Resolving ecosystem complexity in ecological risk assessment for mine site rehabilitation.

CONTEXT: Ecological Risk Assessments (ERAs) are important tools for supporting evidence-based decision making. However, most ERA frameworks rarely consider complex ecological feedbacks, which limit their capacity to evaluate risks at community and ecosystem levels of organisation. METHOD: We used qualitative mathematical modelling to add additional perspectives to previously conducted ERAs for the rehabilitation of the Ranger uranium mine (Northern Territory, Australia) and support an assessment of the cumulative risks from the mine site. Using expert elicitation workshops, separate qualitative models and scenarios were developed for aquatic and terrestrial systems. The models developed in the workshops were used to construct Bayes Nets that predicted whole-of-ecosystem outcomes after components were perturbed. RESULTS: The terrestrial model considered the effect of fire and weeds on established native vegetation that will be important for the successful rehabilitation of Ranger. It predicted that a combined intervention that suppresses both weeds and fire intensity gave similar response predictions as for weed control alone, except for lower levels of certainty to tall grasses and fire intensity in models with immature trees or tall grasses. However, this had ambiguous predictions for short grasses and forbs, and tall grasses in models representing mature vegetation. The aquatic model considered the effects of magnesium (Mg), a key solute in current and predicted mine runoff and groundwater egress, which is known to adversely affect many aquatic species. The aquatic models provided support that attached algae and phytoplankton assemblages are the key trophic base for food webs. It predicted that shifts in phytoplankton abundance arising from increase in Mg to receiving waters, may result in cascading effects through the food-chain. CONCLUSION: The qualitative modelling approach was flexible and capable of modelling both gradual (i.e. decadal) processes in the mine-site restoration and the comparatively more rapid (seasonal) processes of the aquatic ecosystem. The modelling also provides a useful decision tool for identifying important ecosystem sub-systems for further research efforts.

Assessing Different Causes of Crown-of-Thorns Starfish Outbreaks and Appropriate Responses for Management on the Great Barrier Reef.

The crown-of-thorns starfish Acanthaster planci (COTS) has contributed greatly to declines in coral cover on Australia's Great Barrier Reef, and remains one of the major acute disturbances on Indo-Pacific coral reefs. Despite uncertainty about the underlying causes of outbreaks and the management responses that might address them, few studies have critically and directly compared competing hypotheses. This study uses qualitative modelling to compare hypotheses relating to outbreak initiation, explicitly considering the potential role of positive feedbacks, elevated nutrients, and removal of starfish predators by fishing. When nutrients and fishing are considered in isolation, the models indicate that a range of alternative hypotheses are capable of explaining outbreak initiation with similar levels of certainty. The models also suggest that outbreaks may be caused by multiple factors operating simultaneously, rather than by single proximal causes. As the complexity and realism of the models increased, the certainty of outcomes decreased, but key areas that require further research to improve the structure of the models were identified. Nutrient additions were likely to result in outbreaks only when COTS larvae alone benefitted from nutrients. Similarly, the effects of fishing on the decline of corals depended on the complexity of interactions among several categories of fishes. Our work suggests that management approaches which seek to be robust to model structure uncertainty should allow for multiple potential causes of outbreaks. Monitoring programs can provide tests of alternative potential causes of outbreaks if they specifically monitor all key taxa at reefs that are exposed to appropriate combinations of potential causal factors.

Mapping Habitats and Developing Baselines in Offshore Marine Reserves with Little Prior Knowledge: A Critical Evaluation of a New Approach.

The recently declared Australian Commonwealth Marine Reserve (CMR) Network covers a total of 3.1 million km2 of continental shelf, slope, and abyssal habitat. Managing and conserving the biodiversity values within this network requires knowledge of the physical and biological assets that lie within its boundaries. Unfortunately very little is known about the habitats and biological assemblages of the continental shelf within the network, where diversity is richest and anthropogenic pressures are greatest. Effective management of the CMR estate into the future requires this knowledge gap to be filled efficiently and quantitatively. The challenge is particularly great for the shelf as multibeam echosounder (MBES) mapping, a key tool for identifying and quantifying habitat distribution, is time consuming in shallow depths, so full coverage mapping of the CMR shelf assets is unrealistic in the medium-term. Here we report on the results of a study undertaken in the Flinders Commonwealth Marine Reserve (southeast Australia) designed to test the benefits of two approaches to characterising shelf habitats: (i) MBES mapping of a continuous (~30 km2) area selected on the basis of its potential to include a range of seabed habitats that are potentially representative of the wider area, versus; (ii) a novel approach that uses targeted mapping of a greater number of smaller, but spatially balanced, locations using a Generalized Random Tessellation Stratified sample design. We present the first quantitative estimates of habitat type and sessile biological communities on the shelf of the Flinders reserve, the former based on three MBES analysis techniques. We contrast the quality of information that both survey approaches offer in combination with the three MBES analysis methods. The GRTS approach enables design based estimates of habitat types and sessile communities and also identifies potential biodiversity hotspots in the northwest corner of the reserve's IUCN zone IV, and in locations close to shelf incising canyon heads. Design based estimates of habitats, however, vary substantially depending on the MBES analysis technique, highlighting the challenging nature of the reserve's low profile reefs, and improvements that are needed when acquiring MBES data for small GRTS locations. We conclude that the two survey approaches are complementary and both have their place in a successful and flexible monitoring strategy; the emphasis on one method over the other should be considered on a case by case basis, taking into account the survey objectives and limitations imposed by the type of vessel, time available, size and location of the region where knowledge is required.

