Multi-scale marine biodiversity patterns inferred efficiently from habitat image processing

Cost-effective proxies of biodiversity and species abundance, applicable across a range of spatial scales, are needed for setting conservation priorities and planning action. We outline a rapid, efficient, and low-cost measure of spectral signal from digital habitat images that, being an effective proxy for habitat complexity, correlates with species diversity and requires little image processing or interpretation. We validated this method for coral reefs of the Great Barrier Reef (GBR), Australia, across a range of spatial scales (1 m to 10 km), using digital photographs of benthic communities at the transect scale and high-resolution Landsat satellite images at the reef scale. We calculated an index of image-derived spatial heterogeneity, the mean information gain (MIG), for each scale and related it to univariate (species richness and total abundance summed across species) and multivariate (species abundance matrix) measures of fish community structure, using two techniques that account for the hierarchical structure of the data: hierarchical (mixed-effect) linear models and distance-based partial redundancy analysis. Over the length and breadth of the GBR, MIG alone explained up to 29% of deviance in fish species richness, 33% in total fish abundance, and 25% in fish community structure at multiple scales, thus demonstrating the possibility of easily and rapidly exploiting spatial information contained in digital images to complement existing methods for inferring diversity and abundance patterns among fish communities. Thus, the spectral signal of unprocessed remotely sensed images provides an efficient and low-cost way to optimize the design of surveys used in conservation planning. In data-sparse situations, this simple approach also offers a viable method for rapid assessment of potential local biodiversity, particularly where there is little local capacity in terms of skills or resources for mounting in-depth biodiversity surveys.     

Density-dependent biodiversity effects on physical habitat modification by freshwater bivalves

Several decades of research have shown that biodiversity affects ecosystem processes associated with resource capture and the production of biomass within trophic levels. Although there are good reasons to expect that biodiversity influences non-trophic ecosystem processes, such as the physical creation or modification of habitat, studies investigating the role of biodiversity on physical processes are scarce. Here we report the results of a study using artificial streams to test the influence of freshwater mussel biodiversity on gravel erosion during high flows while manipulating mussel abundance. Mussel species vary in traits that should influence their effects on erosion, such as size, shell morphology, and burrowing behavior. We found that mussel species richness was associated with an increase in erosion at both low and high densities. Planned contrasts showed that the erosion observed in species mixtures was purely additive at low density, indicating that erosion in a species polyculture could routinely be predicted by the performance of monocultures. However, at high density certain combinations of species showed nonadditive effects on erosion, suggesting that organism abundance can fundamentally alter biodiversity effects. Although this may have been a result of altered species interactions at high density, our study design cannot confirm this.     

The effects of habitat loss, fragmentation, and community homogenization on resilience in estuaries.

When changes in the frequency and extent of disturbance outstrip the recovery potential of resident communities, the selective removal of species contributes to habitat loss and fragmentation across landscapes. The degree to which habitat change is likely to influence community resilience will depend on metacommunity structure and connectivity. Thus ecological connectivity is central to understanding the potential for cumulative effects to impact upon diversity. The importance of these issues to coastal marine communities, where the prevailing concept of open communities composed of highly dispersive species is being challenged, indicates that these systems may be more sensitive to cumulative impacts than previously thought. We conducted a disturbance-recovery experiment across gradients of community type and environmental conditions to assess the roles of ecological connectivity and regional variations in community structure on the recovery of species richness, total abundance, and community composition in Mahurangi Harbour, New Zealand. After 394 days, significant differences in recovery between sites were apparent. Statistical models explaining a high proportion of the variability (R2 > 0.92) suggested that community recovery rates were controlled by a combination of physical and ecological features operating across spatial scales, affecting successional processes. The dynamic and complex interplay of ecological and environmental processes we observed driving patch recovery across the estuarine landscape are integral to recovery from disturbances in heterogeneous environments. This link between succession/recovery, disturbance, and heterogeneity confirms the utility of disturbance-recovery experiments as assays for cumulative change due to fragmentation and habitat change in estuaries.     

Land change in the southern Yucatán and Calakmul biosphere reserve: effects on habitat and biodiversity.

