Aggregation influences coral species richness at multiple spatial scales

The spatial dispersion of individuals across multiple spatial scales can significantly influence biodiversity patterns. Here we characterize the dispersion of corals in reef assemblages distributed across a 10000-km longitudinal biodiversity gradient from Indonesia to the Society Islands, using a multiscale sampling design. Our results indicate that most coral species were aggregated among 10-m transect samples across this vast distance. Using observed and randomized species sampling curves, we show that aggregation reduced the number of species per transect, site, and island sample on average by 13-27%. Across site, island, and regional scales, aggregation also reduced the area under species sampling curves by an average of 2.7-6.5%. The level of aggregation was relatively constant across spatial scales within regions and did not vary among habitats. However, there was significant variation among regions using transect samples across individual sites. Specifically, aggregation reduced the species richness per transect and the area under species sampling curves nearly twice as much in the Indonesian biodiversity hotspot than in the Society Islands. As a significant component of the spatial structure of coral assemblages, aggregation should be integrated into our understanding of coral community dynamics and the development of conservation strategies designed to protect these communities.     

The application of predicted habitat models to investigate the spatial ecology of demersal fish assemblages

Benthic habitats are known to influence the abundance and richness of demersal fish assemblages; however, little is known about how habitat structure and composition influences these distributions at very fine scales. We examined how the benthic environment structures marine fish assemblages using high-resolution bathymetry and accurate predicted benthic habitat maps. Areas characterised by a mosaic of habitat patches supported the highest richness of demersal fishes. A total of 37.4% of the variation in the distribution of the fish assemblage was attributed to 6 significant variables. Depth explained 23.0% of the variation, with the boulders explaining 12.6% and relief 1.4%. The remaining measures (seawhips, light/exposure and solid reef) provided a small (<1.0%) but significant contribution. Identifying components of the benthic environment important in structuring fish assemblages and understanding how they influence the spatial distribution of marine fishes is imperative for better management of demersal fish populations.     

Scale-dependent variation in coral community similarity across sites, islands, and island groups

Community similarity is the proportion of species richness in a region that is shared on average among communities within that region. The slope of local richness (alpha diversity) regressed on regional richness (gamma diversity) can serve as an index of community similarity across regions with different regional richness. We examined community similarity in corals at three spatial scales (among transects at a site, sites on an island, and islands within an island group) across a 10 000-km longitudinal diversity gradient in the west-central Pacific Ocean. When alpha diversity was regressed on gamma diversity, the slopes, and thus community similarity, increased with scale (0.085, 0.261, and 0.407, respectively) because a greater proportion of gamma diversity was subsumed within alpha diversity as scale increased. Using standard randomization methods, we also examined how community similarity differed between observed and randomized assemblages and how this difference was affected by spatial separation of species within habitat types and specialization of species to three habitat types (reef flats, crests, and slopes). If spatial separation within habitat types and/or habitat specialization (i.e., underdispersion) occurs, fewer species are shared among assemblages than the random expectation. When the locations of individual coral colonies were randomized within and among habitat types, community similarity was 46-47% higher than that for observed assemblages at all three scales. We predicted that spatial separation of coral species within habitat types should increase with scale due to dispersal/extinction dynamics in this insular system, but that specialization of species to different habitat types should not change because habitat differences do not change with scale. However, neither habitat specialization nor spatial separation within habitat types differed among scales. At the two larger scales, each accounted for 22-24% of the difference in community similarity between observed and randomized assemblages. At the smallest scale (transect-site), neither spatial separation within habitat types nor habitat specialization had significant effects on community similarity, probably due to the small size of transect samples. The results suggest that coral species can disperse among islands in an island group as easily as they can among sites on an island over time scales that are relevant to their establishment and persistence on reefs.     

