zeroMay 2022View details →

Linking variation in planktonic primary production to coral reef fish growth and condition

Within low nutrient tropical oceans, islands and atolls with higher primary production support higher reef fish biomass and reef organism abundance. External energy subsidies can be delivered onto reefs via a range of physical mechanisms. However, the influence of spatial variation in primary production on reef fish growth and condition is largely unknown. It is not yet clear how variability in food delivery onto a reef interacts with reef depth and slope, and affects reef fish productivity. Here we test the hypothesis that with increased proximity to deep-water oceanic allochthonous nutrient sources, or at sites where transportation of these water bodies onto reefs is facilitated by shallower reef slopes, parameters of fish growth and condition will be higher, and this pattern will be further emphasised in areas naturally higher in primary production. Contrary to expectations, we found no association between fish growth rate and sites with higher mean chlorophyll values. There were no differences in δ15N or δ13C values in fish collected at greater depths across reefs, suggesting a homogeneous primary production resource. However, the relationship between fish condition and primary production was influenced by depth of collection, driven by higher fish condition at shallow depths within a study site which is a 'hotspot' of primary production. Carbon δ13C values were depleted at sites with increasing primary production, and this trend was reversed by an interactive effect with shallower reef slopes. Our results indicate that deep-water ocean nutrient influences did not translate into observable increases in overall population growth in planktivorous Chromis fieldi within the 10–17.5 m depth range, but show the importance of site specific variation in hydrodynamics and reef physical characteristics influencing fish carbon isotopic composition and condition.

Small predators dominate fish predation in coral reef communities

README File The dataset consists of 4 Excel files of which: -LizardData: is the fish community data collected on Lizard Island. -Metanalysis_dataset: is the gut content metanalysis, used to create the metanalsamps dataset, which is the dataset consisting the resampling and binning into body sizes.  This was then compared to the simnetsamps dataset, which is the resampling and binning from the LizardData file.

opencc-zeroApr 2020View details →

Data from: Fishes alleviate the impacts of sediments on host corals

Mutualisms play a critical role in ecological communities, however the importance and prevalence of mutualistic associations can be modified by external stressors. On coral reefs, elevated sediments are a major stressor, reducing the health of corals and damaging reef resilience. Here, we investigated the influence of sediment stress on the mutualistic relationship between small damselfishes (Dascyllus aruanus and Pomacentrus moluccensis) and their coral host (Pocillopora damicornis). In an aquaria experiment, corals were exposed to sedimentation rates of ~100 mg cm-2 day-1, with and without symbiont fish to test whether: (1) fishes influence the accumulation of sediments on coral hosts, and (2) fishes moderate partial colony mortality and/or condition. Colonies with fishes accumulated much less sediment compared to colonies without fishes, and this effect was strongest for colonies with D. aruanus (five-fold less sediment than controls) as opposed to P. moluccensis (two-fold less sediment than controls). Colonies with symbiont fishes also had up to 10-fold less sediment-induced partial mortality, as well as higher chlorophyll and protein concentrations. These results demonstrate that fish mutualisms vary in the strength of their benefits and indicates that some mutualistic or facilitative interactions might become more important for species health and resilience as stress levels increase.

opencc-zeroSep 2022View details →

Data from: Paternal hatching care regulates the timing, synchrony, and success of hatching in a coral reef fish

In oviparous species, the timing of hatching is a crucial decision, but for developing embryos, assessing cues that indicate the optimal time to hatch is challenging. In species with parental care, parents can assess environmental conditions and induce their offspring to hatch. We provide the first documentation of parental hatching regulation in a coral reef fish, demonstrating that male neon gobies (Elacatinus colini) directly regulate hatching by removing embryos from the clutch and spitting hatchlings into the water column. All male gobies synchronized hatching within 2h of sunrise, regardless of when eggs were laid. Paternally-incubated embryos hatched later in development, more synchronously, and had higher hatching success than artificially-incubated embryos that were shaken to simulate paternal hatching cues or not stimulated. Artificially-incubated embryos displayed substantial plasticity in hatching times (range: 88 – 244 hours post-fertilization), suggesting that males could respond to environmental heterogeneity by modifying the hatching time of their offspring. Finally, paternally-incubated embryos hatched with smaller yolk sacs and larger propulsive areas than artificially-incubated embryos, suggesting that paternal effects on hatchling phenotypes may influence larval dispersal and fitness. These findings highlight the complexity of fish parental care and may have important, and currently unstudied, consequences for fish population dynamics.

opencc-zeroSep 2022View details →

Data for: Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes

Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability. Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks, such as feeding strategy or conspecific detection. By studying all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (lws) opsin is highly expressed in algivorous and less or not expressed in zooplanktivorous species. Lws is also upregulated in species with orange/red colours (reflectance >520 nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling. Character state reconstructions indicate that in the early evolutionary history of damselfishes, there was no lws expression and no orange/red coloration. Omnivory was most often the dominant state. Although herbivory was sometimes dominant, zooplanktivory was never dominant. Sensitivity to long wavelength (increased lws expression) only emerged in association with algivory but never with zooplanktivory. Higher lws expression is also exploited by social signalling in orange/red, which emerged after the transition to algivory. Although the relative timing of traits may deviate by different reconstructions and alternative explanations are possible, our results are consistent with sensory bias whereby social signals evolve as a correlated response to natural selection on sensory system properties in other contexts.

opencc-zeroMay 2024View details →

Out of shape: Ocean acidification simplifies coral reef architecture and reshuffles fish assemblages

Climate change stressors are progressively simplifying biogenic habitats in the terrestrial and marine realms, and consequently altering the structure of associated species communities. Here, we used a volcanic CO2 seep in Papua New Guinea to test in situ if altered reef architecture due to ocean acidification reshuffles associated fish assemblages. We observed replacement of branching corals by massive corals at the seep, with simplified coral architectural complexity driving abundance declines between 60-86% for an assemblage of damselfishes associated with branching corals. An experimental test of habitat preference for a focal species indicated that acidification does not directly affect habitat selection behaviour, with changes in habitat structural complexity consequently appearing to be the stronger driver of assemblage reshuffling. Habitat health affected anti-predator behaviour, with P. moluccensis becoming less bold on dead branching corals relative to live branching corals, irrespective of ocean acidification. We conclude that coral reef fish assemblages are likely to be more sensitive to changes in habitat structure induced by increasing pCO2 than any direct effects on behaviour, indicating that changes in coral architecture and live cover may act as important mediators of reef fish community structures in a future ocean.

opencc-by-4.0Nov 2014View details →

Figure 1 in Diversity of trypanorhynch metacestodes in teleost fishes from coral reefs off eastern Australia and New Caledonia

Figure 1. Collection localities off the east coast of Australia and New Caledonia.

opencc-by-4.0Dec 2020View details →

Fig 6 in The status of coral reefs and reef fishes of Biloro Village, Southern Buru Regency, Indonesia

Fig 6: The percentage of coral reef fish at Biloro Village waters.

opencc-by-4.0Dec 2020View details →

Fig 3 in The status of coral reefs and reef fishes of Biloro Village, Southern Buru Regency, Indonesia

Fig 3: Some of dominated hard coral found in study site.