The southern Yucatán contains the largest expanse of seasonal tropical forests remaining in Mexico, forming an ecocline between the drier north of the peninsula and the humid Petén, Guatemala. The Calakmul Biosphere Reserve resides in the center of this region as part of the Mesoamerican Biological Corridor. The reserve's functions are examined in regard to land changes throughout the region, generated over the last 40 years by increasing settlement and the expansion and intensification of agriculture. These changes are documented from 1987/1988 to 2000, and their implications regarding the capacity of the reserve to protect the ecocline, forest habitats, and butterfly diversity are addressed. The results indicate that the current landscape matrix serves the biotic diversity of the reserve, with several looming caveats involving the loss of humid forests and the interruption of biota flow across the ecocline, and the amount and proximity of older forest patches beyond the reserve. The highly dynamic land cover changes underway in this economic frontier warrant an adaptive management approach that monitors the major changes underway in mature forest types, while the paucity of systematic ecological and environment-development studies is rectified in order to inform policy and practice.     

Predictability of marine nematode biodiversity

In this paper, we investigated: (1) the predictability of different aspects of biodiversity, (2) the effect of spatial autocorrelation on the predictability and (3) the environmental variables affecting the biodiversity of free-living marine nematodes on the Belgian Continental Shelf. An extensive historical database of free-living marine nematodes was employed to model different aspects of biodiversity: species richness, evenness, and taxonomic diversity. Artificial neural networks (ANNs), often considered as “black boxes”, were applied as a modeling tool. Three methods were used to reveal these “black boxes” and to identify the contributions of each environmental variable to the diversity indices. Since spatial autocorrelation is known to introduce bias in spatial analyses, Moran's I was used to test the spatial dependency of the diversity indices and the residuals of the model. The best predictions were made for evenness. Although species richness was quite accurately predicted as well, the residuals indicated a lack of performance of the model. Pure taxonomic diversity shows high spatial variability and is difficult to model. The biodiversity indices show a strong spatial dependency, opposed to the residuals of the models, indicating that the environmental variables explain the spatial variability of the diversity indices adequately. The most important environmental variables structuring evenness are clay and sand fraction, and the minimum annual total suspended matter. Species richness is also affected by the intensity of sand extraction and the amount of gravel of the sea bed.     

Using community‐level metrics to monitor the effects of marine protected areas on biodiversity

Marine protected areas (MPAs) are used to protect species, communities, and their associated habitats, among other goals. Measuring MPA efficacy can be challenging, however, particularly when considering responses at the community level. We gathered 36 abundance and 14 biomass data sets on fish assemblages and used meta‐analysis to evaluate the ability of 22 distinct community diversity metrics to detect differences in community structure between MPAs and nearby control sites. We also considered the effects of 6 covariates—MPA size and age, MPA size and age interaction, latitude, total species richness, and level of protection—on each metric. Some common metrics, such as species richness and Shannon diversity, did not differ consistently between MPA and control sites, whereas other metrics, such as total abundance and biomass, were consistently different across studies. Metric responses derived from the biomass data sets were more consistent than those based on the abundance data sets, suggesting that community‐level biomass differs more predictably than abundance between MPA and control sites. Covariate analyses indicated that level of protection, latitude, MPA size, and the interaction between MPA size and age affect metric performance. These results highlight a handful of metrics, several of which are little known, that could be used to meet the increasing demand for community‐level indicators of MPA effectiveness.     

The Mediterranean intertidal habitat as a natural laboratory to study climate change drivers of geographic patterns in marine biodiversity

Nylon bags containing yellow leaves of Rhizophora apiculata and Avicennia marina, were immersed for 80 days from August to October, 1996. the decomposing leaves were collected every 10 days and analysed for dry weight loss and six biochemical parameters: tannins, total amino acids, total sugars, total nitrogen, total lipids and fatty acid profile. the leaf weight initially decreased very rapidly by about 50% of the start in two species of mangroves within 10 days. Similar changes were observed with tannins, total amino acids and sugars. However, the concentration of nitrogen increased significantly with decomposition. There was no significant change in total lipid and fatty acid profile. the highest concentration of fatty acid in the decomposing leaves was palmitic acid (16:0). Unsaturated fatty acids such as, 18:1 w7c and 18:1 w9c were found to be present in decomposing leaves of both species.     

