Effectiveness of Biological Surrogates for Predicting Patterns of Marine Biodiversity: A Global Meta-Analysis

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 (R2). 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 R2. 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 R2, 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

The effects of climate change on the ecology of fishes

Ocean warming and acidification are set to reshuffle life on Earth and alter ecological processes that underpin the biodiversity, health, productivity, and resilience of ecosystems. Fishes contribute significantly to marine, estuarine, and freshwater species diversity and the functioning of marine ecosystems, and are not immune to climate change impacts. Whilst considerable effort has been placed on studying the effects of climate change on fishes, much emphasis has been placed on their (eco)physiology and at the organismal level. Fishes are affected by climate change through impacts at various levels of biological organisation and through a large variety of traits, making it difficult to make generalisations regarding fish responses to climate change. Here, we briefly review the current state of knowledge of climate change effects on fishes across a wide range of subfields of fish ecology and evaluate these effects at various scales of biological organisation (from genes to ecosystems). We argue that a more holistic synthesis of the various interconnected subfields of fish ecology and integration of responses at different levels of biological organisation are needed for a better understanding of how fishes and their populations and communities might respond or adapt to the multi-stressor effects of climate change. We postulate that studies using natural analogues of climate change, meta-analyses, advanced integrative modelling approaches, and lessons learned from past extreme climate events could help reveal some general patterns of climate change impacts on fishes that are valuable for management and conservation approaches. Whilst these might not reveal many of the underlying mechanisms responsible for observed biodiversity and community change, their insights are useful to help create better climate adaptation strategies for their preservation in a rapidly changing ocean

Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef

Crown-of-thorns starfish (CoTS; Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014

Models of marine fish biodiversity : assessing predictors from three habitat classification schemes

Prioritising biodiversity conservation requires knowledge of where biodiversity occurs. Such knowledge, however, is often lacking. New technologies for collecting biological and physical data coupled with advances in modelling techniques could help address these gaps and facilitate improved management outcomes. Here we examined the utility of environmental data, obtained using different methods, for developing models of both uni- and multivariate biodiversity metrics. We tested which biodiversity metrics could be predicted best and evaluated the performance of predictor variables generated from three types of habitat data: acoustic multibeam sonar imagery, predicted habitat classification, and direct observer habitat classification. We used boosted regression trees (BRT) to model metrics of fish species richness, abundance and biomass, and multivariate regression trees (MRT) to model biomass and abundance of fish functional groups. We compared model performance using different sets of predictors and estimated the relative influence of individual predictors. Models of total species richness and total abundance performed best; those developed for endemic species performed worst. Abundance models performed substantially better than corresponding biomass models. In general, BRT and MRTs developed using predicted habitat classifications performed less well than those using multibeam data. The most influential individual predictor was the abiotic categorical variable from direct observer habitat classification and models that incorporated predictors from direct observer habitat classification consistently outperformed those that did not. Our results show that while remotely sensed data can offer considerable utility for predictive modeling, the addition of direct observer habitat classification data can substantially improve model performance. Thus it appears that there are aspects of marine habitats that are important for modeling metrics of fish biodiversity that are not fully captured by remotely sensed data. As such, the use of remotely sensed data to model biodiversity represents a compromise between model performance and data availability

A novel method for mapping reefs and subtidal rocky habitats using artificial neural networks

