Effects of Ignoring Survey Design Information for Data Reuse

Data are currently being used, and reused, in ecological research at an unprecedented rate. To ensure appropriate reuse however, we need to ask the question: "Are aggregated databases currently providing the right information to enable effective and unbiased reuse?" We investigate this question, with a focus on designs that purposefully favor the selection of sampling locations (upweighting the probability of selection of some locations). These designs are common and examples are those designs that have uneven inclusion probabilities or are stratified. We perform a simulation experiment by creating data sets with progressively more uneven inclusion probabilities and examine the resulting estimates of the average number of individuals per unit area (density). The effect of ignoring the survey design can be profound, with biases of up to 250% in density estimates when naive analytical methods are used. This density estimation bias is not reduced by adding more data. Fortunately, the estimation bias can be mitigated by using an appropriate estimator or an appropriate model that incorporates the design information. These are only available however, when essential information about the survey design is available: the sample location selection process (e.g., inclusion probabilities), and/or covariates used in their specification. The results suggest that such information must be stored and served with the data to support meaningful inference and data reuse.Peer reviewe

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

The use of biological surrogates as proxies for biodiversity patterns is gaining popularity, particularly in marine systems where field surveys can be expensive and species richness high. Yet, uncertainty regarding their applicability remains because of inconsistency of definitions, a lack of standard methods for estimating effectiveness, and variable spatial scales considered. We present a Bayesian meta-analysis of the effectiveness of biological surrogates in marine ecosystems. Surrogate effectiveness was defined both as the proportion of surrogacy tests where predictions based on surrogates were better than random (i.e., low probability of making a Type I error; P) and as the predictability of targets using surrogates (R2). A total of 264 published surrogacy tests combined with prior probabilities elicited from eight international experts demonstrated that the habitat, spatial scale, type of surrogate and statistical method used all influenced surrogate effectiveness, at least according to either P or R2. The type of surrogate used (higher-taxa, cross-taxa or subset taxa) was the best predictor of P, with the higher-taxa surrogates outperforming all others. The marine habitat was the best predictor of R2, with particularly low predictability in tropical reefs. Surrogate effectiveness was greatest for higher-taxa surrogates at a <10-km spatial scale, in low-complexity marine habitats such as soft bottoms, and using multivariate-based methods. Comparisons with terrestrial studies in terms of the methods used to study surrogates revealed that marine applications still ignore some problems with several widely used statistical approaches to surrogacy. Our study provides a benchmark for the reliable use of biological surrogates in marine ecosystems, and highlights directions for future development of biological surrogates in predicting biodiversity

Evolving and Sustaining Ocean Best Practices to Enable Interoperability in the UN Decade of Ocean Science for Sustainable Development

The UN Decade of Ocean Science for Sustainable Development (Ocean Decade) challenges marine science to better inform and stimulate social and economic development while conserving marine ecosystems. To achieve these objectives, we must make our diverse methodologies more comparable and interoperable, expanding global participation and foster capacity development in ocean science through a new and coherent approach to best practice development. We present perspectives on this issue gleaned from the ongoing development of the UNESCO Intergovernmental Oceanographic Commission (IOC) Ocean Best Practices System (OBPS). The OBPS is collaborating with individuals and programs around the world to transform the way ocean methodologies are managed, in strong alignment with the outcomes envisioned for the Ocean Decade. However, significant challenges remain, including: (1) the haphazard management of methodologies across their lifecycle, (2) the ambiguous endorsement of what is "best" and when and where one method may be applicable vs. another, and (3) the inconsistent access to methodological knowledge across disciplines and cultures. To help address these challenges, we recommend that sponsors and leaders in ocean science and education promote consistent documentation and convergence of methodologies to: create and improve context-dependent best practices; incorporate contextualized best practices into Ocean Decade Actions; clarify who endorses which method and why; create a global network of complementary ocean practices systems; and ensure broader consistency and flexibility in international capacity development

Origin of high density seabed pockmark fields and their use in inferring bottom currents

Some of the highest density pockmark fields in the world have been observed on the northwest Australian continental shelf (>700/km2) where they occur in muddy, organic-rich sediment around carbonate banks and paleochannels. Here we developed a semi-automated method to map and quantify the form and density of these pockmark fields (~220,000 pockmarks) and characterise their geochemical, sedimentological and biological properties to provide insight into their formative processes. These data indicate that pockmarks formed due to the release of gas derived from the breakdown of near-surface organic material, with gas accumulation aided by the sealing properties of the sediments. Sources of organic matter include adjacent carbonate banks and buried paleochannels. Polychaetes biodiversity appears to be affected negatively by the conditions surrounding dense pockmark fields since higher biodiversity is associated with low density fields. While regional bi-directionality of pockmark scours corresponds to modelled tidal flow, localised scattering around banks suggests turbulence. This multi-scale information therefore suggests that pockmark scours can act as proxy for bottom currents, which could help to inform modelling of benthic biodiversity pattern

