Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km²). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.     

Quantifying biases in marine-protected-area placement relative to abatable threats

Marine protected areas (MPAs) are a critical defense against biodiversity loss in the world's oceans, but to realize near-term conservation benefits, they must be established where major threats to biodiversity occur and can be mitigated. We quantified the degree to which MPA establishment has targeted stoppable threats (i.e., threats that can be abated through effectively managed MPAs alone) by combining spatially explicit marine biodiversity threat data in 2008 and 2013 and information on the location and potential of MPAs to halt threats. We calculated an impact metric to determine whether countries are protecting proportionally more high- or low-threat ecoregions and compared observed values with random protected-area allocation. We found that protection covered <2% of ecoregions in national waters with high levels of abatable threat in 2013, which is ∼59% less protection in high-threat areas than if MPAs had been placed randomly. Relatively low-threat ecoregions had 6.3 times more strict protection (International Union for Conservation of Nature categories I–II) than high-threat ecoregions. Thirty-one ecoregions had high levels of stoppable threat but very low protection, which presents opportunities for MPAs to yield more significant near-term conservation benefits. The extent of the global MPA estate has increased, but the establishment of MPAs where they can reduce threats that are driving biodiversity loss is now urgently needed.     

Detecting deterrence from patrol data

The threat posed to protected areas by the illegal killing of wildlife is countered principally by ranger patrols that aim to detect and deter potential offenders. Deterring poaching is a fundamental conservation objective, but its achievement is difficult to identify, especially when the prime source of information comes in the form of the patrols’ own records, which inevitably contain biases. The most common metric of deterrence is a plot of illegal activities detected per unit of patrol effort (CPUE) against patrol effort (CPUE-E). We devised a simple, mechanistic model of law breaking and law enforcement in which we simulated deterrence alongside exogenous changes in the frequency of offences under different temporal patterns of enforcement effort. The CPUE-E plots were not reliable indicators of deterrence. However, plots of change in CPUE over change in effort (ΔCPUE-ΔE) reliably identified deterrence, regardless of the temporal distribution of effort or any exogenous change in illegal activity levels as long as the time lag between patrol effort and subsequent behavioral change among offenders was approximately known. The ΔCPUE-ΔE plots offered a robust, simple metric for monitoring patrol effectiveness; were no more conceptually complicated than the basic CPUE-E plots; and required no specialist knowledge or software to produce. Our findings demonstrate the need to account for temporal autocorrelation in patrol data and to consider appropriate (and poaching-activity-specific) intervals for aggregation. They also reveal important gaps in understanding of deterrence in this context, especially the mechanisms by which it occurs. In practical applications, we recommend the use of ΔCPUE-ΔE plots in preference to other basic metrics and advise that deterrence should be suspected only if there is a clear negative slope. Distinct types of illegal activity should not be grouped together for analysis, especially if the signs of their occurrence have different persistence times in the environment.     

Spatial cost–benefit analysis of blue restoration and factors driving net benefits globally

Marine coastal ecosystems, commonly referred to as blue ecosystems, provide valuable services to society but are under increasing threat worldwide due to a variety of drivers, including eutrophication, development, land-use change, land reclamation, and climate change. Ecological restoration is sometimes necessary to facilitate recovery in coastal ecosystems. Blue restoration (i.e., in marine coastal systems) is a developing field, and projects to date have been small scale and expensive, leading to the perception that restoration may not be economically viable. We conducted a global cost–benefit analysis to determine the net benefits of restoring coral reef, mangrove, saltmarsh, and seagrass ecosystems, where the benefit is defined as the monetary value of ecosystem services. We estimated costs from published restoration case studies and used an adjusted-value-transfer method to assign benefit values to these case studies. Benefit values were estimated as the monetary value provided by ecosystem services of the restored habitats. Benefits outweighed costs (i.e., there were positive net benefits) for restoration of all blue ecosystems. Mean benefit:cost ratios for ecosystem restoration were eight to 10 times higher than prior studies of coral reef and seagrass restoration, most likely due to the more recent lower cost estimates we used. Among ecosystems, saltmarsh had the greatest net benefits followed by mangrove; coral reef and seagrass ecosystems had lower net benefits. In general, restoration in nations with middle incomes had higher (eight times higher in coral reefs and 40 times higher in mangroves) net benefits than those with high incomes. Within an ecosystem type, net benefit varied with restoration technique (coral reef and saltmarsh), ecosystem service produced (mangrove and saltmarsh), and project duration (seagrass). These results challenge the perceptions of the low economic viability of blue restoration and should encourage further targeted investment in this field.     