Reefs and subtidal rocky habitats are sites of high biodiversity and productivity which harbour commercially important species of fish and invertebrates. Although the conservation management of reef associated species has been informed using species distribution models (SDM) and community based approaches, to date their use has been constrained to specific regions where the locality and spatial extent of reefs is well known. Much of the world's subtidal habitats remain either undiscovered or unmapped, including coasts of intense human use. Consequently, to facilitate a stronger understanding of species-environmental relationships there is an urgent need for a cost and time effective standard method to map reefs at fine spatial resolutions across broad geographical extents. We used bathymetric data (∼250. m resolution) to calculate the local slope and curvature of the seabed. We then constructed artificial neural networks (ANNs) to forecast the probability of reef occurrence within grid cells as a function of bathymetric and slope variables. Testing over an independent data set not used in training showed that ANNs were able to accurately predict the location of reefs for 86% of all grid cells (Kappa = 0.63) without over fitting. The ANN with greatest support, combining bathymetric values of the target grid cell with the slope of adjacent grid cells, was used to map inshore reef locations around the Southern Australian coastline (∼250. m resolution). Broadly, our results show that reefs are identifiable from coarse-scale bathymetry data of the seabed. We anticipate that our research technique will strengthen systematic conservation planning tools in many regions of the world, by enabling the identification of rocky substratum and mapping in localities that remain poorly surveyed due to logistics or monetary constraints. © 2011 Elsevier B.V.Michael J. Watts, Yuxiao Li, Bayden D. Russell, Camille Mellin, Sean D. Connell, Damien A. Fordha

Outstanding challenges in the transferability of ecological models

Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their ‘transferability’) undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions

Sélection de l'habitat à l'installation et utilisation de l'habitat post-installation chez les poissons récifaux-lagonaires de Nouvelle-Calédonie

Habitat suitability influences the growth and survival of coral reef fish juveniles, and thus the success of their recruitment in adult populations. The ultimate aim of the PhD research was to assess the relationships between the habitat characteristics in the south-west lagoon of New Caledonia at different scales, growth and abundances of juvenile fish. A photographic method was first developed in order to quantify the characteristics of coral microhabitats for juvenile fish. This method was then used for studying the relationship between microhabitat characteristics, growth trajectories back-calculated from otolith analysis, and abundances of juvenile Pomacentrus moluccensis. No significant difference was showed between the growth trajectories of individuals collected from different coral colonies. However, the density-dependent mortality of juveniles increased when the volume of holes of coral colonies decreased. At the spatial scale of two islets of the lagoon, significant spatial differences were observed in back-calculated growth trajectories, size and/or age at settlement of juveniles of Chromis viridis, Lethrinus genivittatus and Siganus fuscescens. A novel statistical procedure revealed the growth-selective mortality of juveniles C. viridis, which had a significant effect on growth trajectories. Significant differences were then showed between juvenile fish assemblages collected from artificial reefs in seaweed beds, seagrass beds and coral patches, and according to the immersion time. In the south-west lagoon of New Caledonia, changes in juvenile habitat use across seasons or during growth were showed for 53% and 39% of the observed juveniles respectively. Lastly, Generalized Linear Models allowed to explain 75% and 52% of variations in the numbers of species and individuals respectively, from a combination of environmental factors recorded at different scales. Predictions were further spatialized using a remotely sensed habitat map.La qualité de l'habitat influence la croissance et la survie des juvéniles des poissons récifaux-lagonaires, et donc le succès de leur recrutement dans les populations adultes. Dans ce contexte, l'objectif général de la thèse était d'étudier les relations entre les caractéristiques de l'habitat dans le lagon sud-ouest de Nouvelle-Calédonie à différentes échelles, la croissance et les abondances des juvéniles. Une méthode photographique a été développée et testée afin d'estimer les caractéristiques du microhabitat corallien des juvéniles. Cette méthode a ensuite été utilisée lors d'une étude de la relation entre les caractéristiques du microhabitat, les trajectoires de croissance rétrocalculées à partir de l'analyse des otolithes, et les abondances des juvéniles de Pomacentrus moluccensis. Aucune différence de croissance n'a été observée chez des individus capturés sur des colonies coralliennes différentes. En revanche, la mortalité densité-dépendante des juvéniles est apparue d'autant plus importante lorsque le volume interstitiel des colonies coralliennes était faible. A l'échelle de deux îlots du lagon, des différences spatiales significatives ont été observées pour les trajectoires de croissance, la taille et/ou l'âge à l'installation rétrocalculés pour des juvéniles de Chromis viridis, Lethrinus genivittatus et Siganus fuscescens. Une nouvelle procédure de traitement des données a révélé une mortalité benthique croissance-sélective pour C. viridis qui a eu un effet significatif sur les trajectoires de croissance. Des assemblages de juvéniles collectés à partir de récifs artificiels immergés sont apparus significativement différents suivant qu'ils étaient immergés dans des algueraies, des herbiers et des récifs coralliens, et selon leur durée d'immersion. Dans le lagon sud-ouest, des changements d'habitat au cours des saisons et au cours de la croissance ont été montrés pour 53% et 39% des juvéniles observés respectivement, à fine et/ou large échelle spatiale. Enfin, des Modèles Linéaires Généralisés ont permis d'expliquer 75% et 52% des variations du nombre d'espèces et d'individus juvéniles respectivement, à partir de facteurs environnementaux à plusieurs échelles. Les prédictions ont été spatialisées grâce au couplage avec les outils de télédétection

