Identifying the species that are at risk of local extinction in highly diverse ecosystems is a big challenge for conservation science. Assessments of species status are costly and difficult to implement in developing countries with diverse ecosystems due to a lack of species-specific surveys, species-specific data, and other resources. Numerous techniques are devised to determine the threat status of species based on the availability of data and budgetary limits. On this basis, we developed a framework that compared occurrence data of historically exploited reef species in Kenya from existing disparate data sources. Occurrence data from archaeological remains (750-1500CE) was compared with occurrence data of these species catch assessments, and underwater surveys (1991-2014CE). This comparison indicated that only 67 species were exploited over a 750 year period, 750-1500CE, whereas 185 species were landed between 1995 and 2014CE. The first step of our framework identified 23 reef species as threatened with local extinction. The second step of the framework further evaluated the possibility of local extinction with Bayesian extinction analyses using occurrence data from naturalists’ species list with the existing occurrence data sources. The Bayesian extinction analysis reduced the number of reef species threatened with local extinction from 23 to 15. We compared our findings with three methods used for assessing extinction risk. Commonly used extinction risk methods varied in their ability to identify reef species that we identified as threatened with local extinction by our comparative and Bayesian method. For example, 12 of the 15 threatened species that we identified using our framework were listed as either least concern, unevaluated, or data deficient in the International Union for the Conservation of Nature red list. Piscivores and macro-invertivores were the only functional groups found to be locally extinct. Comparing occurrence data from disparate sources revealed a large number of historically exploited reef species that are possibly locally extinct. Our framework addressed biases such as uncertainty in priors, sightings and survey effort, when estimating the probability of local extinction. Our inexpensive method showed the value and potential for disparate data to fill knowledge gaps that exist in species extinction assessments.
The following titles are freely-available, or include a link to a preprint or postprint.
Determining what abiotic and biotic factors affect the diversity and abundance of species through time and space is a basic goal of ecology and an integral step in predicting current and future distributions. Given the pervasive effect of humans worldwide, including anthropogenic factors when quantifying community dynamics is needed to understand discrete and emergent effects of humans on marine ecosystems, especially systems with economically important species. However, there are limited studies that combine a large-scale ecological survey with multiple natural and anthropogenic factors to determine the drivers of community dynamics of temperate reef systems. We combined data from a 24-year fish survey on temperate reefs along the Southeast United States coast with information on recreational and commercial fisheries landings, surface and bottom temperature, habitat characteristics, and climate indices to determine what factors may alter the community structure of fishes within this large marine ecosystem. We found that both abundance and richness of temperate reef fishes declined from 1990 to 2013. Climate indices and local temperature explained the greatest variation, and recreational fishing explained slightly more variation compared to commercial fishing in the temperate reef fish community over a multi-decadal scale. When including habitat characteristics in a 3 year analysis, depth, and local temperature explained the greatest variation in fish assemblage, while the influence of habitat was comparatively minimal. Finally, the interaction between predictor variables and fish traits indicated that bigger and longer-lived fishes were positively correlated with depth and winter temperature. Our findings suggest that lesser-studied anthropogenic impacts, such as recreational fishing, may influence communities throughout large ecosystems as much as other well-studied impacts such as climate change and commercial fishing. In addition, climate indices should be considered when assessing changes, natural or anthropogenic, to fish communities.
The European Union (EU) instituted a carding system via its European Commission Regulation (EC) No. 1005/2008 with the goal of incentivizing fish and fish products (fish) exporting countries to the Union to take action to reduce IUU fishing in their waters. This regulation stipulates that the EU will issue warnings, known as a “yellow card,” to countries that perform poorly in the effort to end IUU fishing in their waters. Failure to curb IUU fishing will result in a ban in the export of fish to the EU via the issuance of a red card. Here, I ask the following questions: what is the economic risk of being red carded by the EU? Is the economic risk big enough to significantly reduce IUU fishing in a targeted country’s waters? Would the risk be broad enough to result in a significant reduction in IUU fishing globally? What if the two other leading fish importing countries, i.e., the United States and Japan, also institute a similar carding system as the EU? To address these questions, I develop and compute an economic risk index for the carding system. This study suggests that the impact of an EU only IUU carding system could be significant for some targeted countries but its effect globally, with respect to reducing IUU fishing, would be minimal. However, I find that the economic risk to fish exporting countries would increase significantly if the United States and Japan also instituted similar carding systems, which would in turn help to reduce IUU fishing worldwide. This contribution shows that an IUU carding system could contribute significantly to the elimination of IUU fishing provided a critical mass of top fish importing countries participate in such a system.