Modelling marine protected areas: insights and hurdles.

Models provide useful insights into conservation and resource management issues and solutions. Their use to date has highlighted conditions under which no-take marine protected areas (MPAs) may help us to achieve the goals of ecosystem-based management by reducing pressures, and where they might fail to achieve desired goals. For example, static reserve designs are unlikely to achieve desired objectives when applied to mobile species or when compromised by climate-related ecosystem restructuring and range shifts. Modelling tools allow planners to explore a range of options, such as basing MPAs on the presence of dynamic oceanic features, and to evaluate the potential future impacts of alternative interventions compared with 'no-action' counterfactuals, under a range of environmental and development scenarios. The modelling environment allows the analyst to test if indicators and management strategies are robust to uncertainties in how the ecosystem (and the broader human-ecosystem combination) operates, including the direct and indirect ecological effects of protection. Moreover, modelling results can be presented at multiple spatial and temporal scales, and relative to ecological, economic and social objectives. This helps to reveal potential 'surprises', such as regime shifts, trophic cascades and bottlenecks in human responses. Using illustrative examples, this paper briefly covers the history of the use of simulation models for evaluating MPA options, and discusses their utility and limitations for informing protected area management in the marine realm.

Qualitative mathematical models to support ecosystem-based management of Australia's Northern Prawn Fishery.

A major decline in the catch of the banana prawn [shrimp], Penaeus (Fenneropenaeus) merguiensis, occurred over a six-year period in the Weipa region of the northeastern Gulf of Carpentaria, Australia. Three main hypotheses have been developed to explain this decline: (1) prawn recruitment collapsed due to overfishing; (2) recruitment collapsed due to a change in the prawn's environment; and (3) adult banana prawns were still present, but fishers could no longer effectively find or catch them. Qualitative mathematical models were used to link population biology, environmental factors, and fishery dynamics to evaluate the alternative hypotheses. This modeling approach provides the means to rapidly integrate knowledge across disciplines and consider alternative hypotheses about how the structure and function of an ecosystem affects its dynamics. Alternative models were constructed to address the different hypotheses and also to encompass a diversity of opinion about the underlying dynamics of the system. Key findings from these analyses are that: instability in the system can arise when discarded fishery bycatch supports relatively high predation pressure; system stability can be enhanced by management of fishing effort or stock catchability; catch per unit effort is not necessarily a reliable indicator of stock abundance; a change in early-season rainfall should affect all stages in the banana prawn's life cycle; and a reduced catch in the Weipa region can create and reinforce a shift in fishing effort away from Weipa. Results from the models informed an approach to test the hypotheses (i.e., an experimental fishing program), and promoted understanding of the system among researchers, management agencies, and industry. The analytical tools developed in this work to address stages of a prawn life cycle and fishery dynamics are generally applicable to any exploited natural. resource.

Quantifying fish assemblages in large, offshore marine protected areas: an Australian case study.

As the number of marine protected areas (MPAs) increases globally, so does the need to assess if MPAs are meeting their management goals. Integral to this assessment is usually a long-term biological monitoring program, which can be difficult to develop for large and remote areas that have little available fine-scale habitat and biological data. This is the situation for many MPAs within the newly declared Australian Commonwealth Marine Reserve (CMR) network which covers approximately 3.1 million km2 of continental shelf, slope, and abyssal habitat, much of which is remote and difficult to access. A detailed inventory of the species, types of assemblages present and their spatial distribution within individual MPAs is required prior to developing monitoring programs to measure the impact of management strategies. Here we use a spatially-balanced survey design and non-extractive baited video observations to quantitatively document the fish assemblages within the continental shelf area (a multiple use zone, IUCN VI) of the Flinders Marine Reserve, within the Southeast marine region. We identified distinct demersal fish assemblages, quantified assemblage relationships with environmental gradients (primarily depth and habitat type), and described their spatial distribution across a variety of reef and sediment habitats. Baited videos recorded a range of species from multiple trophic levels, including species of commercial and recreational interest. The majority of species, whilst found commonly along the southern or south-eastern coasts of Australia, are endemic to Australia, highlighting the global significance of this region. Species richness was greater on habitats containing some reef and declined with increasing depth. The trophic breath of species in assemblages was also greater in shallow waters. We discuss the utility of our approach for establishing inventories when little prior knowledge is available and how such an approach may inform future monitoring efforts within the CMR network.

Assessing model structure uncertainty through an analysis of system feedback and Bayesian networks.

