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Distributional shifts in species ranges provide critical evidence of ecological responses to climate change. Assessments of climate-driven changes typically focus on broad-scale range shifts (e.g. poleward or upward), with ecological consequences at regional and local scales commonly overlooked. While these changes are informative for species presenting continuous geographic ranges, many species have discontinuous distributions-both natural (e.g. mountain or coastal species) or human-induced (e.g. species inhabiting fragmented landscapes)-where within-range changes can be significant. Here, we use an ecosystem engineer species (Sabellaria alveolata) with a naturally fragmented distribution as a case study to assess climate-driven changes in within-range occupancy across its entire global distribution. To this end, we applied landscape ecology metrics to outputs from species distribution modelling (SDM) in a novel unified framework. SDM predicted a 27.5% overall increase in the area of potentially suitable habitat under RCP 4.5 by 2050, which taken in isolation would have led to the classification of the species as a climate change winner. SDM further revealed that the latitudinal range is predicted to shrink because of decreased habitat suitability in the equatorward part of the range, not compensated by a poleward expansion. The use of landscape ecology metrics provided additional insights by identifying regions that are predicted to become increasingly fragmented in the future, potentially increasing extirpation risk by jeopardising metapopulation dynamics. This increased range fragmentation could have dramatic consequences for ecosystem structure and functioning. Importantly, the proposed framework-which brings together SDM and landscape metrics-can be widely used to study currently overlooked climate-driven changes in species internal range structure, without requiring detailed empirical knowledge of the modelled species. This approach represents an important advancement beyond predictive envelope approaches and could reveal itself as paramount for managers whose spatial scale of action usually ranges from local to regional.

Joint Species Distribution Models (jSDM) are increasingly used to explain and predict biodiversity patterns. jSDMs account for species co-occurrence patterns and can include phylogeny or functional traits to better capture the processes shaping communities. Yet, several factors may limit or affect the interpretability and predictive ability of jSDMs : missing abiotic predictors, omitting ecologically-important species, or increasing the number of model parameters by adding phylogeny and/or trait information.We assessed how interpretability, explanatory and predictive power of jSDM varied across four alternative models focusing on 99 coastal benthic marine polychaete species: (1) a baseline jSDM with no additional information sources other than abiotic predictors and residual co-occurrence patterns, (2) a jSDM including phylogeny alone or (3) in combination with traits data and (4) a jSDM including monitoring information related to additional species sampled alongside the target assemblage (i.e. non-target species that are not of direct interest but potentially interact with the target assemblage). The four models fitted on both presence/absence and abundance data from a regional monitoring programme were assessed using complementary metrics. We compared performance at both species- and community-level, considering multiple facets of species responses and assemblage diversity.For both presence/absence and abundance data, all models displayed good and similar explanatory power but varied in their interpretability and predictive power. Considering trait data provides insights on species response along environmental gradients, which is a decisive element for model interpretability. Relative to the baseline model, predictive power increased by 26% when including data on additional species, whereas only marginal changes were detected for the two other models. These patterns are explained by changes in the species-environment relationships and residual co-occurrence patterns inferred by these models.Overall, this study highlights that adequate strategy to fit jSDM depends on data at hand, modelling objective and research question. To understand observed community space-time variability, adding phylogenetic or trait information is most effective. Inclusion of non-target species is however a better strategy to predict how the target species assemblage responds to environmental changes. Importantly, we provide a comprehensive toolbox for the comparative assessment of jSDM performance.

Ecosystem-based approaches are increasingly used in fisheries management to account for the direct trophic impacts of fish population harvesting. However, fisheries can also indirectly alter ecosystem structure and functioning, for instance via the provision of new feeding opportunities to marine predators. For instance, marine depredation, where predators feed on fishery catches on fishing gear, is a behaviour developed by many marine species globally. This behaviour can modify both the ecological role of predators and fisheries performance. Yet, these ecosystem-wide effects of depredation are rarely considered holistically. In this study, we explored different ways of incorporating depredation into an Ecopath trophic model. We assessed, through a subantarctic case study, how three alternative model structures can account for depredation effects on fishery catches, predator and non-commercial prey populations, as well as target fish stocks. While none adequately addresses all facets of depredation, the alternative models can to some extent capture how depredation can lead to increased fishing pressure on stocks. As structural specificities of Ecopath prevented us from representing other depredation effects such as provisioning effects for predator populations, we conclude this study with a set of guidance to effectively capture the complex effects of depredation in marine ecosystems and fisheries models.

