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1. Many publications documenting large-scale trends in the distribution of species make use of opportunistic citizen data, that is, observations of species collected without standardized field protocol and without explicit sampling design. It is a challenge to achieve reliable estimates of distribution trends from them, because opportunistic citizen science data may suffer from changes in field efforts over time (observation bias), from incomplete and selective recording by observers (reporting bias) and from geographical bias. These, in addition to detection bias, may lead to spurious trends. 2. We investigated whether occupancy models can correct for the observation, reporting and detection biases in opportunistic data. Occupancy models use detection/nondetection data and yield estimates of the percentage of occupied sites (occupancy) per year. These models take the imperfect detection of species into account. By correcting for detection bias, they may simultaneously correct for observation and reporting bias as well. We compared trends in occupancy (or distribution) of butterfly and dragonfly species derived from opportunistic data with those derived from standardized monitoring data. All data came from the same grid squares and years, in order to avoid any geographical bias in this comparison. 3. Distribution trends in opportunistic and monitoring data were well-matched. Strong trends observed in monitoring data were rarely missed in opportunistic data. 4. Synthesis and applications. Opportunistic data can be used for monitoring purposes if occupancy models are used for analysis. Occupancy models are able to control for the common biases encountered with opportunistic data, enabling species trends to be monitored for species groups and regions where it is not feasible to collect standardized data on a large scale. Opportunistic data may thus become an important source of information to track distribution trends in many groups of species.

1. National and international forest biodiversity assessments largely rely on indirect indicators, based on elements of forest structure that are used as surrogates for species diversity. These proxies are reputedly easier and cheaper to assess than biodiversity. Tree microhabitats - tree-borne singularities such as cavities, conks of fungi or bark characteristics - have gained attention as potential forest biodiversity indicators. However, as with most biodiversity indicators, there is a lack of scientific evidence documenting their quantitative link with the biodiversity they are supposed to assess. 2. We explored the link between microhabitat indices and the richness and abundance of three taxonomic groups: bats, birds, and saproxylic beetles. Using a nation-wide multi-taxon sampling design in France, we compared 213 plots located inside and outside strict forest reserves. We hypothesized that the positive effect setting aside forest reserves has on biodiversity conservation is indirectly due to an increase in the proportion of large structural elements (e.g. living trees, standing and lying deadwood). These, in turn, are likely to favour the quantity and diversity of microhabitats. We analysed the relationship between the abundance and species richness of different groups and guilds (e.g. red-listed species, forest specialists, cavity dwellers) and microhabitat density and diversity. We then used confirmatory structural equation models to assess the direct and indirect effects of management abandonment, large structural elements and microhabitats on the biodiversity of the target species. 3. For several groups of birds and bats, the indirect effect of management abandonment and large structural elements on biodiversity was mediated by microhabitats. However, the magnitude of the link between microhabitat indices and biodiversity was moderate. In particular, saproxylic beetles' biodiversity was poorly explained by microhabitats, large structural elements or management abandonment. 4. Synthesis and applications: Tree microhabitats may serve as indicators for bats and birds, but they are not a universal biodiversity indicator. Rather, compared to large structural elements, they most likely have a complementary role to biodiversity. In terms of forest management and conservation, preserving diversity of microhabitats at the local scale benefits several groups of both bats and birds.

