Assuming independence in spatial latent variable models: Consequences and implications of misspecification.

Multivariate spatial data, where multiple responses are simultaneously recorded across spatially indexed observational units, are routinely collected in a wide variety of disciplines. For example, the Southern Ocean Continuous Plankton Recorder survey collects records of zooplankton communities in the Indian sector of the Southern Ocean, with the aim of identifying and quantifying spatial patterns in biodiversity in response to environmental change. One increasingly popular method for modeling such data is spatial generalized linear latent variable models (GLLVMs), where the correlation across sites is captured by a spatial covariance function in the latent variables. However, little is known about the impact of misspecifying the latent variable correlation structure on inference of various parameters in such models. To address this gap in the literature, we investigate how misspecifying and assuming independence for the latent variables' correlation structure impacts estimation and inference in spatial GLLVMs. Through both theory and numerical studies, we show that performance of maximum likelihood estimation and inference on regression coefficients under misspecification depends on a combination of the response type, the magnitude of true regression coefficient, and the corresponding loadings, and, most importantly, whether the corresponding covariate is (also) spatially correlated. On the other hand, estimation and inference of truly nonzero loadings and prediction of latent variables is consistently not robust to misspecification of the latent variable correlation structure.

Integrated assessment of the spatial distribution and structural dynamics of deep benthic marine communities.

Characterizing the spatial distribution and variation of species communities and validating these characteristics with data from the field are key elements for an ecosystem-based approach to management. However, models of species distributions that yield community structure are usually not linked to models of community dynamics, constraining understanding and management of the ecosystem, particularly in data-poor regions. Here we use a qualitative network model to predict changes in Antarctic benthic community structure between major marine habitats characterized largely by seafloor depth and slope, and use multivariate mixture models of species distributions to validate the community dynamics. We then assess how future increases in primary production associated with anticipated loss of sea-ice may affect the ecosystem. Our study shows how both spatial and structural features of ecosystems in data-poor regions can be analyzed and possible futures assessed, with direct relevance for ecosystem-based management.

Integrating abundance and functional traits reveals new global hotspots of fish diversity.

Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.

Congruence in demersal fish, macroinvertebrate, and macroalgal community turnover on shallow temperate reefs.

To support coastal planning through improved understanding of patterns of biotic and abiotic surrogacy at broad scales, we used gradient forest modeling (GFM) to analyze and predict spatial patterns of compositional turnover of demersal fishes, macroinvertebrates, and macroalgae on shallow, temperate Australian reefs. Predictive models were first developed using environmental surrogates with estimates of prediction uncertainty, and then the efficacy of the three assemblages as biosurrogates for each other was assessed. Data from underwater visual surveys of subtidal rocky reefs were collected from the southeastern coastline of continental Australia (including South Australia and Victoria) and the northern coastline of Tasmania. These data were combined with 0.01 degree-resolution gridded environmental variables to develop statistical models of compositional turnover (beta diversity) using GFM. GFM extends the machine learning, ensemble tree-based method of random forests (RF), to allow the simultaneous modeling of multiple taxa. The models were used to generate predictions of compositional turnover for each of the three assemblages within unsurveyed areas across the 6600 km of coastline in the region of interest. The most important predictor for all three assemblages was variability in sea surface temperature (measured as standard deviation from measures taken interannually). Spatial predictions of compositional turnover within unsurveyed areas across the region of interest were remarkably congruent across the three taxa. However, the greatest uncertainty in these predictions varied in location among the different assemblages. Pairwise congruency comparisons of observed and predicted turnover among the three assemblages showed that invertebrate and macroalgal biodiversity were most similar, followed by fishes and macroalgae, and lastly fishes and invertebrate biodiversity, suggesting that of the three assemblages, macroalgae would make the best biosurrogate for both invertebrate and fish compositional turnover.

Contaminated suspended sediments toxic to an Antarctic filter feeder: aqueous- and particulate-phase effects.