Climate-driven changes in ocean currents have facilitated the range extension of the long-spined sea urchin (Centrostephanus rodgersii) from Australia’s mainland to eastern Tasmania over recent decades. Since its arrival, the destructive grazing of the urchin has led to widespread formation of sea urchin ‘barrens’. The loss of habitat, biodiversity and productivity for important commercial reef species in conjunction with the development of an urchin fishery has led to conflicting objectives among some stakeholders that pose complex challenges for regional management. Stakeholders representatives and managers were engaged via a participatory workshop and subsequent one-on-one surveys to trial a structured decision making process to identify effective ecosystem-based management strategies. We directly and indirectly elicited each preferences for nine alternative management strategies by presenting them with the 10-year consequences of each strategy estimated from an ecosystem model of Tasmanian reef communities. These preferences were included in cost-effectiveness scores that were averaged (across stakeholders) to enable strategy ranking from most to least cost-effective. Rankings revealed strategies that included sea urchin removal or translocation of predatory lobsters were the most cost-effective. However, assessment of stakeholders’ individual cost-effectiveness scores showed some disparity among preferences in high ranking strategies. Additionally, inconsistencies in strategy preferences using alternative (direct or indirect) ranking scores reveal conflicting objectives as the most plausible explanation. Our study illustrates how structured decision making can effectively facilitate ecosystem-based management by engaging stakeholders step-by-step towards management strategy implementation and promoting collective learning.

Aim To investigate some of the environmental variables underpinning the past and present distribution of an ecosystem engineer near its poleward range edge. Location >500 locations spanning >7,400 km around Ireland. Methods We collated past and present distribution records on a known climate change indicator, the reef‐forming worm Sabellaria alveolata (Linnaeus, 1767) in a biogeographic boundary region over 182 years (1836–2018). This included repeat sampling of 60 locations in the cooler 1950s and again in the warmer 2000s and 2010s. Using species distribution modelling, we identified some of the environmental drivers that likely underpin S. alveolata distribution towards the leading edge of its biogeographical range in Ireland. Results Through plotting 981 records of presence and absence, we revealed a discontinuous distribution with discretely bounded sub‐populations, and edges that coincide with the locations of tidal fronts. Repeat surveys of 60 locations across three time periods showed evidence of population increases, declines, local extirpation and recolonization events within the range, but no evidence of extensions beyond the previously identified distribution limits, despite decades of warming. At a regional scale, populations were relatively stable through time, but local populations in the cold Irish Sea appear highly dynamic and vulnerable to local extirpation risk. Contemporary distribution data (2013–2018) computed with modelled environmental data identified specific niche requirements which can explain the many distribution gaps, namely wave height, tidal amplitude, stratification index, then substrate type. Main conclusions In the face of climate warming, such specific niche requirements can create environmental barriers that may prevent species from extending beyond their leading edges. These boundaries may limit a species’ capacity to redistribute in response to global environmental change.

Although colonization of artificial structures by epibenthic communities is well-documented overall, our understanding of colonization processes is largely limited to low-energy environments. In this study, we monitored epibenthic colonization of different structures associated with a tidal energy test site located in a high-energy hydrodynamic environment. Using four years of image-based underwater surveys, we characterized changes through space and time in the taxonomic composition of epibenthic assemblages colonizing two kinds of artificial structures, as well as the surrounding natural habitat. Our results highlight that ecological successions followed similar trends across the two artificial habitats, but that different habitat-specific communities emerged at the end of our survey. Deployment of these artificial structures resulted in the addition of elevated and stable substrata in an environment where natural hard substrates are unstable and strongly exposed to sediment abrasion. Although epibenthic communities colonizing artificial habitats are unlikely to have reached a mature stage at the end of our survey, these supported structurally complex taxa facilitating an overall increase in local diversity. We were able to quantify how epibenthic communities can significantly vary over time in high-energy coastal environment, and our final survey suggests that the ecological succession was still in progress five years after the deployment of artificial reefs. Thus, maintaining long-term continuous survey of coastal artificial reef habitats will be key to better discriminate between long-term ecological successions and shorter-term variability.