1. The challenges associated with monitoring low-density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. Non-invasive sampling techniques and advanced statistical approaches have alleviated some of these challenges and can even allow for spatially explicit estimates of density, one of the most valuable wildlife monitoring tools. 2. For some species, individual identification comes at no cost when unique attributes (e.g. pelage patterns) can be discerned with remote cameras, while other species require viable genetic material and expensive laboratory processing for individual assignment. Prohibitive costs may still force monitoring efforts to use species distribution or occupancy as a surrogate for density, which may not be appropriate under many conditions. 3. Here, we used a large-scale monitoring study of fisher Pekania pennanti to evaluate the effectiveness of occupancy as an approximation to density, particularly for informing harvest management decisions. We combined remote cameras with baited hair snares during 2013-2015 to sample across a 70 096-km² region of western New York, USA. We fit occupancy and Royle-Nichols models to species detection-non-detection data collected by cameras, and spatial capture-recapture (SCR) models to individual encounter data obtained by genotyped hair samples. Variation in the state variables within 15-km² grid cells was modelled as a function of landscape attributes known to influence fisher distribution. 4. We found a close relationship between grid cell estimates of fisher state variables from the models using detection-non-detection data and those from the SCR model, likely due to informative spatial covariates across a large landscape extent and a grid cell resolution that worked well with the movement ecology of the species. Fisher occupancy and density were both positively associated with the proportion of coniferous-mixed forest and negatively associated with road density. As a result, spatially explicit management recommendations for fisher were similar across models, though relative variation was dampened for the detection-non-detection data. 5. Synthesis and applications. Our work provides empirical evidence that models using detection-non-detection data can make similar inferences regarding relative spatial variation of the focal population to models using more expensive individual encounters when the selected spatial grain approximates or is marginally smaller than home range size. When occupancy alone is chosen as a cost-effective state variable for monitoring, simulation and sensitivity analyses should be used to understand how inferences from detection-non-detection data will be affected by aspects of study design and species ecology.

1. Protected areas are the cornerstone of global conservation, yet financial support for basic monitoring infrastructure is lacking in 60% of them. Citizen science holds potential to address these shortcomings in wildlife monitoring, particularly for resource-limited conservation initiatives in developing countries - if we can account for the reliability of data produced by volunteer citizen scientists (VCS).\\ 2. This study tests the reliability of VCS data vs. data produced by trained ecologists, presenting a hierarchical framework for integrating diverse datasets to assess extra variability from VCS data. 3. Our results show that while VCS data are likely to be overdispersed for our system, the overdispersion varies widely by species. We contend that citizen science methods, within the context of East African drylands, may be more appropriate for species with large body sizes, which are relatively rare, or those that form small herds. VCS perceptions of the charisma of a species may also influence their enthusiasm for recording it. 4. Tailored programme design (such as incentives for VCS) may mitigate the biases in citizen science data and improve overall participation. However, the cost of designing and implementing high-quality citizen science programmes may be prohibitive for the small protected areas that would most benefit from these approaches. 5. Synthesis and applications. As citizen science methods continue to gain momentum, it is critical that managers remain cautious in their implementation of these programmes while working to ensure methods match data purpose. Context-specific tests of citizen science data quality can improve programme implementation, and separate data models should be used when volunteer citizen scientists' variability differs from trained ecologists' data. Partnerships across protected areas and between protected areas and other conservation institutions could help to cover the costs of citizen science programme design and implementation.

1. Confronted by significant impacts to ecosystems world-wide, decision makers face the challenge of maintaining both biodiversity and the provision of ecosystem services (ES). However, the objectives of managing biodiversity and supplying ES may not always be in concert, resulting in the need for trade-offs. Understanding these potential trade-offs is crucial for identifying circumstances under which conservation strategies designed to maximise either biodiversity or ES will result in win-win or win-lose outcomes. One important factor that may influence these outcomes are species interactions and the structure of the networks in which they are embedded. 2. We combine optimisation and network theory to investigate the difference in species prioritisation and management outcomes when targeting biodiversity or ES, by considering trophic interactions between species. We analyse 360 simulated ecosystem networks with different ecosystem structures, including the trophic level of the species providing the ES, the number of ES considered, and the food web connectivity. We then illustrate the framework on a saltmarsh case study. 3. We find that trade-offs between biodiversity and ES depend on the network structure of the ecosystem being managed. The trophic level of the species providing the ES is an important determinant of optimal species protection priorities and the biodiversity-ES trade-offs. A strategy targeting ES leads to similar levels of biodiversity conservation (a win-win situation) only when basal species provide the services. In contrast, food web connectivity and the number of services considered have little impact on biodiversity-ES trade-offs. 4. Synthesis and applications. Our research provides the first optimisation model to examine trade-offs between a biodiversity- or ecosystem service-based approach for managing a network of interacting species that provide services. Importantly, results from considering species-services interactions in ecosystem network dynamics can provide managers with quantitative insights to identify opportunities for win-wins and or to avoid win-loss outcomes, by focusing on the trophic level of the species providing services. Future research could build on our model to add multiple interaction types among species, ecosystem functions, and ecosystem services to analyse optimal ecosystem management for multiple conservation objectives.