Ecological predictions and management strategies are sensitive to variability in model parameters as well as uncertainty in model structure. Systematic analysis of the effect of alternative model structures, however, is often beyond the resources typically available to ecologists, ecological risk practitioners, and natural resource managers. Many of these practitioners are also using Bayesian belief networks based on expert opinion to fill gaps in empirical information. The practical application of this approach can be limited by the need to populate large conditional probability tables and the complexity associated with ecological feedback cycles. In this paper, we describe a modeling approach that helps solve these problems by embedding a qualitative analysis of sign directed graphs into the probabilistic framework of a Bayesian belief network. Our approach incorporates the effects of feedback on the model's response to a sustained change in one or more of its parameters, provides an efficient means to explore the effect of alternative model structures, mitigates the cognitive bias in expert opinion, and is amenable to stakeholder input. We demonstrate our approach by examining two published case studies: a host-parasitoid community centered on a nonnative, agricultural pest of citrus cultivars and the response of an experimental lake mesocosm to nutrient input. Observations drawn from these case studies are used to diagnose alternative model structures and to predict the system's response following management intervention.

Understanding and predicting effects of modified interactions through a qualitative analysis of community structure.

Models of ecological communities are traditionally based on relationships between pairs of species, where the strengths of per capita interactions are fixed and independent of population abundance. A growing body of literature, however; describes interactions whose strength is modified by the density of either a third species or by one of the species involved in a pairwise interaction. These modified interactions have been treated as indirect effects, and the terminology addressing them is diverse and overlapping. In this paper we develop a general analytical framework based on a qualitative analysis of community structure to account for the consequence of modified interactions in complex ecological communities. Modified interactions are found to create both direct and indirect effects between species. The sign of a direct effect can change in some instances depending on the magnitude of a key variable or parameter, which leads to a threshold change in system structure and dynamics. By considering alternative structures of a community, we extend our ability to model perturbations that move the system far from a previous equilibrium. Using specific examples, we reinterpret existing results, develop hypotheses to guide experiments or management interventions, and explore the role of modified interactions and positive feedback in creating and maintaining alternative stable states. Through a qualitative analysis of community structure, system feedback is demonstrated as being key in understanding and predicting the dynamics of complex ecological communities.

Qualitative modelling of gold mine impacts on Lihir Island's socioeconomic system and reef-edge fish community.

Inhabitants of Lihir Island, Papua New Guinea, have traditionally relied on reef fishing and rotational farming of slash-burn forest plots for a subsistence diet. However, a new gold mine has introduced a cash economy to the island's socioeconomic system and impacted the fringing coral reef through sedimentation from the near-shore dumping of mine wastes. Studies of the Lihirian people have documented changes in population size, local customs, health, education, and land use; studies of the reef have documented impacts to fish populations in mine affected sites. Indirect effects from these impacts are complex and indecipherable when viewed only from isolated studies. Here, we use qualitative modelling to synthesize the social and biological research programs in order to understand the interaction of the human and ecological systems. Initial modelling results appear to be consistent with differences in fish and macroalgae populations in sites with and without coral degradation due to sedimentation. A greater cash flow from mine expansion is predicted to increase the human population, the intensity of the artisanal fishery, and the rate of sewage production and land clearing. Modelling results are being used to guide ongoing research projects, such as monitoring fish populations and artisanal catch and patterns and intensity of land clearing.

Life expectancy change in perturbed communities: derivation and qualitative analysis.

Pollution, loss of habitat, and climate change are introducing dramatic perturbations to natural communities and affecting public health. Populations in perturbed communities can change dynamically, in both abundance and age structure. While analysis of the community matrix can predict changes in population abundance arising from a sustained or press perturbation, perturbations also have the potential to modify life expectancy, which adds yet another means to falsify experimental hypotheses and to monitor management interventions in natural systems. In some instances, an input to a community will produce no change in the abundance of a population but create a major shift in its mean age. We present an analysis of change in both abundance and life expectancy, leading to a formal quantitative assessment as well as qualitative predictions, and illustrate the usefulness of the technique through general examples relating to vector-borne disease and fisheries.

Qualitative stability and ambiguity in model ecosystems.

Qualitative analysis of stability in model ecosystems has previously been limited to determining whether a community matrix is sign stable or not with little analytical means to assess the impact of complexity on system stability. Systems are seen as either unconditionally or conditionally stable with little distinction and therefore much ambiguity in the likelihood of stability. First, we reexamine Hurwitz's principal theorem for stability and propose two "Hurwitz criteria" that address different aspects of instability: positive feedback and insufficient lower-level feedback. Second, we derive two qualitative metrics based on these criteria: weighted feedback (wF(n)) and weighted determinants (wDelta(n)). Third, we test the utility of these qualitative metrics through quantitative simulations in a random and evenly distributed parameter space in models of various sizes and complexities. Taken together they provide a practical means to assess the relative degree to which ambiguity has entered into calculations of stability as a result of system structure and complexity. From these metrics we identify two classes of models that may have significant relevance to system research and management. This work helps to resolve some of the impasse between theoretical and empirical discussions on the complexity and stability of natural communities.