An increasing number of offshore structures are being deployed worldwide to meet the growing demand for renewable energy. Besides energy production, these structures can also provide new artificial habitats to a diversity of fish and crustacean species. This study characterises how concrete mattresses that stabilise the submarine power cable of a tidal energy test site can increase habitat capacity for benthic megafauna. A five-year monitoring, which relied on both visual counts and video-based surveys by divers, revealed that these mattresses provide a suitable habitat for 5 taxa of large crustaceans and fish. In particular, two commercially valuable species, i.e. the edible crab Cancer pagurus and the European lobster Homarus gammarus, showed a constant occupancy of these artificial habitats throughout the course of the project. The shape and the number of shelters available below individual mattresses largely determine potential for colonisation by mobile megafauna. Local physical characteristics of the implantation site (e.g. substratum type, topography, exposition to current etc.) significantly impact amount and type of shelters provided by the concrete mattresses. Thus, to characterise habitat potential of artificial structures, it is not only essential to consider (i) the design of the structures, but also to (ii) account for their interactions with local environmental conditions when deployed on the seafloor.

Underwater imagery is increasingly used as an effective and repeatable method to monitor benthic ecosystems. Nevertheless, extracting ecologically relevant information from a large amount of raw images remains a time-consuming and somewhat laborious challenge. Thus, underwater imagery processing needs to strike a compromise between time-efficient image annotation and accuracy in quantifying benthic community composition. Designing and implementing robust image sampling and image annotation protocols are therefore critical to rationally address these trade-offs between ecological accuracy and processing time. The aim of this study was to develop and to optimize a reliable image scoring strategy based on the point count method using imagery data acquired on tide-swept macroepibenthic communities. Using a stepwise approach, we define an underwater imagery processing protocol that is effective in terms of (i) time allocated to overall image, (ii) reaching a satisfactory accuracy to estimate the occurrence of dominant benthic taxa, and (iii) adopting a sufficient taxonomic resolution to describe changes in community composition. We believe that our method is well adapted to investigate the composition of epibenthic communities on artificial reefs and can be useful in surveying colonization of other human structures (wind turbine foundations, pipelines, etc.) in coastal areas. Our strategy meets the increasing demand for inexpensive and time-effective tools for monitoring changes in benthic communities in a context of increasing coastal artificialization pressures.

Imagery collected from Autonomous Underwater Vehicles (AUVs) provides a novel means of monitoring changes in benthic ecosystems over large spatial scales and depth ranges. However, for many benthic ecosystems there is little baseline data to quantify temporal and spatial variance for key indicator species. This information is crucial for isolating background “noise” from long-term “signals”. Here we quantify components of variance for five key deep-water sessile invertebrate species across four long-term benthic monitoring sites in a region undergoing strong climate-driven changes. We use linear mixed models to estimate the contribution of sources of spatial and temporal variance in species covers from empirical data. We then combine this information with projected long-term climate-driven changes in the cover of these groups and test the power of various survey designs to detect change through time. Large short-term temporal and spatial variability in the cover of a gorgonian octocoral results in high components of variance that limit the detectability of the projected long-term trend for this species. Conversely, for three of the sponge species high power is achievable with revisits to the four original sites every two years until 2060. By including more sites in the revisit design, high power can be achieved with less frequent revisits. For the fifth species, we find high power is unachievable due to the small trend predicted. Overall, we highlight how examination of components of variance in a system can aid in the selection of suitable indicators and the establishment of effective monitoring programs.

Policy- and decision-makers require assessments of status and trends for marine species, habitats, and ecosystems to understand if human activities in the marine environment are sustainable, particularly in the face of global change. Central to many assessments are statistical and dynamical models of populations, communities, ecosystems, and their socioeconomic systems and management frameworks. The establishment of a national system that could facilitate the development of such model-based assessments has been identified as a priority for addressing management challenges for Australia’s marine environment. Given that most assessments require cross-scale information, individual models cannot capture all of the spatial, temporal, biological, and socioeconomic scales that are typically needed. Coupling or integrating models across scales and domains can expand the scope for developing comprehensive and internally consistent, system-level assessments, including higher-level feedbacks in social–ecological systems. In this article, we summarize: (i) integrated modelling for marine systems currently being undertaken in Australia, (ii) methods used for integration and comparison of models, and (iii) improvements to facilitate further integration, particularly with respect to standards and specifications. We consider future needs for integrated modelling of marine social–ecological systems in Australia and provide a set of recommendations for priority focus areas in the development of a national approach to integrated modelling. These recommendations draw on—and have broader relevance for—international efforts around integrated modelling to inform decision-making for marine systems.

