While ecologists have long recognized the influence of spatial resolution on species distribution models (SDMs), they have given relatively little attention to the influence of temporal resolution. Considering temporal resolutions is critical in distribution modelling of highly mobile marine animals, as they interact with dynamic oceanographic processes that vary at time-scales from seconds to decades. We guide ecologists in selecting temporal resolutions that best match ecological questions and ecosystems, and managers in applying these models. We group the temporal resolutions of environmental variables used in SDMs into three classes: instantaneous, contemporaneous and climatological. We posit that animal associations with fine-scale and ephemeral | 1099MANNOCCI et Al. | INTRODUCTIONHighly mobile marine animals such as marine mammals, seabirds, sea turtles and fish are unevenly distributed in the ocean. Ecologists have long sought to understand and predict their patterns of distributions, particularly for commercially valuable species subject to exploitation (Lehodey, Bertignac, Hampton, Lewis, & Picaut, 1997) and for protected species vulnerable to incidental harm (Reilly, 1990). They often employ species distribution models (SDMs) that statistically relate distribution patterns to environmental conditions by linking animal observations to environmental variables. SDMs have been successfully used to examine many ecological, management and conservation questions (Elith & Leathwick, 2009). In particular, they have been widely used to explain and predict distribution patterns of highly mobile marine animals in a variety of ecosystems (Benson et al., 2011;Forney, Becker, Foley, Barlow, & Oleson, 2015;Hartog, Hobday, Matear, & Feng, 2011;Mannocci et al., 2014).It has become apparent that the hierarchical structure of processes in the marine environment drives the distribution and movement patterns of marine animals at multiple spatio-temporal scales (Benoit-Bird, Battaile, Nordstrom, & Trites, 2013;Fauchald, Erikstad, & Skarsfjord, 2000;Fauchald & Tveraa, 2006;Fritz, Said, & Weimerskirch, 2003;Pinaud & Weimerskirch, 2005) (Figure 1). At fine scales, animals track ephemeral prey patches that extend over tens of metres to satisfy their energy requirements (Goldbogen et al., 2008;Heaslip, Iverson, Bowen, & James, 2012 (Benson et al., 2011;Hobday & Hartog, 2014;Tew Kai & Marsac, 2010). At broad scales, animals associate with persistent water masses and current systems that extend over thousands of kilometres and delimit their geographic ranges or migration routes (Jaquet, Whitehead, & Lewis, 1996;Reygondeau et al., 2012;Shillinger et al., 2008). Thus, the distributions of highly mobile marine animals appear determined by both short-term ocean variability and persistent patterns of longer-term ocean climate.Researchers use a variety of methods to obtain synoptic data on marine animal distributions and the marine environment at a wide range of spatial and temporal extents ( Figure 2, see Appendix S1 in Supporti...

Black band disease (BBD) of corals is characterized as a pathogenic microbial consortium composed of a wide variety of microorganisms. Together, many of these microorganisms contribute to an active sulfur cycle that produces anoxia and high levels of sulfide adjacent to the coral surface, conditions that are lethal to coral tissue. Sulfate-reducing bacteria, as sulfide producers, are an important component of the sulfur cycle and the black band community. Previous molecular survey studies have shown multiple Desulfovibrio species present in BBD but with limited consistency between bacterial species and infections. In this study we compared 16S rRNA gene sequences of sulfate-reducing bacteria selectively cultured from 6 BBD bands on 4 coral species, Diploria clivosa, D. strigosa, D. labyrinthiformes, and Siderastrea siderea, in the Florida Keys and Dominica. The 16S rRNA gene sequences were obtained through direct sequencing of PCR products or by cloning. A BLAST search revealed that 8 out of 10 cultures sequenced were highly homologous to Desulfovibrio sp. strain TBP-1, a strain originally isolated from marine sediment. Although the remaining 2 sequences were less homologous to Desulfovibrio sp. strain TBP-1, they did not match any other sulfate-reducing (or other) species in GenBank.