Trait-based approaches to investigate (short- and long-term) phytoplankton dynamics and community assembly have become increasingly popular in freshwater and marine science. Although the nature of the pelagic habitat and the main phytoplankton taxa and ecology are relatively similar in both marine and freshwater systems, the lines of research have evolved, at least in part, separately. We compare and contrast the approaches adopted in marine and freshwater ecosystems with respect to phytoplankton functional traits. We note differences in study goals relating to functional trait use that assess community assembly and those that relate to ecosystem processes and biogeochemical cycling that affect the type of characteristics assigned as traits to phytoplankton taxa. Specific phytoplankton traits relevant for ecological function are examined in relation to herbivory, amplitude of environmental change and spatial and temporal scales of study. Major differences are identified, including the shorter time scale for regular environmental change in freshwater ecosystems compared to that in the open oceans as well as the type of sampling done by researchers based on site-accessibility. Overall, we encourage researchers to better motivate why they apply trait-based analyses to their studies and to make use of process-driven approaches, which are more common in marine studies. We further propose fully comparative trait studies conducted along the habitat gradient spanning freshwater to brackish to marine systems, or along geographic gradients. Such studies will benefit from the combined strength of both fields.
Exposure to oil from the Deepwater Horizon spill may have lasting impacts on preservation of historic shipwrecks in the Gulf of Mexico. Submerged steel structures, including shipwrecks, serve as artificial reefs and become hotspots of biodiversity in the deep sea. Marine biofilms on submerged structures support settlement of micro- and macro-biota and may enhance and protect against corrosion. Disruptions in the local environment, including oil spills, may impact the role that biofilms play in reef preservation. To determine how the Deepwater Horizon spill potentially impacted shipwreck biofilms and the functional roles of the biofilm microbiome, experiments containing carbon steels disks (CSDs) were placed at five historic shipwreck sites located within, and external to the benthic footprint of the Deepwater Horizon spill. The CSDs were incubated for 16 weeks to enable colonization by biofilm-forming microorganisms and to provide time for in situ corrosion to occur. Biofilms from the CSDs, as well as sediment and water microbiomes, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe community composition and determine the source of taxa colonizing biofilms. Biofilm metagenomes were sequenced to compare differential gene abundances at spill-impacted and reference sites. Biofilms were dominated by Zeta-, Alpha-, Epsilon-, and Gamma-proteobacteria. Sequences affiliated with the Mariprofundus and Sulfurimonas genera were prolific, and Roseobacter, and Colwellia genera were also abundant. Analysis of 16S rRNA sequences from sediment, water, and biofilms revealed sediment to be the main known source of taxa to biofilms at impacted sites. Differential gene abundance analysis revealed the two-component response regulator CreC, a gene involved in environmental stress response, to be elevated at reference sites compared to impacted sites within the spill plume fallout area on the seafloor. Genes for chemotaxis, motility, and alcohol dehydrogenases were differentially abundant at reference vs. impacted sites. Metal loss on CSDs was elevated at sites within the spill fallout plume. Time series images reveal that metal loss at a heavily impacted site, the German Submarine U-166, has accelerated since the spill in 2010. This study provides evidence that spill residues on the seafloor may impact biofilm communities and the preservation of historic steel shipwrecks.