Deep reef assemblages in south-eastern Australia are poorly described, and have been surveyed by only a few studies conducted over small spatial scales. Here, we characterise the composition of deep (~30-90 m depth) sessile invertebrate communities from sub-tropical (27°S) to temperate eastern Australia (43°S). We estimated the cover of 51 preselected invertebrate types from over 1700 seafloor images collected by an autonomous underwater vehicle from >105 km of transects across the study region. Seafloor images were assessed using 3 alternative schemes reflecting different resolution of benthic invertebrate groupings, including the broad- level Collaborative and Automated Tools for Analysis of Marine Imagery project (‘CATAMI’) classification recently developed as a generic scoring approach for seafloor imagery. Ordination using canonical analysis of principal coordinates indicated a clear latitudinal gradient in benthic community composition and, particularly when based on individual morphotypes, 3 distinct community types (sub-tropical, warm temperate and cool temperate). Changes in community structure mostly correlated with primary productivity and the temperature climatology, while local-scale variability in community composition was most related to depth. Along with the gradual shift in deep reef community composition across latitudes, region-specific sessile invertebrates might serve as useful indicators of change in these deep benthic communities under future changes in ocean climate in the region, which has been identified as a global hotspot for ocean warming. Our methodological approach has general applicability for large-scale surveying and monitoring of benthic communities using underwater imagery.

Climate-driven changes in ocean currents have facilitated the range extension of the long-spined sea urchin (Centrostephanus rodgersii) from Australia's mainland to eastern Tasmania over recent decades. Since its arrival, destructive grazing by the urchin has led to widespread formation of sea urchin 'barrens'. The loss of habitat, biodiversity and productivity for important commercial reef species in conjunction with the development of an urchin fishery has led to conflicting objectives among stakeholders, which poses complex challenges for regional management. Stakeholder representatives and managers were engaged via a participatory workshop and subsequent one-on-one surveys to trial a structured decision-making process to identify effective ecosystem-based management strategies. We directly and indirectly elicited each stakeholder's preferences for nine alternative management strategies by presenting them with the 10-year consequences of each strategy estimated from an ecosystem model of Tasmanian reef communities. These preferences were included in cost-effectiveness scores that were averaged (across stakeholders) to enable strategy ranking from most to least cost-effective. Rankings revealed strategies that included sea urchin removal or translocation of predatory lobsters were the most cost-effective. However, assessment of stakeholders' individual cost-effectiveness scores showed some disparity among stakeholders' preferences in high ranking strategies. Additionally, evaluating inconsistencies within some stakeholders' scores that included direct or indirect preferences revealed conflicting objectives and cognitive bias as the most plausible explanations for these inconsistencies. Our study illustrates how structured decision-making can effectively facilitate ecosystem-based management by engaging stakeholders step-by-step towards management strategy implementation, identifying psychological barriers to decision-making and promoting collective learning.

[Departement_IRSTEA]Eaux [TR1_IRSTEA]QUASARE [ADD1_IRSTEA]Dynamique et fonctionnement des écosystèmes; International audience; Trophic ecology is the study of feeding interactions and food acquisition by organisms. It includes the causes and consequences of those behaviours at all levels of biological organisation. As a field of research, it crosses many disciplinary boundaries and provides knowledge that is pertinent to many other areas of ecology. Here we list and categorise the methods available to trophic ecologists whose toolbox has broadened considerably in recent years. They encompass empirical and numerical approaches with focus ranging from molecules to ecosystems. We further examine the relationship of each method to features such as the scale of observation (from microbes to largest organisms) and organisational level (from individuals to ecosystems) as well as the ecological question the method is capable of answering (from detecting predator-prey relationships to studying implications and consequences at different scales). Our survey reveals a very wide range of methodologies, each more-or-less appropriate for a particular line of research. It also identifies deficits, for example, trophic interactions at microscopic scales, for which empirical methods have hardly been used, as well as trophic models that have failed to consider fluxes at the ecosystem scale. Furthermore, we note that the combination of methodologies remains under-exploited despite great opportunities to solve complex ecological questions and to foster the emergence of new insights and hypotheses regarding organism, population and/or ecosystem properties.