Disturbances such as dredging, storms, and bioturbation result in the resuspension of sediments. This may affect sessile organisms that live on hard substrates directly above the sediment. Localized sediment contamination exists around many Antarctic research stations, often resulting in elevated contamination loads in marine sediments. To our knowledge, the potential impact of resuspended contaminated sediments on sessile fauna has not been considered, so in the present study, we assessed the sensitivity of Antarctic spirorbid polychaetes to aqueous metals and to metal-contaminated sediments that had been experimentally resuspended. Worms were first exposed to aqueous metals, both singly and in combination, over 10 d. Spirorbid mortality was tolerant to copper (median lethal concentration [LC50], 570 microg/L), zinc (LC50, > 4,910 microg/L), and lead (LC50, > 2,905 microg/L); however, spirorbid behavior responded to copper concentrations as low as 20 microg/L. When in combination, zinc significantly reduced mortality caused by copper. A novel technique was used to resuspend sediments spiked with four concentrations of three metals (up to 450 microg/g dry wt of copper, 525 micro/g dry wt of lead, and 2,035 microg/g dry wt of zinc). The response of spirorbids to unfiltered suspended sediment solutions and filtered solutions (aqueous metal exposure) was measured. Suspended sediments were toxic to filter-feeding spirorbids at concentrations approximating those found in contaminated Antarctica areas. Toxicity resulted both from aqueous metals and from metals associated with the suspended sediments, although suspended clean sediments had no impact. To our knowledge, the present study is the first to show that resuspension of contaminated sediments can be an important pathway for toxicity to Antarctic hard substrate organisms. Based on the present results, current sediment-quality guidelines used in the evaluation of Australian sediments may be applicable to Antarctic ecosystems.

Phylogenetic and geographic variation in host breadth and composition by herbivorous amphipods in the family Ampithoidae.

Predicting the host range for herbivores has been a major aim of research into plant-herbivore interactions and an important model system for understanding the evolution of feeding specialization. Among many terrestrial insects, host range is strongly affected by herbivore phylogeny and long historical associations between particular herbivore and plant taxa. For small herbivores in marine environments, it is known that the evolution of host use is sculpted by several ecological factors (e.g., food quality, value as a refuge from predators, and abiotic forces), but the potential for phylogenetic constraints on host use remains largely unexplored. Here, we analyze reports of host use of herbivorous amphipods from the family Ampithoidae (102 amphipod species from 12 genera) to test the hypotheses that host breadth and composition vary among herbivore lineages, and to quantify the extent to which nonpolar secondary metabolites mediate these patterns. The family as a whole, and most individual species, are found on a wide variety of macroalgae and seagrasses. Despite this polyphagous host use, amphipod genera consistently differed in host range and composition. As an example, the genus Peramphithoe rarely use available macrophytes in the order Dictyotales (e.g., Dictyota) and as a consequence, display a more restricted host range than do other genera (e.g., Ampithoe, Cymadusa, or Exampithoe). The strong phylogenetic effect on host use was independent of the uneven distribution of host taxa among geographic regions. Algae that produced nonpolar secondary metabolites were colonized by higher numbers of amphipod species relative to chemically poor genera, consistent with the notion that secondary metabolites do not provide algae an escape from amphipod herbivory. In contrast to patterns described for some groups of phytophagous insects, marine amphipods that use chemically rich algae tended to have broader, not narrower, host ranges. This result suggests that an evolutionary advantage to metabolite tolerance in marine amphipods may be that it increases the availability of appropriate algal hosts (i.e., enlarges the resource base).

An evaluation of the error and uncertainty in epibenthos cover estimates from AUV images collected with an efficient, spatially-balanced design.