Global biodiversity patterns of benthic marine algae

Species richness patterns are remarkably similar across many marine taxa, yet explanations of how such patterns are generated and maintained are conflicting. I use published occurrence data to identify previously masked latitudinal and longitudinal diversity gradients for all genera of benthic marine macroalgae and for species in the Order Bryopsidales. I also quantify the size, location, and overlap of macroalgal geographic ranges to determine how the observed richness patterns are generated. Algal genera exhibit an inverse latitudinal gradient, with biodiversity hotspots in temperate regions, while bryopsidalean species reach peak diversity in the tropics. The geographic distribution of range locations results in distinct clusters of range mid-points. In particular, widespread taxa are centered within tight latitudinal and longitudinal bands in the middle of the Indo-Pacific and Atlantic Oceans while small-ranged taxa are clustered in peripheral locations, suggesting that variation in speciation and extinction are important drivers of algal diversity patterns. Hypotheses about factors that regulate diversity contain underlying assumptions about the size and location of geographic ranges, in addition to predictions as to why species numbers will differ among regions. Yet these assumptions are rarely considered in assessing the validity of the prevailing hypotheses. I assess a suite of hypotheses, suggested to explain patterns of marine diversity, by comparing algal-richness patterns in combination with the size and location of algal geographic ranges, to the richness and range locations predicted by these hypotheses. In particular, the results implicate habitat areas and ocean currents as the most plausible drivers of observed diversity patterns.     

Marine biology: the role of accommodation in shaping marine biodiversity

A review of evidence from two kinds of studies conducted in the marine environment suggests a species relationship not previously recognized as being consistent and widespread. In the first instance, observations on species invading from a more diverse ecosystem into a less diverse ecosystem indicate that successful colonizations take place because space is yielded by their ecological equivalents. In the second instance, widespread studies show that any community, rich or poor, located in tropical or cold waters, is vulnerable to invasions by species from a larger, more diverse region. Furthermore, the species richness of a community apparently depends upon that of the region to which it belongs. Together, these observations indicate the existence of a general rule which states that if an invader becomes established, it is permitted to do so by an accommodation on the part of the species that occupies the preferred ecological space. Paleontological data on invasions provide evidence of speciation following accommodation. This leads to the recognition of a three-step process: invasion to accommodation to speciation (IAS). This process, which may be called the IAS mechanism, may have contributed to historical rises of global biodiversity.     

Predicting the distributions of marine organisms at the global scale

We present and evaluate AquaMaps, a presence-only species distribution modelling system that allows the incorporation of expert knowledge about habitat usage and was designed for maximum output of standardized species range maps at the global scale. In the marine environment there is a significant challenge to the production of range maps due to large biases in the amount and location of occurrence data for most species. AquaMaps is compared with traditional presence-only species distribution modelling methods to determine the quality of outputs under equivalently automated conditions. The effect of the inclusion of expert knowledge to AquaMaps is also investigated. Model outputs were tested internally, through data partitioning, and externally against independent survey data to determine the ability of models to predict presence versus absence. Models were also tested externally by assessing correlation with independent survey estimates of relative species abundance. AquaMaps outputs compare well to the existing methods tested, and inclusion of expert knowledge results in a general improvement in model outputs. The transparency, speed and adaptability of the AquaMaps system, as well as the existing online framework which allows expert review to compensate for sampling biases and thus improve model predictions are proposed as additional benefits for public and research use alike.     

Potential effects of forest policies on terrestrial biodiversity in a multi-ownership province.

