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Regime shifts have been observed in marine ecosystems around the globe. These phenomena can result in dramatic changes in the provision of ecosystem services to coastal communities. Accounting for regime shifts in management clearly requires integrative, ecosystem-based management (EBM) approaches. EBM has emerged as an accepted paradigm for ocean management worldwide, yet, despite the rapid and intense development of EBM theory, implementation has languished, and many implemented or proposed EBM schemes largely ignore the special characteristics of regime shifts. Here, we first explore key aspects of regime shifts that are of critical importance to EBM, and then suggest how regime shifts can be better incorporated into EBM using the concept of integrated ecosystem assessment (IEA). An IEA uses approaches that determine the likelihood that ecological or socio-economic properties of systems will move beyond or return to acceptable bounds as defined by resource managers and policy makers. We suggest an approach for implementing IEAs for cases of regime shifts where the objectives are either avoiding an undesired state or returning to a desired condition. We discuss the suitability and short-comings of methods summarizing the status of ecosystem components, screening and prioritizing potential risks, and evaluating alternative management strategies. IEAs are evolving as an EBM approach that can address regime shifts; however, advances in statistical, analytical and simulation modelling are needed before IEAs can robustly inform tactical management in systems characterized by regime shifts.

Objective To support the movement in marine fisheries management toward ecosystem‐based fisheries management by exploring ecosystem‐level reference points (ELRPs) as an option for managing fisheries at the ecosystem level. An ELRP is an ecosystem harvest level or indicator with one or more associated benchmarks or thresholds (i.e., targets, limits) to identify, monitor, or maintain desirable ecosystem conditions and functions. Methods This paper explores the development and implementation of ELRPs in fisheries management to support ecosystem and fisheries sustainability, help identify when ecosystem changes that impact fisheries resources occur, and foster discussions of trade‐offs in management decisions. Result We organize existing and potential ELRPs into five categories (statistical analysis of nonlinear dynamics and tipping points, ecosystem productivity, ecosystem trophic information, biodiversity, and human dimensions), provide an overview of analytical methods that can estimate ELRP benchmarks, provide examples of where ELRP benchmarks are being used today, and evaluate pros and cons of the different ELRP categories. We also attempt to identify potential next steps for fisheries scientists and managers to further the science, development, and application of ELRPs. Conclusion Ecosystem‐level reference points can be used as a proactive accountability mechanism to achieve ecosystem objectives and maintain the ecosystem in a preferred operating space or as an early warning that ecosystem‐level changes (e.g., tipping points) could be imminent if current biological and ecological trends in the system continue. Impact statement Ecosystem‐level reference points (ELRPs) are a fundamental concept in ecosystem‐based fisheries management (EBFM) that are not currently being used to their full potential. Given the challenges associated with managing fisheries in a changing climate, this paper highlights ELRPs as a tool to advance the field of EBFM in the United States and globally.

Marine food webs are structured through a combination of top-down and bottom-up processes. In coral reef ecosystems, fish size is related to life-history characteristics and size-based indicators can represent the distribution and flow of energy through the food web. Thus, size spectra can be a useful tool for investigating the impacts of both fishing and habitat condition on the health and productivity of coral reef fisheries. In addition, coral reef fisheries are often data-limited and size spectra analysis can be a relatively cost-effective and simple method for assessing fish populations. Abundance size spectra are widely used and quantify the relationship between organism size and relative abundance. Previous studies that have investigated the impacts of fishing and habitat condition together on the size distribution of coral reef fishes, however, have aggregated all fishes regardless of taxonomic identity. This leads to a poor understanding of how fishes with different feeding strategies, body size-abundance relationships, or catchability might be influenced by top-down and bottom-up drivers. To address this gap, we quantified size spectra slopes of carnivorous and herbivorous coral reef fishes across three regions of Indonesia representing a gradient in fishing pressure and habitat conditions. We show that fishing pressure was the dominant driver of size spectra slopes such that they became steeper as fishing pressure increased, which was due to the removal of large-bodied fishes. When considering fish functional groups separately, however, carnivore size spectra slopes were more heavily impacted by fishing than herbivores. Also, structural complexity, which can mediate predator-prey interactions and provisioning of resources, was a relatively important driver of herbivore size spectra slopes such that slopes were shallower in more complex habitats. Our results show that size spectra slopes can be used as indicators of fishing pressure on coral reef fishes, but aggregating fish regardless of trophic identity or functional role overlooks differential impacts of fishing pressure and habitat condition on carnivore and herbivore size distributions.