Habitat selection at settlement and post-settlement dynamics in juvenile fish communities in the New Caledonia lagoon

Habitat suitability influences the growth and survival of coral reef fish juveniles, and thus the success of their recruitment in adult populations. The ultimate aim of the PhD research was to assess the relationships between the habitat characteristics in the south-west lagoon of New Caledonia at different scales, growth and abundances of juvenile fish. A photographic method was first developed in order to quantify the characteristics of coral microhabitats for juvenile fish. This method was then used for studying the relationship between microhabitat characteristics, growth trajectories back-calculated from otolith analysis, and abundances of juvenile Pomacentrus moluccensis. No significant difference was showed between the growth trajectories of individuals collected from different coral colonies. However, the density-dependent mortality of juveniles increased when the volume of holes of coral colonies decreased. At the spatial scale of two islets of the lagoon, significant spatial differences were observed in back-calculated growth trajectories, size and/or age at settlement of juveniles of Chromis viridis, Lethrinus genivittatus and Siganus fuscescens. A novel statistical procedure revealed the growth-selective mortality of juveniles C. viridis, which had a significant effect on growth trajectories. Significant differences were then showed between juvenile fish assemblages collected from artificial reefs in seaweed beds, seagrass beds and coral patches, and according to the immersion time. In the southwest lagoon of New Caledonia, changes in juvenile habitat use across seasons or during growth were showed for 53% and 39% of the observed juveniles respectively. Lastly, Generalized Linear Models allowed to explain 75% and 52% of variations in the numbers of species and individuals respectively, from a combination of environmental factors recorded at different scales. Predictions were further spatialized using a remotely sensed habitat map.Camille Mellinhttp://www.mnhn.fr/sfi/cybium/numeros/BilingualAbstracts/332/sommaire332.htm

Seasonal and ontogenetic patterns of habitat use in coral reef fish juveniles

We investigated the diversity of patterns of habitat use by juveniles of coral reef fishes according to seasons and at two spatial scales (10-100 m and 1-10 km). We conducted underwater visual censuses in New Caledonia's Lagoon between 1986 and 2001. Co-inertia analyses highlighted the importance of mid-shelf habitats at large spatial scale (1-10 km) and of sandy and vegetated habitats at small spatial scale (10-100 m) for most juveniles. Among all juvenile species, 53% used different habitats across seasons (e.g. Lutjanus fulviflamma and Siganus argenteus) and 39% used different habitats as they grow (e.g. Lethrinus atkinsoni and Scarus ghobban). During their ontogeny, at large and small scales, respectively, 21% and 33% of the species studied showed an increase in the number of habitats used (e.g. L. fulviflamma, L. atkinsoni), 10% and 3% showed a decrease in. the number of habitats used (e.g. Amphiprion melanopus, Siganus fuscescens), 23% and 3% showed a drastic change of habitat used (e.g. S. ghobban, Scarus sp.) whereas 46% and 61% showed no change of habitat used (e.g. Lethrinus genivittatus, Ctenochaetus striatus). Changes in habitat use at both small and large spatial scales occurred during the ontogeny of several species (e.g. S. ghobban, Scarus sp.). Results pointed out the different spatial and temporal scales of juvenile habitat use to account for in conservation decisions regarding both assemblage and species-specific levels