Reaching protected area (PA) coverage goals is challenged by a lack of sufficient financial resources. This funding gap is particularly pervasive for marine protected areas (MPAs). It has been suggested that marine conservationists examine examples from terrestrial protected areas (TPAs) for potential solutions to better fund MPAs. However, the funding needs for MPAs and TPAs have not been directly compared, and there is risk of management failures if any such differences are not properly considered when designing MPA financial strategies. We perform an in-depth literature review to investigate differences in distribution of costs incurred by MPAs and TPAs across three primary categories; establishment, operational, and opportunity costs. We use our findings to conduct a snapshot quantitative comparison, which we complement with theoretical support to provide preliminary insight into differences between MPA and TPA costs, and how these may influence financial strategies most appropriate for each type of PA. Our research suggests that TPA costs, and thereby funding requirements, are greater for the time period leading up to and including the implementation phase, whereas MPAs have higher financial requirements for meeting long-term annual operational costs. This may be primarily due to the prevalence of private property rights for terrestrial regions, which are less frequently in place for ocean areas, as well as logistical requirements for enforcement and monitoring in a marine environment. To cement these suggestions in greater analytical certainty, we call for more thorough and standardized PA cost reporting at all stages, especially for MPAs and PAs in developing countries. The quantity and quality of such data presently limits research in PA sustainable finance, and will need to be remedied to advance the field in future years.
Despite growing plastic discharge into the environment, researchers have struggled to detect expected increases of marine plastic debris in sea surfaces, sparking discussions about “missing plastics” and final sinks, which are hypothesized to be coastal and deep-sea sediments. While it holds true that the highest concentrations of plastic particles are found in these locations (103-104 particles m-3 in sediments vs. 0.1-1 particles m-3in the water column), our meta-analysis also highlights that in open oceans, microplastic polymer types segregated in the water column according to their density. Lower density polymers, such as polypropylene and polyethylene, dominated sea surface samples (25% and 42%, respectively) but decreased in abundance through the water column (3% and 2% in the deep-sea, respectively), whereas only denser polymers (i.e.polyesters and acrylics) were enriched with depth (5% in surface seawater vs. 77 % in deep-sea locations). Our meta-analysis demonstrates that some of the most abundant and recalcitrant manufactured plastics are more persistent in the sea surface than previously anticipated and that further research is required to determine the ultimate fate of these polymers as current knowledge does not support the deep sea as the final sink for all polymer types.
Coastal wetlands are a significant carbon (C) sink since they store carbon in anoxic soils. This ecosystem service is impacted by hydrologic alteration and management of these coastal habitats. Efforts to restore tidal flow to former salt marshes have increased in recent decades and are generally associated with alteration of water inundation levels and salinity. This study examined the effect of water level and salinity changes on soil organic matter decomposition during a 60‐day incubation period. Intact soil cores from impounded fresh water marsh and salt marsh were incubated after addition of either sea water or fresh water under flooded and drained water levels. Elevating fresh water marsh salinity to 6 to 9 ppt enhanced CO2 emission by 50%−80% and most typically decreased CH4 emissions, whereas, decreasing the salinity from 26 ppt to 19 ppt in salt marsh soils had no effect on CO2 or CH4 fluxes. The effect from altering water levels was more pronounced with drained soil cores emitting ~10‐fold more CO2 than the flooded treatment in both marsh sediments. Draining soil cores also increased dissolved organic carbon (DOC) concentrations. Stable carbon isotope analysis of CO2 generated during the incubations of fresh water marsh cores in drained soils demonstrates that relict peat OC that accumulated when the marsh was saline was preferentially oxidized when sea water was introduced. This study suggests that restoration of tidal flow that raises the water level from drained conditions would decrease aerobic decomposition and enhance C sequestration. It is also possible that the restoration would increase soil C decomposition of deeper deposits by anaerobic oxidation, however this impact would be minimal compared to lower emissions expected due to the return of flooding conditions.