1.A key challenge facing ecologists and ecosystem managers is understanding what drives unexpected shifts in ecosystems and limits the effectiveness of human interventions. Research that integrates and analyses data from natural and social systems can provide important insight for unravelling the complexity of these dynamics. It is, therefore, a critical step towards the development of evidence‐based, whole‐system management approaches. 2.To examine our ability to influence ecosystems that are behaving in unexpected ways, we explore three prominent cases of “ecological surprise.” We captured the social‐ecological systems (SES) using key variables and interactions from Ostrom’s SES framework, which integrates broader ecosystem processes (e.g. climate, connectivity), management variables (e.g. quotas, restrictions, monitoring), resource use behaviours (e.g. harvesting) and the resource unit (e.g. trees, fish, clean water) being managed. 3.Structural equation modelling revealed that management interventions often influenced resource use behaviours (e.g. rules and limits strongly affected harvest or pollution), but they did not have a significant effect on the abundance of the managed resource. Instead, most resource variability was related to ecological processes and feedbacks operating at broader spatial or temporal scales than management interventions, which locked the resource system into the degraded state. 4.Synthesis and applications. Mismatch between the influence of management systems and ecosystem processes can limit the effectiveness of human interventions during periods of ecological surprise. Management strategies should shift from a conventional focus on removal or addition of a single resource towards solutions that influence the broader ecosystem. Operationalizing Ostrom’s framework to quantitatively analyse social‐ecological systems using structural equation models shows promise for testing solutions to navigate these events.

1. The increasing awareness that a fire regime that promotes biodiversity in one system can threaten biodiversity in another has resulted in a shift away from fire management based on vague notions of maximising pyrodiversity, towards determining the optimal fire regime based on the demonstrated requirements of target species. 2. We utilised a long-running, replicated fire experiment on Melville Island, the largest island off the northern Australian coast, to test the importance of pyrodiversity for native mammals in a northern Australian savanna landscape. We first developed statistical models to determine how native mammal abundance has responded to nine years of experimentally-manipulated fire frequency. Next, given each species' modelled response to fire frequency, we identified the level of pyrodiversity and optimal mix of fire frequencies that would be expected to maximise mammal diversity and abundance, and minimise extinction risk. This was done for both the entire mammal assemblage and for the mammal species currently declining on Melville Island. 3. Fire frequency was a significant predictor of abundance of the northern brown bandicoot Isoodon macrourus, black-footed tree-rat Mesembriomys gouldii, brushtailed rabbit-rat Conilurus peniciilatus, grassland melomys Melomys burtoni, pale field-rat Rattus tunneyi, and mice/dunnarts but not for the common brushtail possum Trichosurus vulpecula. 4. The geometric mean abundance (GMA) of the entire mammal assemblage was positively associated with pyrodiversity, but peaked at an intermediate value. Hence, maximising pyrodiversity would reduce native mammal assemblage GMA below its potential maximum. The fire history for an area that maximised the entire native mammal assemblage GMA consisted of 57% long-unburnt, 43% triennially burnt and <1% annually burnt. Pyrodiversity did not reduce the extinction risk, nor increase the GMA of declining mammals above that predicted in areas entirely annually or triennially burnt. 5. Synthesis and applications. We demonstrate a useful approach with which to develop fire management strategies based on the demonstrated requirements of target species. By comparing the optimal fire regime identified for the conservation of threatened species and that identified for the entire mammal assemblage, we demonstrate the flexibility of this approach to tailor fire management to address specific management priorities in other fire-prone environments.