A framework for allocating conservation resources among multiple threats and actions

Land managers decide how to allocate resources among multiple threats that can be addressed through multiple possible actions. Additionally, these actions vary in feasibility, effectiveness, and cost. We sought to provide a way to optimize resource allocation to address multiple threats when multiple management options are available, including mutually exclusive options. Formulating the decision as a combinatorial optimization problem, our framework takes as inputs the expected impact and cost of each threat for each action (including do nothing) and for each overall budget identifies the optimal action to take for each threat. We compared the optimal solution to an easy to calculate greedy algorithm approximation and a variety of plausible ranking schemes. We applied the framework to management of multiple introduced plant species in Australian alpine areas. We developed a model of invasion to predict the expected impact in 50 years for each species-action combination that accounted for each species’ current invasion state (absent, localized, widespread); arrival probability; spread rate; impact, if present, of each species; and management effectiveness of each species-action combination. We found that the recommended action for a threat changed with budget; there was no single optimal management action for each species; and considering more than one candidate action can substantially increase the management plan's overall efficiency. The approximate solution (solution ranked by marginal cost-effectiveness) performed well when the budget matched the cost of the prioritized actions, indicating that this approach would be effective if the budget was set as part of the prioritization process. The ranking schemes varied in performance, and achieving a close to optimal solution was not guaranteed. Global sensitivity analysis revealed a threat's expected impact and, to a lesser extent, management effectiveness were the most influential parameters, emphasizing the need to focus research and monitoring efforts on their quantification.     

Minimizing opportunity costs to aquatic connectivity restoration while controlling an invasive species

Controlling invasive species is critical for conservation but can have unintended consequences for native species and divert resources away from other efforts. This dilemma occurs on a grand scale in the North American Great Lakes, where dams and culverts block tributary access to habitat of desirable fish species and are a lynchpin of long‐standing efforts to limit ecological damage inflicted by the invasive, parasitic sea lamprey (Petromyzon marinus). Habitat restoration and sea‐lamprey control create conflicting goals for managing aging infrastructure. We used optimization to minimize opportunity costs of habitat gains for 37 desirable migratory fishes that arose from restricting sea lamprey access (0–25% increase) when selecting barriers for removal under a limited budget (US$1–105 million). Imposing limits on sea lamprey habitat reduced gains in tributary access for desirable species by 15–50% relative to an unconstrained scenario. Additional investment to offset the effect of limiting sea‐lamprey access resulted in high opportunity costs for 30 of 37 species (e.g., an additional US$20–80 million for lake sturgeon [Acipenser fulvescens]) and often required ≥5% increase in sea‐lamprey access to identify barrier‐removal solutions adhering to the budget and limiting access. Narrowly distributed species exhibited the highest opportunity costs but benefited more at less cost when small increases in sea‐lamprey access were allowed. Our results illustrate the value of optimization in limiting opportunity costs when balancing invasion control against restoration benefits for diverse desirable species. Such trade‐off analyses are essential to the restoration of connectivity within fragmented rivers without unleashing invaders.     

Improving inferences about private land conservation by accounting for incomplete reporting

Private lands provide key habitat for imperiled species and are core components of function protectected area networks; yet, their incorporation into national and regional conservation planning has been challenging. Identifying locations where private landowners are likely to participate in conservation initiatives can help avoid conflict and clarify trade-offs between ecological benefits and sociopolitical costs. Empirical, spatially explicit assessment of the factors associated with conservation on private land is an emerging tool for identifying future conservation opportunities. However, most data on private land conservation are voluntarily reported and incomplete, which complicates these assessments. We used a novel application of occupancy models to analyze the occurrence of conservation easements on private land. We compared multiple formulations of occupancy models with a logistic regression model to predict the locations of conservation easements based on a spatially explicit social–ecological systems framework. We combined a simulation experiment with a case study of easement data in Idaho and Montana (United States) to illustrate the utility of the occupancy framework for modeling conservation on private land. Occupancy models that explicitly accounted for variation in reporting produced estimates of predictors that were substantially less biased than estimates produced by logistic regression under all simulated conditions. Occupancy models produced estimates for the 6 predictors we evaluated in our case study that were larger in magnitude, but less certain than those produced by logistic regression. These results suggest that occupancy models result in qualitatively different inferences regarding the effects of predictors on conservation easement occurrence than logistic regression and highlight the importance of integrating variable and incomplete reporting of participation in empirical analysis of conservation initiatives. Failure to do so can lead to emphasizing the wrong social, institutional, and environmental factors that enable conservation and underestimating conservation opportunities in landscapes where social norms or institutional constraints inhibit reporting.     

