The measurement of ecosystem development in Caribbean coral reefs through topological indices

Functional developmental states of the Greater Caribbean coral reefs

It is now clear that research addressed at a large scale can allow for new insights on complex phenomena taking place in the global ocean. Ecological studies are more and more based on data-driven methodologies that rely on pre-existing datasets. However, open-access, digital and cross-disciplinary datasets are still uncommon for ecology. In the face of the global overexploitation of marine resources and rapid degradation of ecosystem integrity, new research tools are required to tackle these issues and enable new powerful, interdisciplinary research capabilities. We have, in fisheries research generally, and at the Fisheries Centre in particular, broad experience with fisheries data collection, and analysis of food web aspects of ecosystem dynamics. With this report titled EcoBase: a repository solution to gather and communicate information from EwE models, Colleter and colleagues have made a big effort at collecting information from all existing ecosystem models worldwide, built using the Ecopath with Ecosim (EwE) approach. EwE is the world’s most widely used ecological modeling approach, and its development is led by Fisheries Centre researchers, including, Villy Christensen, Daniel Pauly and Carl Walters. A new accomplishment is now achieved with the EcoBase project initiated by the Ecopath Research and Development Consortium (ERDC) and carried out by the authors of this report. The ERDC was initiated at the Fisheries Centre in October 2011, and formally established in Edinburgh, Scotland, in May 2012. It contributes to creating synergies and partnerships between scientists in aquatic ecology, and promotes the EwE modeling approach. The main goals of EcoBase are to (i) gather published EwE models; (ii) communicate on EwE modeling research; (iii) facilitate meta-analyses based on EwE models. EcoBase is meant to be a comprehensive, open-access, digital repository where EwE models are made discoverable, accessible and reusable by the scientific community. The structure, capabilities and current state of the EcoBase models repository are described in further details in this report. This represents new opportunities for research and trans-disciplinary analyses, including, trophic functioning, fisheries impact or economic aspects, for which I commend the authors. U. R. Sumaila, Director, Fisheries Centre, UBC.

The implementation of ecosystem management requires ecosystem modelling within the context of a natural resource management process. Ecopath with Ecosim (EwE) is the most widely used modelling platform for investigating the dynamics of marine ecosystems, but has played a limited role in fisheries management and in multi‐sector resource decision‐making. We review 10 case studies that demonstrate the use of EwE to support operational resource management. EwE models are being used to inform tactical decision‐making in fisheries and other ocean use sectors, as well as to identify key trade‐offs, develop appropriate policy objectives, and reconcile conflicting legislative mandates in a variety of ecosystems. We suggest the following criteria to enhance the use of EwE and other ecosystem models in operational resource management: (1) a clear management objective that can be addressed through modelling; (2) an important trade‐off and a receptive policy context amenable to trade‐off evaluation; (3) an accessible and well‐documented model that follows best practices; (4) early and iterative engagement among scientists, stakeholders, and managers; (5) integration within a collaborative management process; (6) a multi‐model approach; and (7) a rigorous review process. Our review suggests that existing management frameworks are as much or more of a limitation to the operational use of EwE than technical issues related to data availability and model uncertainty. Ecosystem models are increasingly needed to facilitate more effective and transparent decision‐making. We assert that the requisite conditions currently exist for enhanced strategic and tactical use of EwE to support fisheries and natural resource management.

A donor-driven approach to modelling anchovy-sardine dominance shifts in the southern Benguela ecosystem