Since the 1970s, the magnitude of turtle cold-stun strandings have increased dramatically within the northwestern Atlantic. Here, we examine oceanic, atmospheric, and biological factors that may affect the increasing trend of cold-stunned Kemp’s ridleys in Cape Cod Bay, Massachusetts, United States of America. Using machine learning and Bayesian inference modeling techniques, we demonstrate higher cold-stunning years occur when the Gulf of Maine has warmer sea surface temperatures in late October through early November. Surprisingly, hatchling numbers in Mexico, a proxy for population abundance, was not identified as an important factor. Further, using our Bayesian count model and forecasted sea surface temperature projections, we predict more than 2,300 Kemp’s ridley turtles may cold-stun annually by 2031 as sea surface temperatures continue to increase within the Gulf of Maine. We suggest warmer sea surface temperatures may have modified the northerly distribution of Kemp’s ridleys and act as an ecological bridge between the Gulf Stream and nearshore waters. While cold-stunning may currently account for a minor proportion of juvenile mortality, we recommend continuing efforts to rehabilitate cold-stunned individuals to maintain population resiliency for this critically endangered species in the face of a changing climate and continuing anthropogenic threats.
Systematic conservation planning is essential in the justification and design of protected areas, especially in an era where every piece of land or water is at a high premium. We used satellite tracking data and regular monitoring of Greater flamingos into the spatial prioritization planning tool Marxan to identify the most important zones for the conservation of the greater flamingo and many other species of waterbirds and marine habitats in one of the economically important areas in the coastal zone of Abu Dhabi. Locations from 11 satellite tracked flamingos and monthly count data since 2009 in the Bul Syayeef area showed a predominant use of a relatively small area which when integrated in Marxan provided optimum boundary with minimum cost. Marxan identified 1, 5, 10 and 15 ha planning units and provided the best solution with 15 ha. The reduced total area of 145 km2 is nearly 40% of the originally proposed area for protection, is more pragmatic and easy to establish, given the high importance of the area for economic development. Using approximately the same boundary, the proposed area was declared a Ramsar site in September 2016 and was subsequently declared a protected area through a government decree in September 2017.
Ecological theory predicts that ecosystems with multiple basins of attraction can get locked in an undesired state, which has profound ecological and management implications. Despite their significance, alternative attractors have proven to be challenging to detect and characterize in natural communities. On coral reefs, it has been hypothesized that persistent coral-to-macroalgae “phase shifts” that can result from overfishing of herbivores and/or nutrient enrichment may reflect a regime shift to an alternate attractor, but, to date, the evidence has been equivocal. Our field experiments in Moorea, French Polynesia, revealed the following: (i) hysteresis existed in the herbivory–macroalgae relationship, creating the potential for coral–macroalgae bistability at some levels of herbivory, and (ii) macroalgae were an alternative attractor under prevailing conditions in the lagoon but not on the fore reef, where ambient herbivory fell outside the experimentally delineated region of hysteresis. These findings help explain the different community responses to disturbances between lagoon and fore reef habitats of Moorea over the past several decades and reinforce the idea that reversing an undesired shift on coral reefs can be difficult. Our experimental framework represents a powerful diagnostic tool to probe for multiple attractors in ecological systems and, as such, can inform management strategies needed to maintain critical ecosystem functions in the face of escalating stresses.
Natural resource policies enacted to protect environmental integrity play an important role in promoting sustainability. However, when resources are shared ecologically, economically, or through a common, global interest, policies implemented to protect resource sustainability in one domain can displace, and in some cases magnify, environmental degradation to other domains. Although such displacement has been recognized as a fundamental challenge to environmental and conservation policy within some resource sectors, there has been little cross‐disciplinary and cross‐sectoral integration to address the problem. This suggests that siloed knowledge may be impeding widespread recognition of the ubiquity of displacement and the need for mitigation. Here, we connect research across multiple disciplines to promote a broader discussion and recognition of the processes and pathways that can lead to displaced impacts that countermand or undermine resource policy and outline a number of approaches that can mitigate displacement.