Boosting freshwater fish conservation with high-resolution distribution mapping across a large territory

The lack of high-resolution distribution maps for freshwater species across large extents fundamentally challenges biodiversity conservation worldwide. We devised a simple framework to delineate the distributions of freshwater fishes in a high-resolution drainage map based on stacked species distribution models and expert information. We applied this framework to the entire Chinese freshwater fish fauna (>1600 species) to examine high-resolution biodiversity patterns and reveal potential conflicts between freshwater biodiversity and anthropogenic disturbances. The correlations between spatial patterns of biodiversity facets (species richness, endemicity, and phylogenetic diversity) were all significant (r = 0.43–0.98, p < 0.001). Areas with high values of different biodiversity facets overlapped with anthropogenic disturbances. Existing protected areas (PAs), covering 22% of China's territory, protected 25–29% of fish habitats, 16–23% of species, and 30–31% of priority conservation areas. Moreover, 6–21% of the species were completely unprotected. These results suggest the need for extending the network of PAs to ensure the conservation of China's freshwater fishes and the goods and services they provide. Specifically, middle to low reaches of large rivers and their associated lakes from northeast to southwest China hosted the most diverse species assemblages and thus should be the target of future expansions of the network of PAs. More generally, our framework, which can be used to draw high-resolution freshwater biodiversity maps combining species occurrence data and expert knowledge on species distribution, provides an efficient way to design PAs regardless of the ecosystem, taxonomic group, or region considered.     

Effects of urban greenspace configuration and native vegetation on bee and wasp reproduction

Pollinator welfare is a recognized research and policy target, and urban greenspaces have been identified as important habitats. Yet, landscape-scale habitat fragmentation and greenspace management practices may limit a city's conservation potential. We examined how landscape configuration, composition, and local patch quality influenced insect nesting success across inner-city Cleveland, Ohio (U.S.A.), a postindustrial legacy city containing a high abundance of vacant land (over 1600 ha). Here, 40 vacant lots were assigned 1 of 5 habitat treatments (T1, vacant lot; T2, grass lawn; T3, flowering lawn; T4, grass prairie; and T5, flowering prairie), and we evaluated how seeded vegetation, greenspace size, and landscape connectivity influenced cavity-nesting bee and wasp reproduction. Native bee and wasp larvae were more abundant in landscapes that contained a large patch (i.e., >6 ha) of contiguous greenspace, in habitats with low plant biomass, and in vacant lots seeded with a native wildflower seed mix or with fine-fescue grass, suggesting that fitness was influenced by urban landscape features and habitat management. Our results can guide urban planning by demonstrating that actions that maintain large contiguous greenspace in the landscape and establish native plants would support the conservation of bees and wasps. Moreover, our study highlights that the world's estimated 350 legacy cities are promising urban conservation targets due to their high abundance of vacant greenspace that could accommodate taxa's habitat needs in urban areas.     

Diverging response patterns of terrestrial and aquatic species to hydromorphological restoration

Although experiences with ecological restoration continue to accumulate, the effectiveness of restoration for biota remains debated. We complemented a traditional taxonomic analysis approach with information on 56 species traits to uncover the responses of 3 aquatic (fish, macroinvertebrates, macrophytes) and 2 terrestrial (carabid beetles, floodplain vegetation) biotic groups to 43 hydromorphological river restoration projects in Germany. All taxonomic groups responded positively to restoration, as shown by increased taxonomic richness (10–164%) and trait diversity (habitat, dispersal and mobility, size, form, life history, and feeding groups) (15–120%). Responses, however, were stronger for terrestrial than aquatic biota, and, contrary to our expectation, taxonomic responses were stronger than those of traits. Nevertheless, trait analysis provided mechanistic insights into the drivers of community change following restoration. Trait analysis for terrestrial biota indicated restoration success was likely enhanced by lateral connectivity and reestablishment of dynamic processes in the floodplain. The weaker response of aquatic biota suggests recovery was hindered by the persistence of stressors in the aquatic environment, such as degraded water quality, dispersal constraints, and insufficient hydromorphological change. Therefore, river restoration requires combined local- and regional-scale approaches to maximize the response of both aquatic and terrestrial organisms. Due to the contrasting responses of aquatic and terrestrial biota, the planning and assessment of river restoration outcomes should consider effects on both components of riverine landscapes.