Evolving and sustaining ocean best practices and standards for the next decade

The oceans play a key role in global issues such as climate change, food security, and human health. Given their vast dimensions and internal complexity, efficient monitoring and predicting of the planet’s ocean must be a collaborative effort of both regional and global scale. A first and foremost requirement for such collaborative ocean observing is the need to follow well-defined and reproducible methods across activities: from strategies for structuring observing systems, sensor deployment and usage, and the generation of data and information products, to ethical and governance aspects when executing ocean observing. To meet the urgent, planet-wide challenges we face, methods across all aspects of ocean observing should be broadly adopted by the ocean community and, where appropriate, should evolve into “Ocean Best Practices.” While many groups have created best practices, they are scattered across the Web or buried in local repositories and many have yet to be digitized. To reduce this fragmentation, we introduce a new open access, permanent, digital repository of best practices documentation (oceanbestpractices.org) that is part of the Ocean Best Practices System (OBPS). The new OBPS provides an opportunity space for the centralized and coordinated improvement of ocean observing methods. The OBPS repository employs user-friendly software to significantly improve discovery and access to methods. The software includes advanced semantic technologies for search capabilities to enhance repository operations. In addition to the repository, the OBPS also includes a peer reviewed journal research topic, a forum for community discussion and a training activity for use of best practices. Together, these components serve to realize a core objective of the OBPS, which is to enable the ocean community to create superior methods for every activity in ocean observing from research to operations to applications that are agreed upon and broadly adopted across communities. Using selected ocean observing examples, we show how the OBPS supports this objective. This paper lays out a future vision of ocean best practices and how OBPS will contribute to improving ocean observing in the decade to come

Sunburnt Sea Snails: the role of ultraviolet radiation in the development of encapsulated embryos from temperate rocky shores

Ultraviolet radiation (UVR) is an important abiotic stressor for both acquatic and terrestrial organisms. The recent anthropogenic depletion of stratospheric ozone has resulted in elevated levels of potentially damaging UV-B to which organisms are exposed, and global climate change many also herald changes in environmental conditions, particularly temperature, precipitation, and sea level. Thus, organisms may be simultaneously exposed to variable environmental stressors. In the marine environment, embryos and larvae are likely the most vulnerable to the negative effects of these stresses. Moreover, intertidal organisms are particularly vulnerable to UVR because they occur in habitats where little or no UVR is absorbed by the water column, and the effects of UVR are coupled with other potential negative stresses associated with low tides. Surprisingly, little is known about the effects of potential interactions between environmental stressors on marine larvae, particularly involving UVR. This study aims to investigate the role of UVR in the development of encapsulated intertidal embryos through a series of six independent experiments that screen a large number of taxa. In the first four experiments, I explored the direct effects of UVR in isolation and with other stressors (UVR/temperature/salinity and UVR/desiccation), as well as the indirect effects of UVR and fouling. Isolated effects of UVR were investigated on egg masses from 23 marine gastropod species collected from three intertidal habitats (full sun, partial shade, full shade) and exposed to four spectral treatments (full spectrum, no UV-B, no UVR, dark). Embryos from full shade habitats were significantly vulnerable to UVR while those from full sun habitats showed no significant mortality differences between special treatments. Multifactorial experiments were then conducted in which encapsulated embryos of three common rocky shore gastropods were exposed to simultaneous combinations (i) UVR, temperature, and salinity and (ii) UVR and desiccation. Siphonaria denticulate and Bembicium nanum embryos were expected to be tolerant to these negative interactions of stressors as they are routinely deposited on rock platforms exposed to solar radiation. In contrast, Dolabrifera brazieri embryos were predicted to be vulnerable to these stressors as they are deposited in shaded, submerged habitats. I detected species-specific synergistic effects of these stressors, and increases in mortality and retardation of development were generally associated with the most physiologically stressful conditions. Based on laboratory results, embryos of D. brazieri were the most sensitive to all the stressors. In contrast, S. denticulate and B. nanum were vulnerable to negative effects associated with synchronous spectral, thermal, and salinity stress; but they were relatively tolerant to UVR and desiccation. Nevertheless, field results indicate that embryos of these species within desiccated habitats have a significantly higher mortality than those within submerged habitats, suggesting that development on rock platform surfaces may not be optimal for these embryos. The indirect effects of UVR and fouling on encapsulated larval development were investigated on egg masses from 18 species cultured under three spectral treatments (full spectrum, no UV, dark). Algal fouling levels, protest colonization, embryonic mortality, and encapsulation period were recorded, and I found that UVR inhibited algal growth and protest colonization on egg mass surfaces. Although algal fouling was not directly related to embryonic mortality in most species, egg masses colonized by protists had a higher level of algal fouling; and overall, these egg masses had a significantly higher incidence of embryonic mortality. In the last two experiments, I examined potential behavioural and biochemical protection afforded to encapsulated intertidal embryos against UV-induced damage. I conducted surveys of intertidal egg masses in south-eastern Australia over two years to determine if spatial and temporal variation in parental site selection could reduce potential environmental stress to encapsulated embryos. I predicted that eff masses would be predominantly deposited in shaded habitats not prone to environmental extremes. Furthermore, I anticipated that egg masses deposited on rock platform surfaces would be smaller and occur less frequently in these habitats during seasons of high environmental stress. As predicted, most species spawned under boulders, thereby minimizing exposure to environmental stress. Analyses confirmed that summer had the highest UVR index, water temperature, and air temperature, as well as the lowest tides; but assemblages and abundances of egg masses on exposed rock platforms were highest during summer with no change in egg mass sizes. Thus, species spawning on rock platform surfaces do not seem to confer protection to their encapsulated offspring by avoidance of physiologically stressful times or conditions. Alternatively, one or more of these potential stressors are beneficial to embryonic development, and these benefits outweigh negative effects. For example, high temperatures associated with direct sunlight may increase developmental rate and counteract any negative effects associated with UVR. Potential biochemical protection against UV-induced damage was examine by quantifying potential chemical sunscreens, mycosporine-like amino acids (MAAs), in intertidal egg masses from 46 mollusc species, two polychaete species, and one fish species from southeastern Australia. Analyses revealed that egg mass maturity and spawning habitat did not significantly affect MAA composition with egg masses. In contrast, adult diet, phylogeny, and viability significantly affected MAA composition. Herbivores had significantly higher levels of certain MAAs than carnivores, and viable egg masses had higher levels of some MAAs than inviable egg masses. MAAs also occurred in relatively high concentrations in molluscan egg masses when compared to adult mollusks and other common intertidal organisms. Despite the complexity of factors affecting MAA composition, the prevalence of MAAs in some species is consistent with protection afforded to offspring against negative effects of UVR. Results from the experiments comprising this study indicate that encapsulated embryos use behavioural and biochemical protection against UVR and related stressors; and the presence and effectiveness of these mechanisms may be species-specific. Similarly, the species-specific effects of UVR highlight the importance of research on a range of species. Furthermore, the complex outcomes observed on applying multiple stressors could not have been predicted from examining environmental variables in isolation. Results from the single factor study here suggest that UVR does not negatively affect embryos of species that spawn in full sun, but multifactorial experiments revealed that UVR can indeed have negative effects when other stressors are considered. Hence, we may be dramatically underestimating the ecological impacts of climate change and stratospheric ozone depletion by failing to consider the complex interplay of combinations of environmental variables with organisms