South Pacific albacore is a species of primary importance in the longline fishery of a number of Small Island Developing States in the Western and Central Pacific Ocean. Despite the fact that the stock is assessed as not being subject to overfishing and not overfished, economic returns have declined significantly over the past decade. This has led to calls for management intervention. Given stated biological and economic objectives for the fishery, members of the Pacific Islands Forum Fisheries Agency proposed an interim stock target reference point to the Western and Central Pacific Fisheries Commission that would imply a larger stock size, higher catch rates and a more profitable fishery (FFA Members, 2015). The purpose of this study is to examine the biological and economic consequences along the trajectories of two distinct longline effort reduction regimes that achieve the proposed target reference point within 20 years and review the trade-offs in terms of forgone catch or effort and forgone revenue. The two effort regimes examined are a one-off reduction implemented immediately, and a phased reduction under which effort is reduced by a fixed percent each year. The results are discussed in the light of wider Pacific Island objectives for fishery production and fleet profitability and highlights the importance of moving beyond a purely biological stock-based focus when providing management advice.
Dynamic energy budget (DEB) theory offers a comprehensive framework for understanding the overall physiological performance (growth, development, respiration, reproduction, etc.) of an organism over the course of its life cycle. We present here a simplified DEB model for the swimming crab Liocarcinus depurator. To the best of our knowledge, this is the first to be presented for this species. Most applications of the standard DEB model assume continuous growth in all size metrics (length, wet mass, carbon content) of the modelled species. However, in crustaceans growth, measured as an increase of carapace length/width, occurs periodically via moult. To account for this, we have extended the model to track the continuous increase in carbon mass as well as the episodic increase in physical size. Model predictions were consistent with the patterns in the observed data, predicting both the moult increment and the intermoult period of an individual. In addition to presenting the model itself, we also make recommendations for further development, and evaluate the potential applications of such a model, both at the individual level (e.g. aquaculture) and as a potential tool for population level dynamics (e.g. fisheries stock assessment).
In this period of environmental change, understanding how resource users respond to such changes is critical for effective resource management and adaptation planning. Extensive work has focused on natural resource responses to environmental changes, but less has examined the response of resource users to such changes. We used an interdisciplinary approach to analyse changes in resource use among commercial trawl fishing communities in the northwest Atlantic, a region that has shown poleward shifts in harvested fish species. We found substantial community-level changes in fishing patterns since 1996: southern trawl fleets of larger vessels with low catch diversity fished up to 400 km further north, while trawl fleets of smaller vessels with low catch diversity shrank or disappeared from the data set over time. In contrast, trawl fleets (of both large and small vessels) with higher catch diversity neither changed fishing location dramatically or nor disappeared as often from the data set. This analysis suggests that catch diversity and high mobility may buffer fishing communities from effects of environmental change. Particularly in times of rapid and uncertain change, constructing diverse portfolios and allowing for fleet mobility may represent effective adaptation strategies.
The ability to perceive and recognise a reflected mirror image as self (mirror self-recognition, MSR) is considered a hallmark of cognition across species. Although MSR has been reported in mammals and birds, it is not known to occur in any other major taxon. Potentially limiting our ability to test for MSR in other taxa is that the established assay, the mark test, requires that animals display contingency testing and self-directed behaviour. These behaviours may be difficult for humans to interpret in taxonomically divergent animals, especially those that lack the dexterity (or limbs) required to touch a mark. Here, we show that a fish, the cleaner wrasse Labroides dimidiatus, shows behaviour that may reasonably be interpreted as passing through all phases of the mark test: (i) social reactions towards the reflection, (ii) repeated idiosyncratic behaviours towards the mirror, and (iii) frequent observation of their reflection. When subsequently provided with a coloured tag in a modified mark test, fish attempt to remove the mark by scraping their body in the presence of a mirror but show no response towards transparent marks or to coloured marks in the absence of a mirror. This remarkable finding presents a challenge to our interpretation of the mark test—do we accept that these behavioural responses, which are taken as evidence of self-recognition in other species during the mark test, lead to the conclusion that fish are self-aware? Or do we rather decide that these behavioural patterns have a basis in a cognitive process other than self-recognition and that fish do not pass the mark test? If the former, what does this mean for our understanding of animal intelligence? If the latter, what does this mean for our application and interpretation of the mark test as a metric for animal cognitive abilities?