Landscape-level influences of terrestrial snake occupancy within the southeastern United States

Habitat loss and degradation are thought to be the primary drivers of species extirpations, but for many species we have little information regarding specific habitats that influence occupancy. Snakes are of conservation concern throughout North America, but effective management and conservation are hindered by a lack of basic natural history information and the small number of large-scale studies designed to assess general population trends. To address this information gap, we compiled detection/nondetection data for 13 large terrestrial species from 449 traps located across the southeastern United States, and we characterized the land cover surrounding each trap at multiple spatial scales (250-, 500-, and 1000-m buffers). We used occupancy modeling, while accounting for heterogeneity in detection probability, to identify habitat variables that were influential in determining the presence of a particular species. We evaluated 12 competing models for each species, representing various hypotheses pertaining to important habitat features for terrestrial snakes. Overall, considerable interspecific variation existed in important habitat variables and relevant spatial scales. For example, kingsnakes (Lampropeltis getula) were negatively associated with evergreen forests, whereas Louisiana pinesnake (Pituophis ruthveni) occupancy increased with increasing coverage of this forest type. Some species were positively associated with grassland and scrub/shrub (e.g., Slowinski's cornsnake, Elaphe slowinskii) whereas others, (e.g., copperhead, Agkistrodon contortrix, and eastern diamond-backed rattlesnake, Crotalus adamanteus) were positively associated with forested habitats. Although the species that we studied may persist in varied landscapes other than those we identified as important, our data were collected in relatively undeveloped areas. Thus, our findings may be relevant when generating conservation plans or restoration goals. Maintaining or restoring landscapes that are most consistent with the ancestral habitat preferences of terrestrial snake assemblages will require a diverse habitat matrix over large spatial scales.     

Diversity,abundance, and distribution of reef sharks on outer-shelf reefs of the Great Barrier Reef,Australia

Quantifying the distribution and habitat use of sharks is critical for understanding their ecological role and for establishing appropriate conservation and management regimes. On coral reefs, particularly the Great Barrier Reef (GBR), little is known regarding the distribution of sharks across major reef habitat types. In this study, we surveyed shark populations across outer-shelf reefs of the GBR in order to determine the diversity, abundance, and distribution of reef sharks across three major coral reef habitats: (1) the reef slope, (2) the back reef and (3) the reef flat. Model selection revealed that habitat was the principal factor influencing shark distribution and abundance. Specifically, overall shark abundance and diversity were significantly higher on the reef slope (and to a lesser degree, the back reef) than the reef flat. This confirms that shark populations are not homogeneously distributed across coral reefs. Thus, the results presented herein have important implications for shark population assessments. In addition, our results highlight the potential importance of the reef slope, with high levels of live coral cover and structural complexity, for sustaining reef shark populations. As this habitat is highly susceptible to disturbance events, this study provides a useful context for predicting and understanding how environmental degradation may influence reef shark populations in the future.     

Macrofaunal responses to structural complexity are mediated by environmental variability and surrounding habitats

Investigating the context that surrounds each habitat is crucial to understand local responses of assemblages of species to habitats. Here, I tested whether responses of benthic macroinvertebrates to the structural complexity of experimental habitats were mediated by the characteristics of their surrounding habitats (i.e. rockpools or emergent-rock surfaces). Each type of surrounding habitat provided particular biotic (e.g. algal growth) and abiotic (e.g. temperature, water movement) conditions that were expected to affect benthic assemblages. The results show that (1) composition of entire assemblages was affected by the matrix and type of habitat; (2) effects of the matrix on the number of species varied depending on the different types of habitats; (3) abundant species showed specific responses to type of habitat, independently of the matrix; and (4) relationships between numbers of species and two major environmental variables (i.e. micro-algal biomass and sediment) varied depending on the type of habitats and the surrounding matrix. Generally, these findings demonstrate that understanding the consequences of the spatial structure of these habitats is essential to advance our knowledge on patterns of abundance and distributions of functionally important species and ultimately the structure of intertidal assemblages.     

In search of quorum effects in metacommunity structure: species co-occurrence analyses