The oceans are changing more rapidly than ever before. Unprecedented climatic variability is interacting with unmistakable long‐term trends, all against a backdrop of intensifying human activities. What remains unclear, however, is how to evaluate whether conditions have changed sufficiently to provoke major responses of species, habitats, and communities. We developed a framework based on multimodel inference to define ecosystem‐based thresholds for human and environmental pressures in the California Current marine ecosystem. To demonstrate how to apply the framework, we explored two decades of data using gradient forest and generalized additive model analyses, screening for nonlinearities and potential threshold responses of ecosystem states (n = 9) across environmental (n = 6) and human (n = 10) pressures. These analyses identified the existence of threshold responses of five ecosystem states to four environmental and two human pressures. Both methods agreed on threshold relationships in two cases: (1) the winter copepod anomaly and habitat modification, and (2) sea lion pup production and the summer mode of the Pacific Decadal Oscillation (PDO). Considered collectively, however, these alternative analytical approaches imply that as many as five of the nine ecosystem states may exhibit threshold changes in response to negative PDO values in the summer (copepods, scavengers, groundfish, and marine mammals). This result is consistent with the idea that the influence of the PDO extends across multiple trophic levels, but extends current knowledge by defining the nonlinear nature of these responses. This research provides a new way to interpret changes in the intensities of human and environmental pressures as they relate to the ecological integrity of the California Current ecosystem. These insights can be used to make more informed assessments of when and under what conditions intervention, preparation, and mitigation may enhance progress toward ecosystem‐based management goals.

Size spectra are recommended tools for detecting the response of marine communities to fishing or to management measures. A size spectrum succinctly describes how a property, such as abundance or biomass, varies with body size in a community. Required data are often collected in binned form, such as numbers of individuals in 1 cm length bins. Numerous methods have been employed to fit size spectra, but most give biased estimates when tested on simulated data, and none account for the data’s bin structure (breakpoints of bins). Here, we used 8 methods to fit an annual size-spectrum exponent, b, to an example data set (30 yr of the North Sea International Bottom Trawl Survey). The methods gave conflicting conclusions regarding b declining (the size spectrum steepening) through time, and so any resulting advice to ecosystem managers will be highly dependent upon the method used. Using simulated data, we showed that ignoring the bin structure gives biased estimates of b, even for high-resolution data. However, our extended likelihood method, which explicitly accounts for the bin structure, accurately estimated b and its confidence intervals, even for coarsely collected data. We developed a novel visualisation method that accounts for the bin structure and associated uncertainty, provide recommendations concerning different data types and have created an R package (sizeSpectra) to reproduce all results and encourage use of our methods. This work is also relevant to wider applications where a power-law distribution (the underlying distribution for a size spectrum) is fitted to binned data.

Rapid urbanization and growing transportation infrastructure in cities negatively affect ecosystems and their functions. Quantifying these effects is a prerequisite for integrating environmental considerations into all phases of transportation planning. However, in many developing or newly developed countries, research is lacking that helps to understand and manage the ecological impacts of transportation construction under local conditions. Presented research contributed to filling this gap by investigating the implications of growing transportation infrastructure on three ecosystem services: local climate regulation, erosion control, and photosynthesis potential. As a case study, we used spatial indicators to quantify changes in the supply of ecosystem services caused by the development of the 3 rd Bosporus Bridge and its connecting highway in Istanbul, Turkiye. Our results indicate a substantial decrease in ecosystem services close to the transportation infrastructure, including a decrease in local climate regulation (− 5.4%), an increase in erosion (+ 9.4%), and a decline in photosynthesis potential or vegetation health (− 28%). Additionally, hotspots of ES supply change were detected. This study provides a blueprint for planning and impact mitigation studies.