Here we argue that there are two important steps in the decision process to restore ecological system that are often ignored. First, consideration of restoration is in response to observed change in a system, but ecological systems can fluctuate widely in their normal dynamic. Thus, there is an imperative to interpret ecological change; shifts in community structure that represent "typical" fluctuations in a properly functioning ecosystem do not warrant restoration, while change associated with phase shift in the system may well demand restoration action. Second, where restoration effort is warranted, it needs to be determined whether management responses are likely to be successful within resource constraints. Where ecological change involves pronounced hysteresis, even massive effort may have little chance in effecting recovery to a preferred ecosystem state. Theory and models indicate that consideration of the characteristic length scales (CLSs) of ecological systems provides an unambiguous interpretation of ecological change, enabling differentiation of "typical" fluctuations from phase shift, and here we show that CLSs can be calculated for real communities from their species’ dynamics, and that their behavior is as predicted from theory. We also show that for ecological systems where local interactions and forcings are well understood, validated simulation models can provide a ready means to identify hysteresis and estimate its magnitude. We conclude that there are useful tools available for ecologists to address the key questions of (1) whether restoration attempts are warranted in the first place and, if they are, (2) whether it is practical to pursue them.

Remote underwater vehicles are cutting-edge tools for mapping benthic habitats, yet their reliability for detecting patterns in abundance of benthic species remains largely unexplored. Here, we use a stereo-imaging AUV to investigate changes in abundance of the overgrazing sea urchin, Centrostephanus rodgersii , which has undergone climate driven range-extension to Tasmania. As part of ongoing bi-yearly monitoring of urchin impacts (June 2009–2013), the benthic stereo-imaging AUV ( Sirius ) surveyed fixed geo-referenced 25 × 25 m plots (625 m 2 ) on deep "urchin barrens" (25–30 m depth) and shallow barren/kelp transition zones (8–16 m) at two sites at St. Helens, northeast Tasmania (−41.25; 148.34). Coincident with initial AUV deployments, urchin abundance was also estimated in the same reef plots using conventional SCUBA diver belt-transects; with comparison of AUV and diver sampling showing AUV-derived estimates to be ∼ 40% lower; while additional AUV sampling at night (high risk for divers in deep water) detected abundances only ∼16% lower than that measured by daytime divers, demonstrating strong nocturnal emergence of C. rodgersii . Importantly, patterns in C. rodgersii abundance across reefs and depths were similar between methods; and long-term population trends were concordant between diver and AUV methods. At finer-scales, AUV detections were compromised where remnant kelp canopies obscured urchins, indicating divers to be superior for detecting early-warning of population increases within intact kelp beds. Comparison of C. rodgersii with two other macro-invertebrates (sea cucumber Australostichopus mollis and sea urchin Heliocidaris erythrogramma ) revealed that while stereo-imaging AUVs can detect space/time variability in macro-invertebrate abundance, detectability is highly dependent on local ecologies and species-specific behaviours.

The effects of climate-driven ocean change on reef habitat-forming species are diverse1,2 and can be deleterious to the structure and functioning of seafloor communities3–5. Although responses of shallow coral- or seaweed-based reef communities to environmental changes are a focus of ecological research in the coastal zone1,4–6, the ecology of habitat-forming organisms on deeper mesophotic reefs remains poorly known. These reefs are typically highly biodiverse7,8 and productive as a result of massive nutrient recycling9. Based on seafloor imagery obtained from an autonomous underwater vehicle8, we related change in community composition on deep reefs (30–90 m) across a latitudinal gradient (25–45° S) in southeastern Australia to high-resolution environmental and oceanographic data, and predicted future changes using downscaled climate change projections for the 2060s10–12. This region is recognized as a global hotspot for ocean warming13. The models show an overall tropicalization trend in these deep temperate reef communities, but different functional groups associate differentially to environmental drivers and display a diversity of responses to projected ocean change. We predict the emergence of novel deep-reef assemblages by the 2060s that have no counterpart on reefs today, which is likely to underpin shifts in biodiversity and ecosystem functioning. Deep reefs and their inhabitants are diverse, but environmental change, in particular warming, will cause these reefs found along southeastern Australia to tropicalize with different responses across functional groups, resulting in novel communities by the 2060s.