Alternative models of community assembly emphasize regional, stochastic, dispersal-based processes or local, deterministic, niche-based processes. Community ecology's historical focus on local processes implicitly assumes that local processes surpass regional processes over time or across space to derive nonrandom metacommunity structure (i.e., a quorum effect). Quorum effects are expected late in succession among nearby sites, whereas quorum effects are not expected early in succession among distant sites. I conducted a meta-analysis of zooplankton data sets encompassing time scales of one to thousands of years and spatial scales of <1 m to thousands of kilometers. Species co-occurrence analyses statistically evaluated presence/absence patterns relative to random patterns obtained with Monte Carlo null models. A series of weighted analyses was conducted and alternative randomization algorithms and null models were evaluated. Most zooplankton metacommunities were randomly structured in unweighted analyses, and the distribution of significant structure did not follow quorum effect predictions. Weighted analyses (e.g., by habitat area) revealed significant, nonrandom structure in most zooplankton metacommunities, but the distribution of significant structure still did not adhere well to quorum effect predictions. Finally, additional weighting for study scale (number of sites) nullified most significant area-weighted structure, and again, the distribution of significant structure did not follow quorum effect predictions. Overall, a quorum effect was not supported, perhaps related to zooplankton life histories and energetics and/or the quorum effect itself. Results at the presence/absence level of resolution indicated that local processes did not generally override regional processes over time or across space to drive community structure. A full integration of dispersal- and niche-based concepts in metacommunity dynamics will be most fruitful for unraveling community assembly. Species co-occurrence analyses were scale dependent (habitat area and study size). Future analyses should use weights for important factors (e.g., habitat area), and meta-analyses should include study scale as an additional factor contributing to apparent patterns.     

Intertidal assemblages on artificial and natural habitats in marinas on the north-west coast of Italy

Following the progressive expansion of human populations, the number of artificial habitats is increasing in shallow waters of urbanised coastal areas. The comparison of assemblages between natural and artificial habitats is necessary to determine whether there is real loss and fragmentation of natural habitats. This study investigates the changes in intertidal assemblages caused by marinas for tourists, along exposed rocky shores on the north-west coast of Italy. Marinas, being made of transplanted boulders and by internal wave-sheltered seawalls, introduce different types of artificial habitats in a relatively small area. Intertidal assemblages on breakwaters, seawalls and adjacent rocky shores were compared at three locations, thousands of metres apart. To assess the generality of patterns through time, natural and artificial habitats were sampled at three different times, over a period of about 2 years. Data were analysed by means of multivariate and univariate analyses to test the hypotheses that assemblages and abundances of single taxa differed among habitats, consistently among locations and times of sampling. Furthermore, the variability of assemblages at the scales of tens of centimetres and metres was compared among habitats. Assemblages on seawalls were largely distinct from those on rocky shores or breakwaters. Seawalls, which supported a smaller number of species than breakwaters and rocky shores, were dominated by encrusting algae and lacked common species such as Rissoella verrucosa and Patella rustica. The abundance of main-space occupiers did not differ between breakwaters and rocky shores, but there were differences in variability of assemblages at both the spatial scales investigated. This study provides evidence for differences between intertidal assemblages supported by artificial habitats at marinas and those on adjacent rocky shores. Differences in habitat-structure (and/or wave-exposure in the case of seawalls) could explain the occurrence of distinct intertidal assemblages. Despite the nature and magnitude of these differences, varied according to the type of artificial habitat considered, neither breakwaters nor seawalls could be considered surrogates of rocky shores.Communicated by R. Cattaneo-Vietti, Genova     

Integrating larval connectivity into the marine conservation decision-making process across spatial scales

Larval dispersal connectivity is typically integrated into spatial conservation decisions at regional or national scales, but implementing agencies struggle with translating these methods to local scales. We used larval dispersal connectivity at regional (hundreds of kilometers) and local (tens of kilometers) scales to aid in design of networks of no-take reserves in Southeast Sulawesi, Indonesia. We used Marxan with Connectivity informed by biophysical larval dispersal models and remotely sensed coral reef habitat data to design marine reserve networks for 4 commercially important reef species across the region. We complemented regional spatial prioritization with decision trees that combined network-based connectivity metrics and habitat quality to design reserve boundaries locally. Decision trees were used in consensus-based workshops with stakeholders to qualitatively assess site desirability, and Marxan was used to identify areas for subsequent network expansion. Priority areas for protection and expected benefits differed among species, with little overlap in reserve network solutions. Because reef quality varied considerably across reefs, we suggest reef degradation must inform the interpretation of larval dispersal patterns and the conservation benefits achievable from protecting reefs. Our methods can be readily applied by conservation practitioners, in this region and elsewhere, to integrate connectivity data across multiple spatial scales.     

