ALBERT

Description: Ecological Applications, Volume 24, Issue 1, Page 3, January 2014.

Description: Ecological Applications, Volume 24, Issue 1, Page 23-24, January 2014.

Description: Ecological Applications, Volume 24, Issue 1, Page 227-228, January 2014.

Description: Ecological Applications, Volume 24, Issue 1, Page 71-83, January 2014. Concerns about bycatch of protected species have become a dominant factor shaping fisheries management. However, efforts to mitigate bycatch are often hindered by a lack of data on the distributions of fishing effort and protected species. One approach to overcoming this problem has been to overlay the distribution of past fishing effort with known locations of protected species, often obtained through satellite telemetry and occurrence data, to identify potential bycatch hotspots. This approach, however, generates static bycatch risk maps, calling into question their ability to forecast into the future, particularly when dealing with spatiotemporally dynamic fisheries and highly migratory bycatch species. In this study, we use boosted regression trees to model the spatiotemporal distribution of fishing effort for two distinct fisheries in the North Pacific Ocean, the albacore (Thunnus alalunga) troll fishery and the California drift gillnet fishery that targets swordfish (Xiphias gladius). Our results suggest that it is possible to accurately predict fishing effort using

Description: Ecological Applications, Volume 24, Issue 1, Page 4-14, January 2014. Although market-based incentives have helped resolve many environmental challenges, conservation markets still play a relatively minor role in wildlife management. Establishing property rights for environmental goods and allowing trade between resource extractors and resource conservationists may offer a path forward in conserving charismatic species like whales, wolves, turtles, and sharks. In this paper, we provide a conceptual model for implementing a conservation market for wildlife and evaluate how such a market could be applied to three case studies for whales (minke [Balaenoptera acutorostrata], bowhead [Balaena mysticetus], and gray [Eschrictius robustus]). We show that, if designed and operated properly, such a market could ensure persistence of imperiled populations, while simultaneously improving the welfare of resource harvesters.

Description: Ecological Applications, Volume 24, Issue 1, Page 15-23, January 2014. We critique a proposal to use catch shares to manage transboundary wildlife resources with potentially high non-extractive values, and we focus on the case of whales. Because whales are impure public goods, a policy that fails to capture all nonmarket benefits (due to free riding) could lead to a suboptimal outcome. Even if free riding were overcome, whale shares would face four implementation challenges. First, a whale share could legitimize the international trade in whale meat and expand the whale meat market. Second, a legal whale trade creates monitoring and enforcement challenges similar to those of organizations that manage highly migratory species such as tuna. Third, a whale share could create a new political economy of management that changes incentives and increases costs for nongovernmental organizations (NGOs) to achieve the current level of conservation. Fourth, a whale share program creates new logistical challenges for quota definition and allocation regardless of whether the market for whale products expands or contracts. Each of these issues, if left unaddressed, could result in lower overall welfare for society than under the status quo.

Description: Ecological Applications, Volume 24, Issue 1, Page 142-157, January 2014. Global wetland biodiversity loss continues unabated, driven by increased demand for freshwater. A key strategy for conservation management of freshwater systems is to maintain the quantity and quality of the natural water regimes, including the frequency and timing of flows. Formalizing an ecological model depicting the key ecological components and the underlying processes of cause and effect is required for successful conservation management. Models linking hydrology with ecological responses can prove to be an invaluable tool for robust decision-making of environmental flows. Here, we explored alternative water management strategies and identified maximal strategies for successful long-term management of colonial waterbirds in the Macquarie Marshes, Australia. We modeled fluctuations in breeding abundances of 10 colonial waterbird species over the past quarter century (1986–2010). Clear relationships existed between flows and breeding, both in frequencies and total abundances, with a strong linear relationship for flows 〉200 GL. Thresholds emerged for triggering breeding events in all 10 species, but these varied among species. Three species displayed a sharp threshold response between 100 GL and 250 GL. These had a breeding probability of 0.5 when flows were 〉180 GL and a 0.9 probability of breeding with flows 〉350 GL. The remaining species had a probability greater than 0.5 of breeding with flows 〉400 GL. Using developed models, we examined the effects of five environmental flow management strategies on the variability of flows and subsequent likelihood of breeding. Management to different target volumes of environmental flows affected overall and specific breeding probabilities. The likelihood of breeding for all 10 colonial waterbirds increased from a regulated historical mean (±SD) of 0.36 ± 0.09 to 0.53 ± 0.14, an improvement of 47.5% ± 18.7%. Management of complex ecosystems depends on good understanding of the responses of organisms to the main drivers of change. Considerable opportunity exists for implementing similar frameworks for other ecosystem attributes, following understanding of their responses to the flow regime, achieving a more complete model of the entire ecosystem.