As climate-driven environmental changes and anthropogenic perturbations increasingly affect ecological systems, the number of abrupt phase shifts in ecosystem dynamics is rising, with far-reaching ecological, economic and social effects. These shifts are notoriously difficult to study, anticipate and manage. Although indicators of impending phase shifts in ecosystems have been described theoretically, they have only been observed empirically either after the fact or under controlled experiments. Here we demonstrate the usefulness of case-specific simulation models to estimate tipping points in the dynamics of real ecological systems, characterise how these thresholds may vary depending on local conditions and derive safe management targets associated with low risk of undesirable phase shifts. Under the combined effects of ocean changes and fishing, inshore rocky reefs in eastern Tasmania can transition from dense seaweed beds to sea urchin ‘barrens’ habitat, realising severe local loss of habitat, productivity and valuable fisheries. Using Monte-Carlo simulations with a validated model that realistically captures reef dynamics, we characterise the hysteresis in community dynamics and the variability in ecological thresholds along the gradient of environmental conditions. Simulation suggests that prevention of ongoing sea urchin destructive grazing of macroalgal beds is achievable but the yet-to-be-observed restoration of seaweed beds from extensive sea urchin barrens is highly unlikely. To guide management against undesirable phase shifts, we define target points associated with low risk of widespread barrens formation and show that, along with sea urchin culling, recognising the role of lobsters in mitigating sea urchin destructive grazing through predation is key to maintain reef productivity.

Long-term shifts in environmental conditions driven by climate change are predicted to persistently modify the distribution of a multitude of species. These range shifts can have significant effects on the functioning of ecological communities. Ocean warming along the southeast coast of Australia has seen a polewards shift in the distribution of the long-spined sea urchin Centrostephanus rodgersii. Barren areas formed by the destructive overgrazing of kelp beds by invading C. rodgersii are associated with a dramatic loss of habitat, species diversity and productivity. The ongoing range expansion of C. rodgersii will further increase sea urchin densities along the south eastern coast of Tasmania, where ‘incipient’ barrens have started to appear. As restoration of sea urchin barrens over a large-scale is costly and hard to achieve, effective management needs to focus on preventing further formation of extensive barrens. This study examines whether systematic culling of C. rodgersii in spatially discrete areas is effective to control their abundance. We show that systematic culling was highly effective in significantly reducing the mean density and aggregation of urchins in a discrete area which persisted for at least 12 months. Notably, there was no significant difference in the reduction of urchin density and aggregation when plots were culled twice rather than once. There was however an edge effect indicating a slow incursion of urchins back into the treatment plots. We also show that divers follow a classic prey-predator interaction with culling efficiency increasing with urchin density. Ultimately our results demonstrate that systematic culling is an effective method for controlling urchin abundance in discrete areas. The high cost and logistical constraints limit the application of a culling programme over large areas of reef. Culling, therefore, needs to be considered along with other management measures to control the effects of overgrazing by urchins over large scales.

As a consequence of global climate-driven changes, marine ecosystems are experiencing polewards redistributions of species - or range shifts - across taxa and throughout latitudes worldwide. Research on these range shifts largely focuses on understanding and predicting changes in the distribution of individual species. The ecological effects of marine range shifts on ecosystem structure and functioning, as well as human coastal communities, can be large, yet remain difficult to anticipate and manage. Here, we use qualitative modelling of system feedback to understand the cumulative impacts of multiple species shifts in south-eastern Australia, a global hotspot for ocean warming. We identify range-shifting species that can induce trophic cascades and affect ecosystem dynamics and productivity, and evaluate the potential effectiveness of alternative management interventions to mitigate these impacts. Our results suggest that the negative ecological impacts of multiple simultaneous range shifts generally add up. Thus, implementing whole-of-ecosystem management strategies and regular monitoring of range-shifting species of ecological concern are necessary to effectively intervene against undesirable consequences of marine range shifts at the regional scale. Our study illustrates how modelling system feedback with only limited qualitative information about ecosystem structure and range-shifting species can predict ecological consequences of multiple co-occurring range shifts, guide ecosystem-based adaptation to climate change and help prioritise future research and monitoring.