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The world’s coral reefs appear to be in a global decline, yet most previous research on coral reefs has taken place at depths shallower than 30 m. Mesophotic coral ecosystem (depths deeper than ~30 m) studies have revealed extensive, productive habitats and rich communities. Despite recent advances, mesophotic coral ecosystems remain understudied due to challenges with sampling at deeper depths. The few previous studies of mesophotic coral ecosystems have shown variation across locations in depth-specific species composition and assemblage shifts, potentially a response to differences in habitat or light availability/water clarity. This study utilized scuba to examine fish and benthic communities from shallow and upper mesophotic (to 45 m) zones of Flower Garden Banks National Marine Sanctuary (FGBNMS, 28°0ʹN; 93°50ʹW) from 2010–2012. Dominant planktivores were ubiquitous in shallow and upper mesophotic habitats, and comparisons with previous shallow research suggest this community distribution has persisted for over 30 years. Planktivores were abundant in shallow low-relief habitats on the periphery of the coral reef, and some of these sites that contained habitat transitioning from high to low relief supported high biomass of benthic predators. These peripheral sites at FGBNMS may be important for the trophic transfer of oceanic energy to the benthic coral reef. Distinct differences between upper mesophotic and shallow communities were also observed. These included greater overall fish (as well as apex predator) biomass in the upper mesophotic, differences in apex predator community composition between depth zones, and greater percent cover of algae, rubble, sand, and sponges in the upper mesophotic. Greater fish biomass in the upper mesophotic and similar fish community composition between depth zones provide preliminary support that upper mesophotic habitats at FGBNMS have the capacity to serve as refugia for the shallow-water reefs. Diving surveys of the upper mesophotic and shallow-water coral reef have revealed valuable information concerning the reef fish community in the northern Gulf of Mexico, with implications for the conservation of apex predators, oceanic coral reefs, and the future management of FGBNMS.

a b s t r a c tWhen coral reefs held in United States public trust are injured by incidents such as vessel groundings or oil spills, a natural resource damage assessment (NRDA) process may be conducted to quantify the resource service loss. Coral cover has been used as an indicator metric to represent lost services in habitat equivalency analyses for determination of compensatory restoration. Depending on the injury and habitat, however, lost services may be more comprehensively represented by alternative approaches such as composite metrics which incorporate other coral reef community characteristics, or a resourcescale approach utilizing size-frequency distributions of injured organisms. We describe the evolving state of practice for capturing coral reef ecosystem services within the natural resources damage assessment context, explore applications and limitations of current metrics, and suggest future directions that may increase the likelihood that NRDA metrics more fully address ecosystem services affected by an injury.Published by Elsevier Ltd.

Resource managers in the United States and worldwide are tasked with identifying and mitigating trade-offs between human activities in the deep sea (e.g., fishing, energy development, and mining) and their impacts on habitat-forming invertebrates, including deep-sea corals, and sponges (DSCS). Related management decisions require information about where DSCS occur and in what densities. Species distribution modeling (SDM) provides a cost-effective means of identifying potential DSCS habitat over large areas to inform these management decisions and data collection. Here we describe good practices for DSCS SDM, especially in the context of data collection and management applications. Managers typically need information regarding DSCS encounter probabilities, densities, and sizes, defined at sub-regional to basin-wide scales and validated using subsequent, targeted data collections. To realistically achieve these goals, analysts should integrate available data sources in SDMs including fine-scale visual sampling and broad-scale resource surveys (e.g., fisheries trawl surveys), include environmental predictor variables representing multiple spatial scales, model residual spatial autocorrelation, and quantify prediction uncertainty.Winship et al. Deep-Sea Coral Modeling Good PracticesWhen possible, models fitted to presence-absence and density data are preferred over models fitted only to presence data, which are difficult to validate and can confound estimated probability of occurrence or density with sampling effort. Ensembles of models can provide robust predictions, while multi-species models leverage information across taxa, and facilitate community inference. To facilitate the use of models by managers, predictions should be expressed in units that are widely understood and validated at an appropriate spatial scale using a sampling design that provides strong statistical inference. We present three case studies for the Pacific Ocean that illustrate good practices with respect to data collection, modeling, and validation; these case studies demonstrate it is possible to implement our good practices in real-world settings.

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