Efficient monitoring of organisms is at the foundation of protected area and biodiversity management. Such monitoring programs are based on a systematically selected set of survey locations that, while able to track trends at those locations through time, lack inference for the overall region being "monitored". Advances in spatially-balanced sampling approaches offer alternatives but remain largely untested in marine ecosystems. This study evaluated the merit of using a two-stage, spatially-balanced survey framework, in conjunction with generalized additive models, to estimate epifauna cover at a reef-wide scale for mesophotic reefs within a large, cross-shelf marine park. Imagery acquired by an autonomous underwater vehicle was classified using a hierarchical scheme developed under the Collaborative and Automated Tools for Analysis of Marine Imagery (CATAMI). At a realistic image subsampling intensity, the two-stage, spatially-balanced framework provided accurate and precise estimates of reef-wide cover for a select number of epifaunal classes at the coarsest CATAMI levels, in particular bryozoan and porifera classes. However, at finer hierarchical levels, accuracy and/or precision of cover estimates declined, primarily because of the natural rarity of even the most common of these classes/morphospecies. Ranked predictor importance suggested that bathymetry, backscatter and derivative terrain variables calculated at their smallest analysis window scales (i.e. 81 m2) were generally the most important variables in the modeling of reef-wide cover. This study makes an important step in identifying the constraints and limitations that can be identified through a robust statistical approach to design and analysis. The two-stage, spatially-balanced framework has great potential for effective quantification of epifaunal cover in cross-shelf mesophotic reefs. However, greater image subsampling intensity than traditionally applied is required to ensure adequate observations for finer-level CATAMI classes and associated morphospecies.

Interactive responses of primary producers and grazers to pollution on temperate rocky reefs.

Macroalgal beds provide important habitat structure and support primary production for rocky reef communities, but are increasingly degraded as a result of human pressures. Various sources of pollution can have both direct and interactive effects on stressed ecosystems. In particular, interactions involving invertebrate grazers could potentially weaken or strengthen the overall impact of pollution on macroalgal beds. Using a paired impact-control experimental design, we tested the effects of multiple pollution sources (fish farms, marinas, sewerage, and stormwater) on translocated and locally established algal assemblages, while also considering the influence of invertebrate grazers. Marinas directly affected algal assemblages and also reduced densities of amphipods and other invertebrate mesograzers. Fish farms and sewerage outfalls tended to directly increase local establishment of foliose and leathery algae without any indication of changes in herbivory. Overall, pollution impacts on algae did not appear to be strongly mediated by changes in grazer abundance. Instead, mesograzer abundance was closely linked to availability of more complex algal forms, with populations likely to decline concurrently with loss of complex algal habitats. Macrograzers, such as sea urchins, showed no signs of a negative impact from any pollution source; hence, the influence of this group on algal dynamics is probably persistent and independent of moderate pollution levels, potentially adding to the direct impacts of pollution on algal beds in urbanised environments.

Abundance and richness of key Antarctic seafloor fauna correlates with modelled food availability.

Most seafloor communities at depths below the photosynthesis zone rely on food that sinks through the water column. However, the nature and strength of this pelagic-benthic coupling and its influence on the structure and diversity of seafloor communities is unclear, especially around Antarctica where ecological data are sparse. Here we show that the strength of pelagic-benthic coupling along the East Antarctic shelf depends on both physical processes and the types of benthic organisms considered. In an approach based on modelling food availability, we combine remotely sensed sea-surface chlorophyll-a, a regional ocean model and diatom abundances from sediment grabs with particle tracking and show that fluctuating seabed currents are crucial in the redistribution of surface productivity at the seafloor. The estimated availability of suspended food near the seafloor correlates strongly with the abundance of benthic suspension feeders, while the deposition of food particles correlates with decreasing suspension feeder richness and more abundant deposit feeders. The modelling framework, which can be modified for other regions, has broad applications in conservation and management, as it enables spatial predictions of key components of seafloor biodiversity over vast regions around Antarctica.

Seawater temperature effect on metal accumulation and toxicity in the subantarctic Macquarie Island isopod, Exosphaeroma gigas.