Description: Ecological Applications, Volume 24, Issue 1, Page 84-93, January 2014. Information on landscape-scale patterns in species distributions and community types is vital for ecological science and effective conservation assessment and planning. However, detailed maps of plant community structure at landscape scales seldom exist due to the inability of field-based inventories to map a sufficient number of individuals over large areas. The Carnegie Airborne Observatory (CAO) collected hyperspectral and lidar data over Kruger National Park, South Africa, and these data were used to remotely identify 〉500 000 tree and shrub crowns over a 144-km2 landscape using stacked support vector machines. Maps of community compositional variation were produced by ordination and clustering, and the importance of hillslope-scale topo-edaphic variation in shaping community structure was evaluated with redundancy analysis. This remote species identification approach revealed spatially complex patterns in woody plant communities throughout the landscape that could not be directly observed using field-based methods alone. We estimated that topo-edaphic variables representing catenal sequences explained 21% of species compositional variation, while we also uncovered important community patterns that were unrelated to catenas, indicating a large role for other soil-related factors in shaping the savanna community. Our results demonstrate the ability of airborne species identification techniques to map biodiversity for the evaluation of ecological controls on community composition over large landscapes.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Vegetation-type conversions between grasslands and shrublands have occurred worldwide in semi-arid regions over the last 150 years. Areas once covered by drought deciduous shrubs in Southern California (Coastal Sage Scrub) are converting to grasslands dominated by non-native species. Increasing fire frequency, drought, and nitrogen deposition have all been hypothesized as causes of this conversion, though there is little direct evidence. We constructed rain-out shelters in a Coastal Sage Scrub community following a wildfire, manipulated water and nitrogen input in a split plot design, and collected annual data on community composition for four years. While shrub cover increased through time in all plots during the post-fire succession, both drought and nitrogen significantly slowed recovery. Four years after the fire, average native shrub cover ranged from over 80% in water addition, ambient nitrogen plots to 20% in water reduction, nitrogen addition plots. European grass cover was high following the fire and remained high in the water reduction plots through the third spring after the fire before decreasing in the fourth year of the study. Adding nitrogen decreased the cover of native plants and increased the cover of Eurasian grasses, but also increased growth of crown-sprouting individuals of one shrub species. Our results suggest that extreme drought during post-fire succession may slow or alter succession, possibly facilitating vegetation-type conversion of Coastal Sage Scrub to grassland. Nitrogen addition slowed succession and, when combined with drought, significantly decreased native cover and increased grass cover. Fire, drought, and atmospheric N deposition are widespread aspects of environmental change that occur simultaneously in this system. Our results suggest these drivers of change may reinforce each other, leading to a continued decline of native shrubs and conversion to annual grassland.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially-explicit, individual-based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement -- a function of water temperature, fluvial distance, and physical barriers -- might influence demogenetic connectivity and hence population vulnerability. We present demographic metrics (abundance, immigration, and change in abundance) and also genetic metrics (diversity, differentiation, and change in differentiation), and combine them into a single vulnerability index for identifying populations at risk of extirpation. We considered four realistic scenarios that illustrate the relative sensitivity of these metrics for early detection of reduced connectivity: (1) maximum resistance due to high water temperatures throughout the network, (2) minimum resistance due to low water temperatures throughout the network, (3) increased resistance at a tributary junction caused by a partial barrier, and (4) complete isolation of a tributary, leaving resident individuals only. We then apply this demogenetic framework using empirical data for a bull trout metapopulation in the upper Flathead River system, Canada and USA, to assess how current and predicted future stream warming may influence population vulnerability. Results suggest that warmer water temperatures and associated barriers to movement (e.g., low flows, de-watering) are predicted to fragment suitable habitat for migratory salmonids, resulting in the loss of genetic diversity and reduced sizes in certain vulnerable population. This demogenetic simulation framework, which is illustrated in a web-based interactive mapping prototype (http://ptolemy.dbs.umt.edu/pvm/), should be useful for evaluating population vulnerability in a wide variety of dendritic and fragmented riverscapes, helping to guide conservation and management efforts for freshwater species.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Tree and shrub abundance has increased in many grasslands causing changes in ecosystem carbon and nitrogen pools that are related to patterns of woody plant distribution. However, with regard to spatial patterns of shrub proliferation, little is known about (i) how they are influenced by grazing or (ii) the extent to which they are influenced by intraspecific interactions. We addressed these questions by quantifying changes in the spatial distribution of Prosopis velutina (mesquite) shrubs over 74 years on grazed and protected grasslands. Livestock are effective agents of mesquite dispersal and mesquite plants have lateral roots extending well beyond the canopy. We therefore hypothesized that mesquite distributions would be (a) random on grazed areas mainly due to cattle dispersion and clustered on protected areas due to decreased dispersal and interspecific interference with grasses; and (b) that clustered or random distributions at early stages of encroachment would give way to regular distributions as stands matured and density-dependent interactions intensified. Assessments in 1932, 1948 and 2006 supported the first hypothesis, but we found no support for the second. In fact, clustering intensified with time on the protected area and the pattern remained random on the grazed site. Although shrub density increased on both areas between 1932 and 2006, we saw no progression toward a regular distribution indicative of density-dependent interactions. We propose that processes related to seed dispersal, grass-shrub seedling interactions, and hydrological constraints on shrub size interact to determine vegetation structure in grassland-to-shrubland state changes with implications for ecosystem function and management.