The restoration of degraded lands has received increased attention in recent years and many commitments have been made as part of global and regional restoration initiatives. Well-informed policy decisions that support land restoration, require spatially explicit information on restoration potentials to guide the design and implementation of restoration interventions in the context of limited resources. This study assessed ecosystems indicators of land degradation using a systematic approach that combines field surveys and remote sensing data into a set of multi-criteria analyses to map restoration potentials in the semi-arid areas. The indicators considered were soil organic carbon, erosion prevalence, enhanced vegetation index, Normalized differences water index and the Net Primary productivity. Three classes of restoration potential were established: (1) areas not in need of immediate restoration due low degradation status, (2) areas with high potential for restoration with moderate efforts required and (3) areas in critical need of restoration and require high level of efforts. Of the total area of the study site estimated at 88,344 km2, 59,146.12 km2, or 66.94% of the theoretically recoverable area, was considered suitable for restoration, of which 38% required moderate efforts while 28% require less efforts. The recoverable areas suitable for restoration could be restored through tree planting, soil and water conservation practices, farmers managed natural regeneration, and integrated soil fertility management. These results can help to spatially identify suitable multifunctional restoration and regeneration hotspots as an efficient way to prioritize restoration interventions in the context of limited resources.

The seminal work of Lindeman (1942), 'The trophic-dynamic aspect of ecology' (Ecology 23:399), has been an important starting point for the holistic view of ecosystem trophodynamics, but it was initially seldom applied to marine ecosystems. Over the past 70 years, research on marine trophodynamics has become more widespread, producing a variety of analytical methods, and increasing our understanding of marine ecosystem functioning. Yet difficulties remain in transforming this body of knowledge into operational management of marine ecosystems and marine resources. This Theme Section on 'Trophodynamics in marine ecology' documents recent advances and lessons learned over the past 70 years, and provides an opportunity to reflect on future directions for marine research.

Ecosystem change is an everyday reality, and assessment of its ability to provide men with products and services of the ecosystem (fresh water, climate, soil fertility, etc.), which are necessary for human welfare, is an urgent applied issue. The question as to “whether changes in the loss of biological diversity will affect the functioning of local ecosystems” is attracting increasing attention. In this first paper, we consider modern approaches to ecosystem monitoring. The concept of historical and novel ecosystems, ecosystem resilience, threshold effects, theory-driven restoration, and social–ecological considerations are reviewed. The principles of indication, requirements for indicators, possibilities, and prospects for the use of small mammals as indicators of the dynamics of local ecosystems are considered.

Marine ecosystems are influenced by drivers that operate and interact over multiple scales, resulting in nonlinear or abrupt responses to perturbation. Because of the inherent complexity of marine ecosystems, progress towards an understanding of factors that affect fisheries production will be most efficient if researchers adopt a comparative approach across ecosystems using suites of indicators. The goals of this study were to explore a suite of biomass- and catchbased ecosystem response indicators for 9 northern hemisphere ecosystems relative to indices that capture the influence of fisheries, trophodynamic and environmental drivers, and to compare the relative influence of the triad of drivers. Partial least squares regression was used to explore relationships between the ecosystem response indicators and predictor drivers and to estimate the relative importance of each of the triad of drivers. Across ecosystems we have identified a few common observations: (1) environmental drivers, particularly temperature-related independent variables, are most likely related to total system biomass and biomass of specific biological groups (e.g. gadoid or clupeid fishes); (2) trophodynamic drivers are most relevant to the mean trophic level of community and the demersal-to-pelagic biomass ratio; and (3) fisheries drivers tend to be related to the catch-based indicators, such as fishing-in-balance and percent of primary production required to support fisheries. Overall, each of the triad of drivers was important for all ecosystems; however, the relative importance of each driver and the indicators they most affected varied among ecosystems, suggesting that an examination of a suite of indicators and drivers is required. A key finding is that fishing is categorically an important driver, but to explain biomass trends it is very important to consider environmental drivers as well.