Forecasting population trend from the scaling pattern of occupancy

Forecasting the temporal trend of a focal species, its range expansion or retraction, provides crucial information regarding population viability. To this end, we require the accumulation of temporal records which is evidently time consuming. Progress in spatial data capturing has enabled rapid and accurate assessment of species distribution across large scales. Therefore, it would be appealing to infer the temporal trends of populations from the spatial structure of their distributions. Based on a combination of models from the fields of range dynamics, occupancy scaling and spatial autocorrelation, here I present a model for forecasting the population trend solely from its spatial distribution. Numerical tests using cellular automata confirm a positive correlation, as inferred from the model, between the temporal change in species range sizes and the exponent of the power-law scaling pattern of occupancy. The model is thus recommended for rapid estimation of species range dynamics from a single snapshot of its current distribution. Further applications in biodiversity conservation could provide a swift risk assessment, especially, for endangered and invasive species.     

Bioengineers and their associated fauna respond differently to the effects of biogeography and upwelling

Temperature and primary production (often linked to nutrient supply) are two of the few factors influencing species diversity and abundances across mesoscale gradients, while at smaller scales the habitat complexity offered by bioengineers is important. Previous studies have illustrated effects of upwelling and biogeography on intertidal bioengineers, but it is not known if these processes influence assemblages associated with those bioengineers in a similar way. We examined the habitat structure offered by two species of mussels and their associated fauna in five regions across 3000 km and three biogeographic provinces of the South African coast, replicating upwelling and non-upwelling areas within each region. Upwelling and region influenced the structure of mussel beds (the density and size of mussels). In contrast, upwelling did not influence mesoscale differences in composition, abundance, and numbers of species of crustaceans, mollusks, or polychaetes in mussel beds. Regardless of trophic level or mode of reproduction, mussel bed fauna were influenced only by region. Regional differences were strongly influenced by biogeography. The associated fauna was, however, also strongly correlated with the structure of the habitats created by mussels. Our results support the importance of upwelling to a critical ecosystem engineer, but show that these effects do not extend directly to the assemblages of associated fauna, which are more influenced by regional-scale effects and biogeography. We suggest that mesoscale patterns in the associated fauna of this bioengineered habitat are driven by the direct effects of biogeography, combined with the influence of biogeography and upwelling on mussel bed structure.     

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.     

Reef size and isolation determine the temporal stability of coral reef fish populations

Temporal variance in species abundance, a potential driver of extinction, is linked to mean abundance through Taylor's power law, the empirical observation of a linear log-log relationship with a slope between 1 and 2 for most species. Here we test the idea that the slope of Taylor's power law can vary both among species and spatially as a function of habitat area and isolation. We used the world's most extensive database of coral reef fish communities comprising a 15-year series of fish abundances on 43 reefs of Australia's Great Barrier Reef. Greater temporal variances were observed at small and isolated reefs, and lower variances at large and connected ones. The combination of reef area and isolation was associated with an even greater effect on temporal variances, indicating strong empirical support for the idea that populations on small and isolated reefs will succumb more frequently to local extinction via higher temporal variability, resulting in lower resilience at the community level. Based on these relationships, we constructed a regional predictive map of the dynamic fragility of coral reef fish assemblages on the Great Barrier Reef.     

Climate, habitat, and species interactions at different scales determine the structure of a Neotropical bat community

Climate, habitat, and species interactions are factors that control community properties (e.g., species richness, abundance) across various spatial scales. Usually, researchers study how a few properties are affected by one factor in isolation and at one scale. Hence, there are few multi-scale studies testing how multiple controlling factors simultaneously affect community properties at different scales. We ask whether climate, habitat structure, or insect resources at each of three spatial scales explains most of the variation in six community properties and which theory best explains the distribution of selected community properties across a rainfall gradient. We studied a Neotropical insectivorous bat ensemble in the Isthmus of Panama with acoustic monitoring techniques. Using climatological data, habitat surveys, and insect captures in a hierarchical sampling design we determined how much variation of the community properties was explained by the three factors employing two approaches for variance partitioning. Our results revealed that most of the variation in species richness, total abundance, and feeding activity occurred at the smallest spatial scale and was explained by habitat structure. In contrast, climate at large scales explained most of the variation in individual species' abundances. Although each species had an idiosyncratic response to the gradient, species richness peaked at intermediate levels of precipitation, whereas total abundance was very similar across sites, suggesting density compensation. All community properties responded in a different manner to the factor and scale under consideration.     