This study addressed whether grazing by the sea urchin Diadema antillarum influenced rates of nitrogen fixation by algal turf communities on Caribbean coral reefs. Because the turfs were nitrogen-limited, we also assessed whether newly-fixed nitrogen was important for supporting net primary productivity by the turfs. We measured acetylene reduction in turfs grown in treatments excluding or including D. antillarum in the presence of other herbivores at 3 m water depth on Tague Bay forereef, St. Croix, U.S. Virgin Islands. These were the first measurements of acetylene reduction on coral reefs under quasi-natural conditions of high water-flow and photosynthetic oxygen generation. Rates of acetylene reduction under these conditions were as high as any measured previously in coral reef communities (mean 7.6 nmol C2H4 cm−2 h−1). Algal turfs grazed by D. antillarum and other herbivores had chlorophyll-specific acetylene reduction rates up to three times higher than when D. antillarum was excluded. High rates of nitrogen fixation by the turfs were sufficient to meet <2% of the nitrogen required to support net chlorophyll-specific primary productivity over 24 h. Grazer-mediated increases in nitrogen fixation do not appear responsible for a parallel enhancement of net primary productivity. Algal turfs at this site must be dependent primarily on external sources of nitrogen.

To explore the historical evolution and current status of the EwE (Ecopath with Ecosim) modelling research, the core dataset and extended dataset were collected by topic retrieval and citation indexing methods from the "Web of Science" from 1984 to 2020. The bibliometric analysis and mapping knowledge were performed by CiteSpace software, focusing on literature distribution, research forces, research theme, and hotspot evolution. The results showed that the annual publications in the EwE model researches were increasing, covering multi-disciplinary fields. Christensen, Walters, and Pauly were representative scholars with an important role in model development and relevant international cooperation. In the early stage, EwE model was usually applied to solve ecosystem problems, including spatial-temporal dynamic of structure and function, and the ecosystem effects of fisheries. Currently, marine resource management, ecosystem modelling, marine protected areas and ecosystem indicators had become the key themes. The research hotspots shifted from model development and food web structure to ecosystem forecasting and resource management, which would provide scientific evidence for ecosystem-based aquatic resource management and the construction of protected area in marine.

We investigated the variations of reef fish assemblages on coral reefs that experience different turbidity regimes, by assessing the association between the vertical extinction coefficient for photosynthetically active radiation (K d PAR ) and communities of fishes and corals at 21 reef sites in La Parguera, southwest Puerto Rico. Statistical correlations and non-metric multidimensional scaling (NMS) identified turbidity as an important environmental parameter affecting ecological processes on coral reefs, as reflected by changes in the composition and abundance of reef fishes and benthic communities. Lower fish density and species richness was found at turbid sites. Turbidity was also negatively correlated to percent coral cover, which together with rugosity, were additional habitat parameters shaping reef fish assemblages. Bluehead wrasse Thalassoma bifasciatum and yellowtail damselfish Microspathodon chrysurus were species rarely present at turbid sites and abundant at clear ones. The yellowtail hamlet Hypoplectrus chlorurus and sharknose goby Elacatinus evelynae had the opposite distribution along the turbidity gradient. We identified seawater turbidity as an additional predictor of the reef fish community structure in La Parguera, in addition to live coral cover and reef rugosity. Because coral reefs and reef fishes were less complex (lower rugosity, less species richness, less diversity) in more turbid sites, managing for clear water conditions within the coastal area of La Parguera should lead to improved ecosystem resilience and stability, and should become a primary goal of management.

Coral reef diversity is correlated with the depth at which the reefs are found, the energy available for biological processes, and the species’ roles and presence throughout the food chain. Can a specific species activity alter the whole ecosystem? Can a small-scale, short-term activity such as fish behaviour have a long-term effect on a larger scale, that of the reef? Can the life stage of a species mediate substrate competition? The three-spot damselfish (Stegastes planifrons) is hypothesized to regulate competition between substrate coverage by actively farming – protecting from herbivores and weeding – in order to regulate the algal species composition and percent coverage of the reef. This behaviour is observed in both juvenile and adult fish. Deeper patches are predicted to have less coral diversity and higher algal diversity; juvenile fish are predicted to have less diversity in their patches than adults. Coral and algal diversity are hypothesized to be negatively correlated. In this study, behaviour of the S. planifrons was classified into one of four categories (active patrolling, passing patrolling, farming, and hiding) and palatable algae surface area coverage was digitized from photographs; life stage was either juvenile or adult. Coral and algal genus diversity were measured along a depth gradient of 0-16 m where the diversity of the reef was thought to be the highest. A three-way ANCOVA was performed to test whether fish behaviour (a small-scale, short-term process), depth, or fish development stage (juvenile or adult) had a significant effect on coral or algal diversity (a large-scale, long-term process). Results showed a significant effect of fish behaviour category on algal genera diversity, and a significant effect of depth on both algal and coral genera diversity. Farming yielded significantly more algal coverage than hiding. This study shows that small-scale, short-term behaviours by S. planifrons can have an effect on algal genera diversity on coral reefs in Utila, Honduras.&#x0D; &#x0D; Keywords: Stegastes planifrons (three-spotted damselfish); behaviours (short-term, small-scale); stage of development (juvenile, adult); depth; coral reef and algal diversity (long-term, large-scale); damselfish territories

