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
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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 trawling is widespread globally and impacts seabed habitats. However, risks from trawling remain unquantified at large scales in most regions. We address these issues by synthesizing evidence ...on the impacts of different trawl-gear types, seabed recovery rates, and spatial distributions of trawling intensity in a quantitative indicator of biotic status (relative amount of pretrawling biota) for sedimentary habitats, where most bottom-trawling occurs, in 24 regions worldwide. Regional average status relative to an untrawled state (=1) was high (>0.9) in 15 regions, but <0.7 in three (European) regions and only 0.25 in the Adriatic Sea. Across all regions, 66% of seabed area was not trawled (status = 1), 1.5% was depleted (status = 0), and 93% had status > 0.8. These assessments are first order, based on parameters estimated with uncertainty from meta-analyses; we recommend regional analyses to refine parameters for local specificity. Nevertheless, our results are sufficiently robust to highlight regions needing more effective management to reduce exploitation and improve stock sustainability and seabed environmental status-while also showing seabed status was high (>0.95) in regions where catches of trawled fish stocks meet accepted benchmarks for sustainable exploitation, demonstrating that environmental benefits accrue from effective fisheries management. Furthermore, regional seabed status was related to the proportional area swept by trawling, enabling preliminary predictions of regional status when only the total amount of trawling is known. This research advances seascape-scale understanding of trawl impacts in regions around the world, enables quantitative assessment of sustainability risks, and facilitates implementation of an ecosystem approach to trawl fisheries management globally.
The Great Barrier Reef (GBR) provides a globally significant demonstration of the effectiveness of large-scale networks of marine reserves in contributing to integrated, adaptive management. ...Comprehensive review of available evidence shows major, rapid benefits of no-take areas for targeted fish and sharks, in both reef and nonreef habitats, with potential benefits for fisheries as well as biodiversity conservation. Large, mobile species like sharks benefit less than smaller, site-attached fish. Critically, reserves also appear to benefit overall ecosystem health and resilience: outbreaks of coral-eating, crown-of-thorns starfish appear less frequent on no-take reefs, which consequently have higher abundance of coral, the very foundation of reef ecosystems. Effective marine reserves require regular review of compliance: fish abundances in no-entry zones suggest that even no-take zones may be significantly depleted due to poaching. Spatial analyses comparing zoning with seabed biodiversity or dugong distributions illustrate significant benefits from application of best-practice conservation principles in data-poor situations. Increases in the marine reserve network in 2004 affected fishers, but preliminary economic analysis suggests considerable net benefits, in terms of protecting environmental and tourism values. Relative to the revenue generated by reef tourism, current expenditure on protection is minor. Recent implementation of an Outlook Report provides regular, formal review of environmental condition and management and links to policy responses, key aspects of adaptive management. Given the major threat posed by climate change, the expanded network of marine reserves provides a critical and cost-effective contribution to enhancing the resilience of the Great Barrier Reef.
Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk ...of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental datasets, that these types of designs usually give less biased estimates than simpler observational designs. We propose a model-based approach to combine study estimates that may suffer from different levels of study design bias, discuss the implications for evidence synthesis, and how to facilitate the use of more credible study designs.
1. Environmental variables are often used as indirect surrogates for mapping biodiversity because species survey data are scant at regional scales, especially in the marine realm. However, ...environmental variables are measured on arbitrary scales unlikely to have simple, direct relationships with biological patterns. Instead, biodiversity may respond nonlinearly and to interactions between environmental variables. 2. To investigate the role of the environment in driving patterns of biodiversity composition in large marine regions, we collated multiple biological survey and environmental data sets from tropical NE Australia, the deep Gulf of Mexico and the temperate Gulf of Maine. We then quantified the shape and magnitude of multispecies responses along > 30 environmental gradients and the extent to which these variables predicted regional distributions. To do this, we applied a new statistical approach, Gradient Forest, an extension of Random Forest, capable of modelling nonlinear and threshold responses. 3. The regional-scale environmental variables predicted an average of 13—35% (up to 50—85% for individual species) of the variation in species abundance distributions. Important predictors differed among regions and biota and included depth, salinity, temperature, sediment composition and current stress. The shapes of responses along gradients also differed and were nonlinear, often with thresholds indicative of step changes in composition. These differing regional responses were partly due to differing environmental indicators of bioregional boundaries and, given the results to date, may indicate limited scope for extrapolating bio-physical relationships beyond the region of source data sets. 4. Synthesis and applications. Gradient Forest offers a new capability for exploring relationships between biodiversity and environmental gradients, generating new information on multispecies responses at a detail not available previously. Importantly, given the scarcity of data, Gradient Forest enables the combined use of information from disparate data sets. The gradient response curves provide biologically informed transformations of environmental layers to predict and map expected patterns of biodiversity composition that represent sampled composition better than uninformed variables. The approach can be applied to support marine spatial planning and management and has similar applicability in terrestrial realms.
