Using Cumulative Impact Mapping to Prioritize Marine Conservation Efforts in Equatorial Guinea

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData Availability Statement Ensemble ecological niche models (EENMs) and threat maps (anthropogenic footprint, cumulative impact, and cumulative utilization and impact) for each species (Atlantic humpback dolphin Sousa teuszii; bottlenose dolphin Tursiops truncatus; humpback whale Megaptera novaeangliae; leatherback Dermochelys coriacea; and olive ridley sea turtle Lepidochelys olivacea) are available from the Dryad Digital Repository doi: 10.5061/dryad.v6wwpzgr9 (Trew et al., 2019).Marine biodiversity is under extreme pressure from anthropogenic activity globally, leading to calls to protect at least 10% of the world’s oceans within marine protected areas (MPAs) and other effective area-based conservation measures. Fulfilling such commitments, however, requires a detailed understanding of the distribution of potentially detrimental human activities, and their predicted impacts. One such approach that is being increasingly used to strengthen our understanding of human impacts is cumulative impact mapping; as it can help identify economic sectors with the greatest potential impact on species and ecosystems in order to prioritize conservation management strategies, providing clear direction for intervention. In this paper, we present the first local cumulative utilization impact mapping exercise for the Bioko-Corisco-Continental area of Equatorial Guinea’s Exclusive Economic Zone – situated in the Gulf of Guinea, one of the most important and least studied marine regions in the Eastern Central Atlantic. This study examines the potential impact of ten direct anthropogenic activities on a suite of key marine megafauna species and reveals that the most suitable habitats for these species, located on the continental shelf, are subject to the highest threat scores. However, in some coastal areas, the persistence of highly suitable habitat subject to lower threat scores suggests that there are still several strategic areas that are less impacted by human activity that may be suitable sites for protected area expansion. Highlighting both the areas with potentially the highest impact, and those with lower impact levels, as well as particularly damaging activities can inform the direction of future conservation initiatives in the region.Waitt FoundationWildlife Conservation SocietyDarwin InitiativeDepartment for Environment, Food and Rural Affairs (Defra)Waterloo FoundationNatural Environment Research Council (NERC)Marine Turtle Conservation Fund (United States Fish and Wildlife Service, United States Department of the Interior)Vaalco EnergyHarvest Natural ResourcesSea World and Busch Gardens Conservation FundTullow OilOld Dominion UniversityWWFWildlife Conservation SocietyUniversity of Exete

Diversification of refugia types needed to secure the future of coral reefs subject to climate change

Identifying locations of refugia from the thermal stresses of climate change for coral reefs and better managing them is one of the key recommendations for climate change adaptation. We review and summarize approximately 30 years of applied research focused on identifying climate refugia to prioritize the conservation actions for coral reefs under rapid climate change. We found that currently proposed climate refugia and the locations predicted to avoid future coral losses are highly reliant on excess heat metrics, such as degree heating weeks. However, many existing alternative environmental, ecological, and life-history variables could be used to identify other types of refugia that lead to the desired diversified portfolio for coral reef conservation. To improve conservation priorities for coral reefs, there is a need to evaluate and validate the predictions of climate refugia with long-term field data on coral abundance, diversity, and functioning. There is also the need to identify and safeguard locations displaying resistance toprolonged exposure to heat waves and the ability to recover quickly after thermal exposure. We recommend using more metrics to identify a portfolio of potential refugia sites for coral reefs that can avoid, resist, and recover from exposure to high ocean temperatures and the consequences of climate change, thereby shifting past efforts focused on avoidance to a diversified risk-spreading portfolio that can be used to improve strategic coral reef conservation in a rapidly warming climate

Effectiveness of Biodiversity Surrogates for Conservation Planning: Different Measures of Effectiveness Generate a Kaleidoscope of Variation

Conservation planners represent many aspects of biodiversity by using surrogates with spatial distributions readily observed or quantified, but tests of their effectiveness have produced varied and conflicting results. We identified four factors likely to have a strong influence on the apparent effectiveness of surrogates: (1) the choice of surrogate; (2) differences among study regions, which might be large and unquantified (3) the test method, that is, how effectiveness is quantified, and (4) the test features that the surrogates are intended to represent. Analysis of an unusually rich dataset enabled us, for the first time, to disentangle these factors and to compare their individual and interacting influences. Using two data-rich regions, we estimated effectiveness using five alternative methods: two forms of incidental representation, two forms of species accumulation index and irreplaceability correlation, to assess the performance of ‘forest ecosystems’ and ‘environmental units’ as surrogates for six groups of threatened species—the test features—mammals, birds, reptiles, frogs, plants and all of these combined. Four methods tested the effectiveness of the surrogates by selecting areas for conservation of the surrogates then estimating how effective those areas were at representing test features. One method measured the spatial match between conservation priorities for surrogates and test features. For methods that selected conservation areas, we measured effectiveness using two analytical approaches: (1) when representation targets for the surrogates were achieved (incidental representation), or (2) progressively as areas were selected (species accumulation index). We estimated the spatial correlation of conservation priorities using an index known as summed irreplaceability. In general, the effectiveness of surrogates for our taxa (mostly threatened species) was low, although environmental units tended to be more effective than forest ecosystems. The surrogates were most effective for plants and mammals and least effective for frogs and reptiles. The five testing methods differed in their rankings of effectiveness of the two surrogates in relation to different groups of test features. There were differences between study areas in terms of the effectiveness of surrogates for different test feature groups. Overall, the effectiveness of the surrogates was sensitive to all four factors. This indicates the need for caution in generalizing surrogacy tests

Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias

Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB

Performance and Consistency of Indicator Groups in Two Biodiversity Hotspots

In a world limited by data availability and limited funds for conservation, scientists and practitioners must use indicator groups to define spatial conservation priorities. Several studies have evaluated the effectiveness of indicator groups, but still little is known about the consistency in performance of these groups in different regions, which would allow their a priori selection.We systematically examined the effectiveness and the consistency of nine indicator groups in representing mammal species in two top-ranked Biodiversity Hotspots (BH): the Brazilian Cerrado and the Atlantic Forest. To test for group effectiveness we first found the best sets of sites able to maximize the representation of each indicator group in the BH and then calculated the average representation of different target species by the indicator groups in the BH. We considered consistent indicator groups whose representation of target species was not statistically different between BH. We called effective those groups that outperformed the target-species representation achieved by random sets of species. Effective indicator groups required the selection of less than 2% of the BH area for representing target species. Restricted-range species were the most effective indicators for the representation of all mammal diversity as well as target species. It was also the only group with high consistency.We show that several indicator groups could be applied as shortcuts for representing mammal species in the Cerrado and the Atlantic Forest to develop conservation plans, however, only restricted-range species consistently held as the most effective indicator group for such a task. This group is of particular importance in conservation planning as it captures high diversity of endemic and endangered species

Quantification of codon selection for comparative bacterial genomics

<p>Abstract</p> <p>Background</p> <p>Statistics measuring codon selection seek to compare genes by their sensitivity to selection for translational efficiency, but existing statistics lack a model for testing the significance of differences between genes. Here, we introduce a new statistic for measuring codon selection, the Adaptive Codon Enrichment (ACE).</p> <p>Results</p> <p>This statistic represents codon usage bias in terms of a probabilistic distribution, quantifying the extent that preferred codons are over-represented in the gene of interest relative to the mean and variance that would result from stochastic sampling of codons. Expected codon frequencies are derived from the observed codon usage frequencies of a broad set of genes, such that they are likely to reflect nonselective, genome wide influences on codon usage (<it>e.g</it>. mutational biases). The relative adaptiveness of synonymous codons is deduced from the frequency of codon usage in a pre-selected set of genes relative to the expected frequency. The ACE can predict both transcript abundance during rapid growth and the rate of synonymous substitutions, with accuracy comparable to or greater than existing metrics. We further examine how the composition of reference gene sets affects the accuracy of the statistic, and suggest methods for selecting appropriate reference sets for any genome, including bacteriophages. Finally, we demonstrate that the ACE may naturally be extended to quantify the genome-wide influence of codon selection in a manner that is sensitive to a large fraction of codons in the genome. This reveals substantial variation among genomes, correlated with the tRNA gene number, even among groups of bacteria where previously proposed whole-genome measures show little variation.</p> <p>Conclusions</p> <p>The statistical framework of the ACE allows rigorous comparison of the level of codon selection acting on genes, both within a genome and between genomes.</p

Accommodating Dynamic Oceanographic Processes and Pelagic Biodiversity in Marine Conservation Planning

Pelagic ecosystems support a significant and vital component of the ocean's productivity and biodiversity. They are also heavily exploited and, as a result, are the focus of numerous spatial planning initiatives. Over the past decade, there has been increasing enthusiasm for protected areas as a tool for pelagic conservation, however, few have been implemented. Here we demonstrate an approach to plan protected areas that address the physical and biological dynamics typical of the pelagic realm. Specifically, we provide an example of an approach to planning protected areas that integrates pelagic and benthic conservation in the southern Benguela and Agulhas Bank ecosystems off South Africa. Our aim was to represent species of importance to fisheries and species of conservation concern within protected areas. In addition to representation, we ensured that protected areas were designed to consider pelagic dynamics, characterized from time-series data on key oceanographic processes, together with data on the abundance of small pelagic fishes. We found that, to have the highest likelihood of reaching conservation targets, protected area selection should be based on time-specific data rather than data averaged across time. More generally, we argue that innovative methods are needed to conserve ephemeral and dynamic pelagic biodiversity

The Nature Index: A General Framework for Synthesizing Knowledge on the State of Biodiversity

The magnitude and urgency of the biodiversity crisis is widely recognized within scientific and political organizations. However, a lack of integrated measures for biodiversity has greatly constrained the national and international response to the biodiversity crisis. Thus, integrated biodiversity indexes will greatly facilitate information transfer from science toward other areas of human society. The Nature Index framework samples scientific information on biodiversity from a variety of sources, synthesizes this information, and then transmits it in a simplified form to environmental managers, policymakers, and the public. The Nature Index optimizes information use by incorporating expert judgment, monitoring-based estimates, and model-based estimates. The index relies on a network of scientific experts, each of whom is responsible for one or more biodiversity indicators. The resulting set of indicators is supposed to represent the best available knowledge on the state of biodiversity and ecosystems in any given area. The value of each indicator is scaled relative to a reference state, i.e., a predicted value assessed by each expert for a hypothetical undisturbed or sustainably managed ecosystem. Scaled indicator values can be aggregated or disaggregated over different axes representing spatiotemporal dimensions or thematic groups. A range of scaling models can be applied to allow for different ways of interpreting the reference states, e.g., optimal situations or minimum sustainable levels. Statistical testing for differences in space or time can be implemented using Monte-Carlo simulations. This study presents the Nature Index framework and details its implementation in Norway. The results suggest that the framework is a functional, efficient, and pragmatic approach for gathering and synthesizing scientific knowledge on the state of biodiversity in any marine or terrestrial ecosystem and has general applicability worldwide

Compositional analysis of bacterial communities in seawater, sediment, and sponges in the Misool coral reef system, Indonesia

Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges.publishe