We used spatial simulation models to evaluate how current and two alternative policies might affect potential biodiversity over 100 years in the Coast Ranges Physiographic Province of Oregon. This 2.3-million-ha province is characterized by a diversity of public and private forest owners, and a wide range of forest policy and management objectives. We evaluated habitat availability for seven focal species representing different life histories. We also examined how policies affected old-growth stand structure, age distributions relative to the historical range of variability, and landscape patterns of forest types. Under the current policy scenario, the area of habitat for old-growth forest structure and associated species increased over time, the habitat for some early-successional associates remained stable, and the area of hardwood vegetation and diverse early-successional stages declined. The province is projected to move toward but not reach the historical range of variation of forest age classes that may have occurred under the wildfire regimes of the pre-Euroamerican settlement period. Ownership explained much of the pattern of biodiversity in the province, and under the current policy scenario, its effect increased over time as the landscape diverged into highly contrasting forest structures and ages. Patch type diversity declined slightly overall but declined strongly within ownerships. Most of the modeled change in biodiversity over time resulted from policies on public forest lands that were intended to increase the area of late-successional forests and species. One of the alternative policies, increased retention of wildlife trees on private lands, reduced the contrast between ownerships and increased habitat availability over time for both early- and late-successional species. Analysis of another alternative, stopping thinning of plantations on federal lands, indicated that current thinning regimes improve habitat for the Olive-sided Flycatcher, but the no-thinning alternative had no effect on the habitat scores for the late-successional species in the 100-year simulation. A comparison of indicators of biological diversity suggests that using focal species and forest structural measures can provide complementary information on biodiversity. The multi-ownership perspective provided a more complete synthesis of province-wide biodiversity patterns than assessments based on single ownerships.     

Predicting biodiversity change: outside the climate envelope, beyond the species-area curve

Efforts to anticipate threats to biodiversity take the form of species richness predictions (SRPs) based on simple correlations with current climate and habitat area. We review the major approaches that have been used for SRP, species-area curves and climate envelopes, and suggest that alternative research efforts may provide more understanding and guidance for management. Extinction prediction suffers from a number of limitations related to data and the novelty of future environments. We suggest additional attention to (1) identification of variables related to biodiversity that are diagnostic and potentially more predictable than extinction, (2) constraints on species dispersal and reproduction that will determine population persistence and range shifts, including limited sources or potential immigrants for many regions, and (3) changes in biotic interactions and phenology. We suggest combinations of observational and experimental approaches within a framework available for ingesting heterogeneous data sources. Together, these recommendations amount to a shift in emphasis from prediction of extinction numbers to identification of vulnerabilities and leading indicators of change, as well as suggestions for surveillance tools needed to evaluate important variables and the experiments likely to provide most insight.     

Testing the presence of marine protected areas against their ability to reduce pressures on biodiversity

Marine protected areas (MPAs) are the preferred tool for preventing marine biodiversity loss, as reflected in international protected area targets. Although the area covered by MPAs is expanding, there is a concern that opposition from resource users is driving them into already low-use locations, whereas high-pressure areas remain unprotected, which has serious implications for biodiversity conservation. We tested the spatial relationships between different human-induced pressures on marine biodiversity and global MPAs. We used global, modeled pressure data and the World Database on Protected Areas to calculate the levels of 15 different human-induced pressures inside and outside the world's MPAs. We fitted binomial generalized linear models to the data to determine whether each pressure had a positive or negative effect on the likelihood of an area being protected and whether this effect changed with different categories of protection. Pelagic and artisanal fishing, shipping, and introductions of invasive species by ships had a negative relationship with protection, and this relationship persisted under even the least restrictive categories of protection (e.g., protected areas classified as category VI under the International Union for Conservation of Nature, a category that permits sustainable use). In contrast, pressures from dispersed, diffusive sources (e.g., pollution and ocean acidification) had positive relationships with protection. Our results showed that MPAs are systematically established in areas where there is low political opposition, limiting the capacity of existing MPAs to manage key drivers of biodiversity loss. We suggest that conservation efforts focus on biodiversity outcomes and effective reduction of pressures rather than prescribing area-based targets, and that alternative approaches to conservation are needed in areas where protection is not feasible.     