Very little is currently known of subantarctic nearshore invertebrates' sensitivity to environmental metals and the role of temperature in this relationship. This study investigated Cu and Zn toxicity in the common subantarctic intertidal isopod, Exosphaeroma gigas, and the influence of temperature on Cu toxicity and bioaccumulation kinetics. Adult E. gigas are insensitive to Cu and Zn at concentrations of 3200 and 7400µg/L respectively in non-renewal tests at 5.5°C (ambient subtidal temperature) over 14days. Under renewed exposures over the same temperature and time period the LC50 for copper was 2204µg/L. A 10-fold increase in Cu body burden occurred relative to zinc, indicating E. gigas has different strategies for regulating the two metals. Copper toxicity and time to mortality both increased with elevated temperature. However, temperature did not significantly affect Cu uptake rate and efflux rate constants derived from biodynamic modelling at lower Cu concentrations. These results may be attributable to E. gigas being an intertidal species with physiological mechanisms adapted to fluctuating environmental conditions. Cu concentrations required to elicit a toxicity response indicates that E. gigas would not be directly threatened by current levels of Cu or Zn present in Macquarie Island intertidal habitats, with the associated elevated temperature fluctuations. This study provides evidence that the sensitivity of this subantarctic intertidal species to metal contaminants is not as high as expected, and which has significance for the derivation of relevant guidelines specific to this distinct subpolar region of the world.

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.

Loss of native rocky reef biodiversity in Australian metropolitan embayments.

Urbanisation of the coastal zone represents a key threat to marine biodiversity, including rocky reef communities which often possess disproportionate ecological, recreational and commercial importance. The nature and magnitude of local urban impacts on reef biodiversity near three Australian capital cities were quantified using visual census methods. The most impacted reefs in urbanised embayments were consistently characterised by smaller, faster growing species, reduced fish biomass and richness, and reduced mobile invertebrate abundance and richness. Reef faunal distribution varied significantly with heavy metals, local population density, and proximity to city ports, while native fish and invertebrate communities were most depauperate in locations where invasive species were abundant. Our study adds impetus for improved urban planning and pollution management practises, while also highlighting the potential for skilled volunteers to improve the tracking of changes in marine biodiversity values and the effectiveness of management intervention.

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.

Beyond the bed: effects of metal contamination on recruitment to bedded sediments and overlying substrata.

Metal-contaminated sediments pose a recognised threat to sediment-dwelling fauna. Re-mobilisation of contaminated sediments however, may impact more broadly on benthic ecosystems, including on diverse assemblages living on hard substrata patches immediately above sediments. We used manipulative field experiments to simultaneously test for the effects of metal contamination on recruitment to marine sediments and overlying hard substrata. Recruitment to sediments was strongly and negatively affected by metal contamination. However, while assemblage-level effects on hard-substratum fauna and flora were observed, most functional groups were unaffected or slightly enhanced by exposure to contaminated sediments. Diversity of hard-substratum fauna was also enhanced by metal contamination at one site. Metal-contaminated sediments appear to pose less of a hazard to hard-substratum than sediment-dwelling assemblages, perhaps due to a lower direct contaminant exposure or to indirect effects mediated by contaminant impacts on sediment fauna. Our results indicate that current sediment quality guidelines are protective of hard-substrata organisms.

Physico-chemical changes in metal-spiked sediments deployed in the field: implications for the interpretation of in situ studies.

Manipulative field studies are useful for investigating cause-effect relationships between contamination and benthic community health. However, there are many challenges for creating environmentally relevant exposures and determining what measurements are necessary to correctly interpret the results. This study describes the physical and chemical changes in the properties of metal-spiked marine sediments deployed in four different locations for up to 11 months. The test sediments lost between 20% and 75% of their volume during the deployment period, with the greatest losses occurring at sites affected by strong hydrodynamic activity. More sediment was lost from clean treatments than those spiked with high metal concentrations and corresponded with differential recruitment of infauna to these treatments. In general, a greater proportion of spiked-metals remained at lower energy sites (48-85%) than at higher energy sites (15-48%). The decreased metal concentrations were attributed mostly to the loss of the metal-spiked sediments (through resuspension) and their dilution with sediments depositing from the surrounding environment. A range of recommendations are made for optimising the information gained from field-based studies using metal-spiked sediments. These include the careful documentation of physico-chemical sediment properties pre- and post-deployment, the use of co-located sediment traps and knowledge of site-specific hydrodynamic processes.