Encouraging people’s pro-environmental behaviors is an objective of Education for Sustainable Development. In the context of small-scale fisheries, unsustainable fishing practices are compromising the integrity of coastal communities and ecosystems. Ecopath with Ecosim (EwE) is an ecosystem modeling software that presents interactions/changes in the food web as a result of fishing. Despite the multiple applications of EwE in fisheries management, it is unknown from a quantitative perspective whether the application of EwE trophic modeling in environmental education processes and management produces effects on norms and ecological beliefs, and if it alters behavioral intentions of the participants receiving ecosystem modeling information. We conducted a behavior change intervention with gillnet fishers in the Gulf of Nicoya, Costa Rica, to compare antecedents of pro-environmental behavior between participants who received an ecosystem-based intervention (lectures containing EwE models; treatment) and those who received lectures that didn’t involve EwE (control). Based on theories of environmental psychology, we used a pre–post survey design, to evaluate changes between control/treatment, and to assess the influence of psychometric constructs and fishing characteristics on the behavioral intentions to support sustainable fishing measures and owning a fishing license (revealed behavior). Personal norms and values were significant at explaining management measures’ support, along with some fishing characteristics (e.g., fishing site). Deliberating about possible future scenarios (via EwE-modeling) helped reduce uncertainties, increasing legitimacy and a perceived behavioral control (PBC) to support measures. Currently, licenses in the Gulf aren’t granted under defined ecological criteria, and although altruistic-biospheric values scored highly before the intervention began, due to mistrust and high illegal-unlicensed fishing, fishers may be underestimating how much others care about the environment. Value-oriented and ecosystem-based interventions may assist to effectively redesign the licensing system and encourage fishers to support sustainable measures. Our research indicates the importance of education interventions that teach about the impacts of fishing in the ecosystem while helping participants to perceive themselves as capable of implementing actions (PBC) and expressing biospheric-altruistic values to restore trust. Redirecting human behaviors to reconnect with ecosystem resilience can be a leverage point for sustainability and for the compliance of small-scale fisheries management measures.

That coral reefs are in decline worldwide, particularly in the Caribbean, will come as no surprise. This decades-long decline has reached a potential tipping point as the weight of the effects of climate change have come decidedly to bear on the planet’s most diverse marine ecosystem. Whether coral reefs can persist without restorative intervention is debatable, which has prompted a surge in coral reef restoration projects focusing primarily on the cultivation and transplantation of coral fragments onto degraded reefs. But that widespread approach does little to address the underlying causes of coral loss, one of which is the proliferation of macroalgae that are deleterious to corals. An emerging solution to this problem is the enhancement of herbivory on coral reefs through improved management of herbivores, artificial enhancement of herbivore settlement, or their mariculture and subsequent stocking. This review explores the nuances of the biology of well-studied Caribbean coral reef herbivores (fishes, sea urchins, and crabs) as it relates to their mariculture and investigates the promise of herbivore stocking onto coral reefs as a restoration strategy. Fish, urchin, and crab herbivores differ appreciably in life histories, which confers advantages and disadvantages with respect to their mariculture and effectiveness as grazers. Mariculture of herbivorous marine fish for reef restoration is essentially non-existent so the reestablishment of grazing fish abundance on coral reefs focuses primarily on their protection through fishery regulations, but only at a few locations in the Caribbean. Mariculture of herbivorous urchins and crabs for restoration purposes is in its infancy, but promising especially for crabs whose larval rearing is less difficult. Perhaps the biggest challenge for the mariculture of either taxon is “scaling-up” from research settings to large-scale mariculture needed for stocking. Numerous studies extol the benefits of functional redundancy and complementarity for coral reef ecosystem stability, but whether this principal applies to the restoration of grazing function is untested. We identify gaps in our knowledge of best practices for the restoration of grazing function on coral reefs and conclude with some practical guidance on the establishment of targets for macroalgal reduction, along with strategic advice on grazer stocking in a given reef habitat.