While they can be useful tools to support decision-making in ecosystem management, robust simulation models of ecosystems with alternative states are challenging to build and validate. Because of the possibility of alternative states in model dynamics, no trivial criteria can provide reliable and useful metrics to assess the goodness-of-fit of such models. This paper outlines the development of the model TRITON, and presents simulation-based validation and analysis of model sensitivity to input parameters. TRITON captures the local dynamics of seaweed-based rocky reef communities in eastern Tasmania, which now occur in two alternative persistent states: (1) either as dense and productive seaweed beds, (2) or as sea urchin ‘barrens’ habitat, i.e. bare rock largely denuded of macroalgae and benthic invertebrates due to destructive grazing by sea urchins. Pattern-oriented-modelling, i.e. comparing patterns in model dynamics across Monte–Carlo simulations with direct observations of Tasmanian reef communities over large scales, provides a valuable approach to calibrate the dynamics of TRITON. Using the computationally efficient, model-independent extended Fourier amplitude sensitivity test, we identify fishing down of predatory lobsters, sea urchin recruitment rate, as well as seaweed growth rate as key parameters of influence on overall model behaviour. Through a set of independent sensitivity tests, we isolate different sets of drivers facilitating the ‘forward’ shift from the seaweed bed to the urchin-dominated state, and the reverse or ‘backward’ shift from denuded sea urchin barren to recovery of seaweed cover. The model suggests that rebuilding populations of large rock lobsters, which predate the urchins, will be effective in limiting ongoing formation of sea urchins barrens habitat, but that the chances of restoring seaweed beds from extensive barrens are relatively low if management relies solely on rebuilding stocks of large rock lobsters. Moreover, even when it does occur, seaweed bed restoration takes up to three decades in the simulations and so is arguably unrealistic to implement under short-term fishery management plans. The process of model validation provided both a better understanding of the key drivers of community dynamics (e.g. fishing of predatory lobsters), and an assessment of priority areas for future research.

Large marine animals may play a crucial role in storing and recycling bioavailable iron in surface waters by consuming iron-rich prey and subsequent defecation of iron that is excess to their requirements. This biological recycling of iron could enhance primary productivity in iron-limited waters. However, quantifying the effects of marine animals on ocean primary productivity remains challenging because of a limited understanding of the key biogeochemical processes involved. In this paper, we develop a preliminary model that explores these uncertainties and examines the potential effects of historical populations of blue, fin and humpback whales, and the biomass of Antarctic krill required to support the whale populations, on primary productivity in the Southern Ocean. Our results suggest that, despite conservative estimates for key processes in our model, pre-exploitation populations of blue whales and, to a lesser extent fin and humpback whales, could have contributed to iron recycling, resulting in enhanced phytoplankton production in iron-limited Southern Ocean waters. Iron-rich defecation by un-exploited whale populations in the Southern Ocean, and the biomass Antarctic krill required to support them, could have resulted in a contribution to primary productivity of between 1.5 × 10 −4 to 23.4 g C m −2 yr −1 (blue whales), 1.4 × 10 −4 to 13.9 g C m −2 yr −1 (fin whales), and 2.4 × 10 −5 to 1.7 g C m −2 yr −1 (humpback whales). However, only when all parameter estimates are at their upper limits does there appear to be this significant role for whales in enhancing primary productivity, and thus we need to assess the likelihood of these values arising. The high degree of uncertainty around the magnitude of these increases in primary productivity is mainly due to our limited quantitative understanding of key biogeochemical processes. To reduce uncertainty regarding the effect of whales on Southern Ocean primary productivity, future research will need to refine our understanding of five influential model parameters: iron content in krill; krill consumption rates by whales; persistence of whale faecal iron in the photic zone; bioavailability of this retained iron; and the carbon-to-iron ratio of phytoplankton.

Low-trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.

The individual-based trophic model Osmose is applied to the upwelling marine ecosystem off the coast of Peru. The dynamics and life cycle of eight major species of the Peruvian marine ecosystem are explicitly considered in the model. Reference simulations provide an overview of the trophic structure of the Peruvian ecosystem during the period 2000–2006. Results of model calibration and simulations are discussed in the light of current empirical knowledge on the trophic functioning of the Peruvian ecosystem and are compared to outputs obtained recently using the trophic model Ecopath. The impacts on the ecosystem of restoration plans for the depleted hake ( Merluccius gayi peruanus ) population are explored through two management scenarios: a) a long term reduction of fishing effort targeting hake and b) a moratorium on the hake fishery. The simulations help better understand the recent failure of a 20 month hake moratorium and provide long-term strategic support to ecosystem-based management. Limits of our approach are discussed and recommendations are detailed for future developments of the Osmose model and ecosystem approach to fishery management in the Peruvian context.