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Mounting evidence now shows that fishing activity modifies both heritable life-history traits and ecological processes in harvested populations. However, ecological and evolutionary changes are intimately linked and can occur on the same time-scale, and few studies have investigated their combined effect on fish population dynamics. Here, we contrast two population subunits of a harvested fish species in the Northeast Atlantic, the European hake (Merluccius merluccius), in the light of the emerging field of evolutionary demography, which considers the interacting processes between ecology and evolution. The two subunits experienced similar age/size truncation due to size-selective fishing, but displayed differences in key ecological processes (recruitment success) and phenotypic characteristics (maturation schedule). We investigate how temporal variation in maturation and recruitment success interactively shape the population dynamics of the two subunits. We document that the two subunits of European hake displayed different responses to fishing in maturation schedules, possibly because of the different level of adaptive phenotypic plasticity. Our results also suggest that high phenotypic plasticity can dampen the effects of fisheries-induced demographic truncation on population dynamics, whereas a population subunit characterized by low phenotypic plasticity may suffer from additive effects of ecological and life-history responses. Similar fishing pressure may thus trigger contrasting interactions between life history variation and ecological processes within the same population. The presented findings improve our understanding of how fishing impacts eco-evolutionary dynamics, which is a keystone for a more comprehensive management of harvested species.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Conservation practitioners, faced with managing multiple threats to biodiversity and limited funding, must prioritize investment in different management actions. From an economic perspective, it is routine practice to invest where the highest rate of return is expected. This return-on-investment (ROI) thinking can also benefit species conservation, and researchers are developing sophisticated approaches to support decision-making for cost-effective conservation. However, applied use of these approaches is limited. Managers may be wary of 'black-box' algorithms or complex methods that are difficult to explain to funding agencies. As an alternative, we demonstrate the use of a basic ROI analysis for determining where to invest in cost-effective management to address threats to species. This method can be applied using basic geographic information system and spread sheet calculations. We illustrate the approach in a management-action prioritization for a biodiverse region of eastern Australia. We use ROI to prioritize management actions for two threats to a suite of threatened species: habitat degradation by cattle grazing and predation by invasive red foxes (Vulpes vulpes). We show how decisions based on cost-effective threat management depend upon how expected benefits to species are defined and how benefits and costs co-vary. By considering a combination of species richness, restricted habitats, species vulnerability, and costs of management actions, small investments can result in greater expected benefit compared with management decisions that consider only species richness. Furthermore, a landscape management strategy that implements multiple actions is more efficient than managing only for one threat or more traditional approaches that don't consider ROI. Our approach provides transparent and logical decision-support for prioritizing different actions intended to abate threats associated with multiple species; it is of use when managers need a justifiable and repeatable approach to investment.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Fire is becoming a pervasive driver of environmental change in Amazonia and is expected to intensify, given projected reductions in precipitation and forest cover. Understanding of the influence of post-deforestation land cover change on fires in Amazonia is limited, even though fires in cleared lands constitute a threat for ecosystems, agriculture, and human health. We used MODIS satellite data to map burned areas annually between 2001 and 2010. We then combined these maps with land cover and climate information to understand the influence of land cover change in cleared lands and dry season severity on fire occurrence and spread in a focus area in the Peruvian Amazon. Fire occurrence, quantified as the probability of burning of individual 232m spatial resolution MODIS pixels was modeled as a function of the area of land cover types within each pixel, drought severity, and distance to roads. Fire spread, quantified as the number of pixels burned in 3x3 pixel windows around each focal burned pixel, was modeled as a function of land cover configuration and area, dry season severity, and distance to roads. We found that vegetation regrowth and oil palm expansion are significantly correlated with fire occurrence but that the magnitude and sign of the correlation depend on drought severity, successional stage of regrowing vegetation and oil palm age. Burning probability increased with the area of non-degraded pastures, fallow, and young oil palm and decreased with larger extents of degraded pastures, secondary forests and adult oil palm plantations. Drought severity had the strongest influence on fire occurrence overriding the effectiveness of secondary forests but not of adult plantations to reduce fire occurrence in severely dry years. Overall, irregular and scattered land cover patches reduced fire spread but irregular and dispersed fallows and secondary forests increased fire spread during dry years. Results underscore the importance of land cover management for reducing fire proliferation in this landscape. Incentives for promoting natural regeneration and perennial crops in cleared lands might help reduce fire risk if those areas are protected against burning in early stages of development and during severely dry years.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. There is a growing need for operational biodiversity mapping methods to quantify and to assess the impact of climate change, habitat alteration and human activity on ecosystem composition and function. Here, we present an original method for the estimation of α- and β-diversity of tropical forests based on high-fidelity imaging spectroscopy. We acquired imagery acquired over high-diversity Amazonian tropical forest landscapes in Perú with the Carnegie Airborne Observatory and developed an unsupervised method to estimate the Shannon Index (H') and variations in species composition using Bray-Curtis Dissimilarity (BC) and non-metric multidimensional scaling (NMDS). An extensive field plot network was used for the validation of remotely sensed α- and β-diversity. Airborne maps of H' were highly correlated with field α-diversity estimates (r = 0.86), and BC was estimated with demonstrable accuracy (r = 0.61-0.76). Our findings are the first direct and spatially-explicit remotely sensed estimates of α- and β-diversity of humid tropical forests, paving the way for new applications using airborne and space-based imaging spectroscopy.