Predicting occurrence of juvenile shark habitat to improve conservation planning

Fishing and habitat degradation have increased the extinction risk of sharks, and conservation strategies recognize that survival of juveniles is critical for the effective management of shark populations. Despite the rapid expansion of marine protected areas (MPAs) globally, the paucity of shark‐monitoring data on large scales (100s–1000s km) means that the effectiveness of MPAs in halting shark declines remains unclear. Using data collected by baited remote underwater video systems (BRUVS) in northwestern Australia, we developed generalized linear models to elucidate the ecological drivers of habitat suitability for juvenile sharks. We assessed occurrence patterns at the order and species levels. We included all juvenile sharks sampled and the 3 most abundant species sampled separately (grey reef [Carcharhinus amblyrhynchos], sandbar [Carcharhinus plumbeus], and whitetip reef sharks [Triaenodon obesus]). We predicted the occurrence of juvenile sharks across 490,515 km² of coastal waters and quantified the representation of highly suitable habitats within MPAs. Our species‐level models had higher accuracy (? ≥ 0.69) and deviance explained (≥48%) than our order‐level model (? = 0.36 and deviance explained of 10%). Maps of predicted occurrence revealed different species‐specific patterns of highly suitable habitat. These differences likely reflect different physiological or resource requirements between individual species and validate concerns over the utility of conservation targets based on aggregate species groups as opposed to a species‐focused approach. Highly suitable habitats were poorly represented in MPAs with the most restrictions on extractive activities. This spatial mismatch possibly indicates a lack of explicit conservation targets and information on species distribution during the planning process. Non‐extractive BRUVS provided a useful platform for building the suitability models across large scales to assist conservation planning across multiple maritime jurisdictions, and our approach provides a simple for method for testing the effectiveness of MPAs.     

Trends in biodiversity and habitat quantification tools used for market-based conservation in the United States

Market-based conservation mechanisms are designed to facilitate the mitigation of harm to and conservation of habitats and biodiversity. Their potential is partly hindered, however, by the quantification tools used to assess habitat quality and functionality. Of specific concern are the lack of transparency and standardization in tool development and gaps in tool availability. To address these issues, we collected information via internet and literature searchers and through conversations with tool developers and users on tools used in U.S. conservation mechanisms, such as payments for ecosystem services (PES) and ecolabel programs, conservation banking, and habitat exchanges. We summarized information about tools and explored trends among and within mechanisms based on criteria detailing geographic, ecological, and technical features of tools. We identified 69 tools that assessed at least 34 species and 39 habitat types. Where tools reported pricing, 98% were freely available. More tools were applied to states along the U.S. West Coast than elsewhere, and the level of tool transferability varied markedly among mechanisms. Tools most often incorporated conditions at numerous spatial scales, frequently addressed multiple risks to site viability, and required 1–83 data inputs. Most tools required a moderate or greater level of user skill. Average tool-complexity estimates were similar among all mechanisms except PES programs. Our results illustrate the diversity among tools in their ecological features, data needs, and geographic application, supporting concerns about a lack of standardization. However, consistency among tools in user skill requirements, incorporation of multiple spatial scales, and complexity highlight important commonalities that could serve as a starting point for establishing more standardized tool development and feature-incorporation processes. Greater standardization in tool design may expand market participation and facilitate a needed assessment of the effectiveness of market-based conservation.     

Using habitat suitability index and particle dispersion models for early detection of marine invaders.

