In ecological analyses of species and community distributions there is interest in the nature of their responses to environmental gradients and in identifying the most important environmental variables, which may be used for predicting patterns of biodiversity. Methods such as random forests already exist to assess predictor importance for individual species and to indicate where along gradients abundance changes. However, there is a need to extend these methods to whole assemblages, to establish where along the range of these gradients the important compositional changes occur, and to identify any important thresholds or change points. We develop such a method, called "gradient forest," which is an extension of the random forest approach. By synthesizing the cross-validated R2 and accuracy importance measures from univariate random forest analyses across multiple species, sampling devices, and surveys, gradient forest obtains a monotonic function of each predictor that represents the compositional turnover along the gradient of the predictor. When applied to a synthetic data set, the method correctly identified the important predictors and delineated where the compositional change points occurred along these gradients. Application of gradient forest to a real data set from part of the Great Barrier Reef identified mud fraction of the sediment as the most important predictor, with highest compositional turnover occurring at mud fraction values around 25%, and provided similar information for other predictors. Such refined information allows for more accurate capturing of biodiversity patterns for the purposes of bioregionalization, delineation of protected areas, or designing of biodiversity surveys.

Bottom trawling is the most widespread human activity affecting seabed habitats. Here, we collate all available data for experimental and comparative studies of trawling impacts on whole communities of seabed macroinvertebrates on sedimentary habitats and develop widely applicable methods to estimate depletion and recovery rates of biota after trawling. Depletion of biota and trawl penetration into the seabed are highly correlated. Otter trawls caused the least depletion, removing 6% of biota per pass and penetrating the seabed on average down to 2.4 cm, whereas hydraulic dredges caused the most depletion, removing 41% of biota and penetrating the seabed on average 16.1 cm. Median recovery times posttrawling (from 50 to 95% of unimpacted biomass) ranged between 1.9 and 6.4 y. By accounting for the effects of penetration depth, environmental variation, and uncertainty, the models explained much of the variability of depletion and recovery estimates from single studies. Coupled with large-scale, high-resolution maps of trawling frequency and habitat, our estimates of depletion and recovery rates enable the assessment of trawling impacts on unprecedented spatial scales.

Bottom‐contact fishing gears are globally the most widespread anthropogenic sources of direct disturbance to the seabed and associated biota. Managing these fishing disturbances requires quantification of gear impacts on biota and the rate of recovery following disturbance. We undertook a systematic review and meta‐analysis of 122 experiments on the effects‐of‐bottom fishing to quantify the removal of benthos in the path of the fishing gear and to estimate rates of recovery following disturbance. A gear pass reduced benthic invertebrate abundance by 26% and species richness by 19%. The effect was strongly gear‐specific, with gears that penetrate deeper into the sediment having a significantly larger impact than those that penetrate less. Sediment composition (% mud and presence of biogenic habitat) and the history of fishing disturbance prior to an experimental fishing event were also important predictors of depletion, with communities in areas that were not previously fished, predominantly muddy or biogenic habitats being more strongly affected by fishing. Sessile and low mobility biota with longer life‐spans such as sponges, soft corals and bivalves took much longer to recover after fishing (>3 year) than mobile biota with shorter life‐spans such as polychaetes and malacostracans (<1 year). This meta‐analysis provides insights into the dynamics of recovery. Our estimates of depletion along with estimates of recovery rates and large‐scale, high‐resolution maps of fishing frequency and habitat will support more rigorous assessment of the environmental impacts of bottom‐contact gears, thus supporting better informed choices in trade‐offs between environmental impacts and fish production.

Summary1. Impacts of bottom fishing, particularly trawling and dredging, on seabed (benthic) habitats are commonly perceived to pose serious environmental risks. Quantitative ecological risk assessment can be used to evaluate actual risks and to help guide the choice of management measures needed to meet sustainability objectives. 2. We develop and apply a quantitative method for assessing the risks to benthic habitats by towed bottom-fishing gears. The method is based on a simple equation for relative benthic status (RBS), derived by solving the logistic population growth equation for the equilibrium state. Estimating RBS requires only maps of fishing intensity and habitat type -and parameters for impact and recovery rates, which may be taken from meta-analyses of multiple experimental studies of towed-gear impacts. The aggregate status of habitats in an assessed region is indicated by the distribution of RBS values for the region. The application of RBS is illustrated for a tropical shrimp-trawl fishery. 3. The status of trawled habitats and their RBS value depend on impact rate (depletion per trawl), recovery rate and exposure to trawling. In the shrimp-trawl fishery region, gravel habitat was most sensitive, and though less exposed than sand or muddy-sand, was most affected overall (regional RBS = 91% relative to un-trawled RBS = 100%). Muddy-sand was less sensitive, and though relatively most exposed, was less affected overall (RBS = 95%). Sand was most heavily trawled but least sensitive and least affected overall (RBS = 98%). Region-wide, >94% of habitat area had >80% RBS because most trawling and impacts were confined to small areas. RBS was also applied to the region's benthic invertebrate communities with similar results. 4. Conclusions. Unlike qualitative or categorical trait-based risk assessments, the RBS method provides a quantitative estimate of status relative to an unimpacted baseline, with minimal requirements for input data. It could be applied to bottom-contact fisheries world-wide, including situations where detailed data on characteristics of seabed habitats, or the abundance of seabed fauna are not available. The approach supports assessment against sustainability criteria and evaluation of alternative management strategies (e.g. closed areas, effort management, gear modifications).

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Summary1. Spatial management is used extensively in natural resource management to address sustainability and biodiversity issues, for example through declaration of terrestrial National Parks and marine protected areas (MPAs). 2. Spatial management is used also to optimize yields or protect key parts of the life cycle of species that are utilized (hunted, farmed or fished), for example through rotational harvesting. 3. To evaluate the effectiveness of marine spatial closures with conflicting fisheries and conservation objectives, a series of marine fisheries closures are here analysed using an integrative modelling tool known as management strategy evaluation (MSE). 4. This modelling framework combines a food web model of a tropical ecosystem fished by a prawn (shrimp) fishery that emulates the resource being managed, together with the present management system and risk-based tools of fishing the prawn species at maximum economic yield. 5. A series of spatial closures are designed and tested with the aim of investigating trade-offs among biodiversity (MPA), benthic impacts, ecosystem function, key species at risk to fishing, economic and sustainability objectives. 6. Synthesis and applications. This paper illustrates that existing tools often available in actively managed fisheries can be linked together into an effective management strategy evaluation framework. Spatial closures tended to succeed with respect to their specific design objective, but this benefit did not necessarily flow to other broad-scale objectives. This demonstrates that there is no single management tool which satisfies all objectives, and that a suite of management tools is needed.

Numerous studies have quantified trawl impacts at small scales. However, effective management of trawl impacts requires synthesis of experimental results (biomass depletion per tow and subsequent recovery) and application at fishery scales — realistically, this is achievable only in a modelling framework. We present a method for scaling up experimental results for management applications that incorporates a benthic biomass model having exponential trawl depletion and logistic recovery. Ultra-fine trawl-track data, supported by simulations, show that realistic trawling can be represented by a negative-binomial stochastic process, with intensity governed by large-scale effort and aggregation by a tunable parameter. Two mechanisms of the process are considered: aggregations in space (hot spots) and aggregations in time (hot times), which yields a logistic differential equation for the large-scale biomass over time. The model shows that scaling from fine scale to fishery scale depends on the degree of aggregation of fishing, with increasing aggregation lowering depletion rates at fishery scales. This model is a fundamental step in enabling assessment of large-scale implications and evaluating alternative management strategies.