The territorial waters and the EEZ of the Netherlands form a part of the southern North Sea. The area is intensely used and for several of these uses considerable growth is forecast. For years, industrial freedom and market forces prevailed during discussions on marine spatial planning in the Netherlands. But in 2005 it became clear that this might lead to increasing conflicts with the environment and between users. The introduction of a new spatial planning framework was in response to an increasing interest in new developments and a growing demand for governmental coordination of these developments. During the years after, societal demands changed rapidly, especially with regard to renewable energy and demand for sand to strengthen the coast. At a regular interval of 6 years, revised Marine Spatial Plans have been developed which are adapted to the new knowledge and experience acquired and the new societal demands. Each cycle has a strong stakeholder involvement, both informal and formal.
Implementing a governance transformation entails the creation of a new institutional system when ecological, economic, or social structures make the existing system untenable. It involves building capacities, establishing viable formal and informal institutions, and triggering major societal changes. Early assessments (EAs) provide a mechanism to fine-tune and support institutional learning processes, which are needed to provide legitimacy and political acceptability of transformational change. We performed an EA of a governance transformation aimed at implementing ecosystem-based, multilevel participatory fisheries management in Chile. We performed individual interviews and workshops and synthesized existing reports to assess the main challenges of the institutionalization of the new policy. Results showed that successful implementation of the governance transformation would need to address key issues related to building trust and improving transparency, including clear protocols for cocreating knowledge and securing resources and capacities. The EA allowed us to define specific recommendations associated with legal reforms, issuing of new executive orders to clarify implementation, and improvement in operational standards by government agencies. EAs provide a fundamental tool that helps build legitimacy and sustainability of new governance systems. They bring a sense of reality, informed by social science, that allows us to understand progress in the implementation of governance transformations, by identifying rigidities that fail to accommodate emerging realities.
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological oceanography, as it is capable of identifying a huge phylogenetic range of organisms to species level. Here we develop and apply a novel multi-gene molecular toolkit to eDNA isolated from bulk plankton samples collected over a five-year period from a single site. This temporal scale and level of detail is unprecedented in eDNA studies. We identified consistent seasonal assemblages of zooplankton species, which demonstrates the ability of our toolkit to audit community composition. We were also able to detect clear departures from the regular seasonal patterns that occurred during an extreme marine heatwave. The integration of eDNA analyses with existing biotic and abiotic surveys delivers a powerful new long-term approach to monitoring the health of our world’s oceans in the context of a rapidly changing climate.
Understanding the mechanisms which determine the capacity of any species to adapt to changing environmental conditions is one of the foremost requirements in accurately predicting which populations, species and clades are likely to survive ongoing, rapid climate change. The polar oceans are amongst the most rapidly changing environments on Earth with reduced regional sea ice duration and extent, and their fauna's expected sensitivity to warming and acidification. These changes potentially pose a significant threat to a number of polar fauna. There is, therefore, a critical need to assess the vulnerability of a wide range of species to determine the tipping points or weak links in marine assemblages. Knowledge of the effect of multiple stressors on polar marine fauna has advanced over the last 40 years, but there are still many data gaps. This study applies ecological risk assessment techniques to the increasing knowledge of polar species' physiological capacities to identify their exposure to climate change and their vulnerability to this exposure. This relatively rapid, semi-quantitative assessment provides a layer of vulnerability on top of climate envelope models, until such times as more extensive physiological data sets can be produced. The risk assessment identified more species that are likely to benefit from the near-future predicted change (the winners), especially predators and deposit feeders. Fewer species were scored at risk (the losers), although animals that feed on krill scored consistently as under the highest risk.