Eradication and control of invasive species are often possible only if populations are detected when they are small and localized. To be efficient, detection surveys should be targeted at locations where there is the greatest risk of incursions. We examine the utility of habitat suitability index (HSI) and particle dispersion models for targeting sampling for marine pests. Habitat suitability index models are a simple way to identify suitable habitat when species distribution data are lacking. We compared the performance of HSI models with statistical models derived from independent data from New Zealand on the distribution of two nonindigenous bivalves: Theora lubrica and Musculista senhousia. Logistic regression models developed using the HSI scores as predictors of the presence/absence of Theora and Musculista explained 26.7% and 6.2% of the deviance in the data, respectively. Odds ratios for the HSI scores were greater than unity, indicating that they were genuine predictors of the presence/ absence of each species. The fit and predictive accuracy of each logistic model were improved when simulated patterns of dispersion from the nearest port were added as a predictor variable. Nevertheless, the combined model explained, at best, 46.5% of the deviance in the distribution of Theora and correctly predicted 56% of true presences and 50% of all cases. Omission errors were between 6% and 16%. Although statistical distribution models built directly from environmental predictors always outperformed the equivalent HSI models, the gain in model fit and accuracy was modest. High residual deviance in both types of model suggests that the distributions realized by Theora and Musculista in the field data were influenced by factors not explicitly modeled as explanatory variables and by error in the environmental data used to project suitable habitat for the species. Our results highlight the difficulty of accurately predicting the distribution of invasive marine species that exhibit low habitat occupancy and patchy distributions in time and space. Although the HSI and statistical models had utility as predictors of the likely distribution of nonindigenous marine species, the level of spatial accuracy achieved with them may be well below expectations for sensitive surveillance programs.     

Assessing the effects of climate change on the distribution of pulmonate freshwater snail biodiversity

Global warming is expected to profoundly change the characteristics of freshwater habitats. Increasing evaporation, lower oxygen concentration due to increased water temperatures and changes in precipitation pattern are likely to affect the survival and reproduction of pulmonate freshwater gastropods. Our statistical niche modelling analysis suggests that for a great proportion of the North-West European genera, the range sizes were predicted to decrease by 2,080, even if unlimited dispersal was assumed. The forecasted warming in the cooler northern ranges predicted the emergence of new suitable areas, as well as drastically reduced available habitat in the southern part of the studied region. Phylogenetic signal was inferred for one dimension of the climatic niche. Independent contrast analyses, taking into account the phylogenetic relationships between the taxa, showed a positive correlation between the genera’s climate niche width and the size of future suitable area. In summary, the results predict a profound faunal freshwater gastropod shift for Central Europe, either permitting the establishment of species currently living south of the studied region or permitting the proliferation of organisms relying on the same food resources, if dispersal abilities do not match the rate of climate change.     

Inhibitory effects of copper on marine dinoflagellates

The effect of copper on three species of marine dinoflagellates [Scrippsiella faeroense (Paulsen) Balech et Soares, Prorocentrum micans Ehrenberg, Gymnodinium splendens Lebour] was studied. It inhibited the growth of all species and was lethal to one species in batch cultures. The effect was more pronounced in semicontinuous culture than in batch cultures. Chlorophyll concentrations and rate of uptake of radioactive carbon by cells of S. faeroense were affected in a manner similar to cell numbers. Copper inhibited growth of cells, most probably either by arresting cell division or by penetrating inside the cell and affecting metabolism.     

The effectiveness of marine reserve systems constructed using different surrogates of biodiversity

Biological sampling in marine systems is often limited, and the cost of acquiring new data is high. We sought to assess whether systematic reserves designed using abiotic domains adequately conserve a comprehensive range of species in a tropical marine inter‐reef system. We based our assessment on data from the Great Barrier Reef, Australia. We designed reserve systems aiming to conserve 30% of each species based on 4 abiotic surrogate types (abiotic domains; weighted abiotic domains; pre‐defined bioregions; and random selection of areas). We evaluated each surrogate in scenarios with and without cost (cost to fishery) and clumping (size of conservation area) constraints. To measure the efficacy of each reserve system for conservation purposes, we evaluated how well 842 species collected at 1155 sites across the Great Barrier Reef seabed were represented in each reserve system. When reserve design included both cost and clumping constraints, the mean proportion of species reaching the conservation target was 20–27% higher for reserve systems that were biologically informed than reserves designed using unweighted environmental data. All domains performed substantially better than random, except when there were no spatial or economic constraints placed on the system design. Under the scenario with no constraints, the mean proportion of species reaching the conservation target ranged from 98.5% to 99.99% across all surrogate domains, whereas the range was 90–96% across all domains when both cost and clumping were considered. This proportion did not change considerably between scenarios where one constraint was imposed and scenarios where both cost and clumping constraints were considered. We conclude that representative reserve systems can be designed using abiotic domains; however, there are substantial benefits if some biological information is incorporated.