Notes on the egg capsule and variable embryonic development of Nerita melanotragus (Gastropoda: Neritidae)

The black nerite Nerita melanotragus (previously known as N. atramentosa) occurs along the rocky intertidal shores of New Zealand and southeastern Australia. Although commonly used in ecological studies, recent observations suggest that the species may not be strictly planktonic as previously recorded. The current study investigates whether only planktonic larvae emerge from N. melanotragus egg capsules in the field by analyzing encapsulation period, developmental stage, temperature and salinity through the digital monitoring of 386 individual egg capsules over 65 days. The persistence of egg capsules in rock pools was highly variable (1-54 days). Encapsulation period was strongly related to developmental stage (Adjusted R 2 = 0.8293, p \u3c 0.0001), and competent larvae and post-metamorphic juveniles were recorded from some capsules after an encapsulation period of 35 or more days. Encapsulation period was significantly and parabolically related to both temperature and salinity, with encapsulation period decreasing during extreme conditions. Results indicate that egg capsules can persist for much longer than would be expected with a strict planktonic developmental mode, thereby challenging the status of N. melanotragus as a consistent planktonic developer. The potential of this species for poecilogony or hatching plasticity is discussed in light of recent studies examining the role of larval dispersal and biogeographic barriers in structuring rocky intertidal communities. C 2011 Malacological Society of Australasia & Society for the Study of Molluscan Diversity

A short note on heavy cunjevoi growth observed on commercial scallops (Pecten fumatus)

Commercial scallops (Pecten fumatus) were collected from Bass Strait, Australia from 41 dredge tows. Of these, four dredges undertaken in February 2016 at 46 m depth returned scallops that were covered by ascidians of the Pyura stolonifera species complex, commonly known as cunjevoi. There were no obvious signs of immediate ill health in the scallops, with meat being assessed as normal quality and all scallops requiring force to separate the shells. Ascidian-encrusted scallops were significantly smaller, and previous tows in the same location ten and eight months earlier returned far fewer scallops with clean shells and no signs of ascidians. This suggests that both both scallop and ascidian recruitment and growth occurred during the period between sampling events. Future research combining laboratory experiments and field observations is recommended to understand this relationship and its potential impacts on scallop populations