Caribbean coral reefs, particularly those in the Florida Keys, are experiencing significant degradation driven by anthropogenic stressors. The most prominent of these is the phase-shift from coral-dominated to macroalgae-dominated ecosystems. These ecosystems are shaped by complex ecological interactions among reef organisms, with community composition varying between day and night. Many reef species exhibit different behaviors or become cryptic at night, leading to biases in traditional visual surveys and incomplete biodiversity assessments.Environmental DNA (eDNA) has emerged as a transformative tool for biodiversity monitoring. This non-invasive molecular technique captures genetic material (e.g., skin cells, mucus) shed by organisms into their environment, enabling the detection of species presence and the identification of cryptic or elusive species that traditional survey methods might miss. While eDNA has been successfully applied in terrestrial and freshwater ecosystems, its use in marine environments, particularly coral reefs, remains an evolving field.This study represents a novel application of eDNA to explore temporal variations in biodiversity on coral reefs, focusing on differences between diurnal and nocturnal periods in the Florida Keys. The primary objectives of this research are: (1) to investigate potential differences in eDNA profiles between day and night sampling, and (2) to complement traditional visual surveys with genetic data, potentially uncovering hidden species that might otherwise be overlooked. Water samples were collected from 13 reefs across the northern Florida Keys, using a Smith-Root eDNA backpack sampler, during both daylight and nighttime. Samples were filtered through self-preserving filters and analyzed by Jonah Ventures for DNA extraction and sequencing. Three genetic markers (16S, 18S, and COI) were used to characterize biodiversity across samples.This study is innovative in its approach to understanding the full extent of biodiversity on coral reefs by integrating both temporal and genetic dimensions. The comparison of eDNA profiles between day and night sampling periods not only highlights the limitations of current eDNA practices but also underscores the necessity of accounting for temporal biodiversity shifts in monitoring efforts. By facilitating biodiversity assessments during nocturnal periods—when many species are most active—our approach aims to enhance the accuracy and completeness of biodiversity data. Furthermore, by generating genetic data from a broad spectrum of species, including those that are nocturnal or cryptic, this study will contribute to expanding eDNA reference libraries. A more comprehensive reference library enables more accurate species identification, which is essential for improving the reliability and scope of future eDNA studies across diverse marine ecosystems. This is critical for more effective conservation and management of vulnerable coral reef ecosystems.Incorporating eDNA into coral reef monitoring offers a holistic, less invasive, view of species diversity and ecosystem health, providing insights that can inform restoration efforts and conservation strategies. By addressing the often-overlooked nocturnal component of reef biodiversity, this work contributes to a more nuanced understanding of ecosystem dynamics. Ultimately, this research will help refine eDNA methodology in marine environments and guide more targeted conservation and management practices for the coral reefs of the Florida Keys, and similar ecosystems globally.

Ecosystem modelling of data-limited fisheries: How reliable are Ecopath with Ecosim models without historical time series fitting?

Wetland ecosystem status and restoration using the Ecopath with Ecosim (EWE) model

Modeling species invasions in Ecopath with Ecosim: An evaluation using Laurentian Great Lakes models

An original model of the northern Gulf of Mexico using Ecopath with Ecosim and its implications for the effects of fishing on ecosystem structure and maturity