Summary
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.
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.
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.
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).
Aim: To examine whether benthic assemblages are more diverse in a region of high topographic and oceanographic complexity by comparing benthic invertebrate assemblages across continental margins with ...contrasting environments. Location: Challenger Plateau and Chatham Rise, to the west and east of New Zealand, respectively. Methods: Benthic faunal data were sourced from extensive seabed surveys in 2007, when both margins were sampled with an epibenthic sled and a towed video system. Three methods were used to investigate benthic assemblages in relation to environmental variables: one based on individual species distribution models (SDMs) using boosted regression trees analysis (BRT), and two community-based modelling methods using generalized dissimilarity modelling (GDM) and gradient forest analysis (GF), respectively. Each method was used to model and predict the turnover in assemblages with respect to environment — the 'biophysical patterns' — across the study region. Results: Across Chatham Rise, a complex oceanographic environment arising from steep gradients in productivity and temperature at the Subtropical Front produced a high diversity of assemblages associated with the sub-Antarctic water mass, the Subtropical Front, steep-sloping regions and fast tidal currents. In contrast, Challenger Plateau lies entirely beneath a single (subtropical) water mass, and assemblage diversity was lower, with a distinctive assemblage on the plateau itself and a deep-water assemblage similar to the northern deep-water assemblage of Chatham Rise. Across both regions, assemblage turnover was fastest in cold waters, at shallow depths and in deep mixed layers. Main conclusions: Benthic assemblages were more varied on Chatham Rise than on Challenger Plateau, supporting the hypothesis that environmentally heterogeneous margins have higher assemblage diversity. Differing assemblages on the northern and southern flanks of Chatham Rise suggest a biogeographical boundary for benthic taxa across the Subtropical Front. These results demonstrate that oceanographically and topographically complex margins have a diverse assemblage structure that should be considered in planning for the sustainable management of diversity.
The use of biological surrogates as proxies for biodiversity patterns is gaining popularity, particularly in marine systems where field surveys can be expensive and species richness high. Yet, ...uncertainty regarding their applicability remains because of inconsistency of definitions, a lack of standard methods for estimating effectiveness, and variable spatial scales considered. We present a Bayesian meta-analysis of the effectiveness of biological surrogates in marine ecosystems. Surrogate effectiveness was defined both as the proportion of surrogacy tests where predictions based on surrogates were better than random (i.e., low probability of making a Type I error; P) and as the predictability of targets using surrogates (R(2)). A total of 264 published surrogacy tests combined with prior probabilities elicited from eight international experts demonstrated that the habitat, spatial scale, type of surrogate and statistical method used all influenced surrogate effectiveness, at least according to either P or R(2). The type of surrogate used (higher-taxa, cross-taxa or subset taxa) was the best predictor of P, with the higher-taxa surrogates outperforming all others. The marine habitat was the best predictor of R(2), with particularly low predictability in tropical reefs. Surrogate effectiveness was greatest for higher-taxa surrogates at a <10-km spatial scale, in low-complexity marine habitats such as soft bottoms, and using multivariate-based methods. Comparisons with terrestrial studies in terms of the methods used to study surrogates revealed that marine applications still ignore some problems with several widely used statistical approaches to surrogacy. Our study provides a benchmark for the reliable use of biological surrogates in marine ecosystems, and highlights directions for future development of biological surrogates in predicting biodiversity.
Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once ...in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Chile, and Gulf of Alaska to >50% in some European seas. Overall, 14% of the 7.8 million-km² study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when high-resolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, therewas >95% probability that >90% of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.
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