Method of estimating the standing stock of Trochus niloticus incorporating Landsat satellite data,with application to the trochus resources of the Bourke Isles,Torres Strait,Australia

The habitat of Trochus niloticus in the Bourke Isles, Torres Strait, was classified into areas of a Landsat image, using high-ratio values of green (Band 2) to red (Band 3) light, along the windward reef margins. These shallow-water (< 15 m) areas have a coral and rubble/algal pavement cover, which constitutes the optimal habitat for this gastropod. The habitat was sampled to estimate the abundance of T. niloticus. The proportion of commercial-sized individuals was estimated by measuring the basal width of all individuals in a sample. A multistage sample design incorporating three spatial scales -100 m² (transect), 1500 m² (site) and 1 km² (reef) — was used to provide variance estimates for sample-design optimisation and to provide data on the spatial variation of abundance. Most variation (68%) in abundance was within reefs and was attributable to differences in reef cover. Variations in abundance and time costs for sampling 2 and 4 m transects were compared; the 2 m transect was more efficient than the 4 m transect. The abundance estimates were combined with habitat-area estimates and the proportion of commerical-sized individuals was estimated at a standing stock of 186000 (24% precision), or 14 t of commerical-sized T. niloticus.     

The use of clear-water non-estuarine mangroves by reef fishes on the Great Barrier Reef

Within the tropics, mangroves and coral reefs represent highly productive biomes. Although these habitats are often within close proximity, the role and importance of mangrove habitats for reef fish species remains unclear. Throughout the Indo-Pacific, reef fish species appear to have few links with estuarine mangrove habitats. In contrast, clear-water non-estuarine mangrove habitats throughout the Caribbean support many reef fish species and may be fundamental for sustaining reef fish populations. But how important are clear-water non-estuarine mangroves for reef fishes within the Indo-Pacific? Using visual surveys during diurnal high tide, the fish assemblages inhabiting clear-water mangrove and adjacent reef habitats of Orpheus Island, Great Barrier Reef, were recorded. Of the 188 species of fishes that were recorded, only 38 were observed to inhabit both habitats. Of these, only eight were observed more than five times within each habitat. These observations provide little indication that the clear-water mangroves are an important habitat for reef fish species. In addition, although based on just a 3-month survey period, we found little evidence to suggest that these areas are important nurseries for reef fish species. The clear-water mangroves of Orpheus Island may, however, provide an additional foraging area for the few reef fish species that were observed to utilize these habitats during high tide. The difference in the importance of clear-water mangroves for reef fishes within this study compared with clear-water mangrove counterparts within the Caribbean is surprising. Although only preliminary, our observations would support suggestions that the patterns reflect the different hydrological characteristics and evolutionary histories of these two biogeographic regions.     

Biodiversity of coastal polyclad flatworm assemblages in the wider Caribbean

Polyclads are mobile predators and possibly an important functional component of hard substrate marine environments globally. To understand the natural patterns of spatial differences, polyclad assemblages were sampled in seven coastal regions across the wider Caribbean spanning 15° latitude and 24° longitude between May and June 2005 and May and September 2006. In total, 67 species in 28 genera and 17 families were recorded from 62 sites. Only two species were found in all surveyed regions, Melloplana ferruginea and Pseudoceros bicolor. Conversely, 41 species were restricted to one or two sites, and 34 species were represented by one or two individuals. The distribution and abundance of species varied between the two suborders. Cotyleans were most species rich and had a higher number of species of restricted range, while Acotylea showed a higher proportion of rare species; however, two species were highly abundant comprising over half of the individuals counted. In most habitats, polyclads were rare, but in some intertidal habitats two species, Styloplanocera fasciata and Boninia divae were densely aggregated and dominant members of the benthic epifauna. Alpha diversity was variable but showed no evidence of a relationship with latitude, longitude or depth. Beta diversity increased with the number of habitats sampled and was highest for cotyleans. Highest gamma diversity was recorded in Jamaica and the US Virgin Islands and was not significantly correlated to alpha diversity. Overall assemblages from the seven regions were similar, revealing faunal homogeneity across the wider region. Reef assemblages were distinct from other habitats dominated by species of the Cotylea. Reefs from Panama and the US Virgin Islands were the most species rich. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.