1. Nutrient over-enrichment increasingly threatens global water resources. Stressor-response studies specifically designed to identify levels of nutrients strongly associated with undesirable ecological conditions are needed to inform numeric nutrient criteria that protect inland waters. 2. Diatoms are important components of aquatic life, which support higher trophic levels and are sensitive to nutrient enrichment. We tested a framework that relies on stressor-response modelling of phosphorus (P) enrichment and stream diatom assemblages across many field locations, multiple years and seasons within years, and under controlled experimental conditions to inform nutrient criteria development. 3. Diatom species composition was nonlinearly correlated with total phosphorus (TP) throughout the 2-year field study. This occurred despite temporal shifts in species composition between two hydrologically distinct years and over eight seasons. 4. Species assemblages on rocks transplanted from a low P stream to mesocosms representing a P enrichment gradient (8,20 and 100 μg/L) shifted into two groups over time. Species composition on rocks in low (20 μg/L) and high (100 μg/L) P mesocosms was consistent with assemblages at P-enriched field sites, whereas rocks in control (8 μg/L) mesocosms had significantly different species composition, consistent with low P field sites. Species composition on rocks transplanted from high P streams did not shift as dramatically and were not significantly different after exposure to different treatments in mesocosms. 5. Threshold Indicator Taxa Analysis identified synchronous declines in several diatom species that culminated in assemblage thresholds associated with TP concentrations >20 and 25 μg/L for 2006 and 2007 respectively. 6. Synthesis and applications. Diatom assemblages show consistent responses to nutrient enrichment despite temporal shifts associated with confounding factors common in stream ecosystems. Regulators should include diatom assemblage responses when developing numeric nutrient criteria. We present a framework that includes spatial, temporal and experimental components, and has broad applicability for use in different ecological settings to evaluate ecological endpoints and set limits for a variety of contaminants threatening freshwater ecosystems throughout the world.

1. Atlas data provide biodiversity information at a relatively fine spatial grain over a broad spatial extent and, increasingly, at multiple points in time, which make them invaluable for understanding processes that affect species distributions over time. The effect of survey effort on species detection has long been appreciated and Atlases typically include survey standards and records of effort, but challenges remain in analysing Atlas data that have not been collected using a repeated sampling protocol designed to correct for imperfect detection. 2. We developed a single-visit dynamic occupancy model to quantify the effects of climatic and land-use drivers on local species extinction and colonization while accounting for imperfect detection using repeat Atlas data. We evaluated model stability using data simulated under alternative scenarios and, ultimately, applied the model to empirical data for Canada warbler Cardellina canadensis, a wide-spread species exhibiting a long-term population decline 3. At sample sizes that are realistic for many Atlases (n = 1000-10 000 independent survey blocks), our models produced unbiased estimates of detection, occupancy, colonization and extinction parameters. Slope estimates for explanatory covariates were somewhat less stable than overall occupancy, colonization and extinction rates, with covariate effects being sensitive to the total number of, and relationships among, explanatory variables. 4. In comparison to other analyses of Canada warbler distributions that indicated minor changes over time, our approach identified a widespread decline in occupancy probability across New York, consistent with the broader population trend, particularly in the areas where it was initially more likely to occur. 5. Synthesis and applications. A single-visit dynamic occupancy model is a novel method for analysing common, ecologically valuable datasets, such as Atlases, that lack repeated sampling necessary to correct for imperfect detection using alternative multi-season occupancy modelling approaches. As a result, using this method can improve understanding of species distributions and factors that shape them over time, thereby providing more accurate information to guide conservation and management.

1. Considerable debate surrounds the extent to which tropical forests can be managed for resource extraction while conserving biodiversity and ecosystem properties, which depend on functional composition. Here we evaluate the compatibility of these aims by examining the effects of logging on taxonomic and functional diversity and composition in a tropical forest. 2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps and adjacent undisturbed areas, and we integrated a database of 13 functional traits describing leaf and wood economics of tropical trees. 3. We found no differences in taxonomic and functional richness among habitats, but logging gaps had significantly higher taxonomic and functional evenness. 4. Logging also effected striking, long-term changes in both species and functional composition. In particular, the xylem density of recruits in logging gaps was 6% less than in unlogged forests, leaves were 11% less tough and had 6—13% greater mineral nutrient concentrations. 5. Synthesis and applications. Our results suggest that managers of tropical forests should limit overall surface area converted to logging gaps by creating fewer, larger gaps during selective logging, to reduce impacts on the taxonomic and functional composition of the regenerating stand.