Description: Ecological Applications, Volume 24, Issue 1, Page 229-233, January 2014.

Description: Ecological Applications, Volume 24, Issue 1, Page 181-195, January 2014. Stable isotopes are valuable tools for partitioning the components contributing to ecological processes of interest, such as animal diets and trophic interactions, plant resource use, ecosystem gas fluxes, streamflow, and many more. Stable isotope data are often analyzed with simple linear mixing (SLM) models to partition the contributions of different sources, but SLM models cannot incorporate a mechanistic understanding of the underlying processes and do not accommodate additional data associated with these processes (e.g., environmental covariates, flux data, gut contents). Thus, SLM models lack predictive ability. We describe a process-based mixing (PBM) model approach for integrating stable isotopes, other data sources, and process models to partition different sources or process components. This is accomplished via a hierarchical Bayesian framework that quantifies multiple sources of uncertainty and enables the incorporation of process models and prior information to help constrain the source-specific proportional contributions, thereby potentially avoiding identifiability issues that plague SLM models applied to “too many” sources. We discuss the application of the PBM model framework to three diverse examples: temporal and spatial partitioning of streamflow, estimation of plant rooting profiles and water uptake profiles (or water sources) with extension to partitioning soil and ecosystem CO2 fluxes, and reconstructing animal diets. These examples illustrate the advantages of the PBM modeling approach, which facilitates incorporation of ecological theory and diverse sources of information into the mixing model framework, thus enabling one to partition key process components across time and space.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e. cyanobacteria, lichens and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte) and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently-aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: 1) species with high resistance and resilience to grazing, 2) species with high resistance but low resilience, 3) species with low resistance but high resilience, and 4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. The American pika (Ochotona princeps) has become a species of concern for its sensitivity to warm temperatures and potential vulnerability to global warming. We explored the value of radiocarbon dating of fecal pellets to address questions of population persistence and timing of site extirpation. Carbon was extracted from pellets collected at 43 locations in the western Great Basin, USA, including 3 known occupied sites and 40 sites of uncertain status at range margins or where previous studies indicated the species is vulnerable. We resolved calibrated dates with high precision (within several years), most of which fell in the period of the mid-late 20th century "bomb curve." The two-sided nature of the bomb curve renders "far-" and "near-side" dates of equal probability, which are separated by 1-4 decades. We document methods for narrowing resolution to one age range, including stratigraphic analysis of vegetation collected from pika haypiles. No evidence was found for biases in atmospheric 14C levels due to fossil-derived or industrial CO2 contamination. Radiocarbon dating indicated that pellets can persist for 〉59 years; known-occupied sites resolved contemporary dates. Using combined evidence from field observations and radiocarbon-dating, and the Bodie Mountains (Mtns) as an example, we propose a historical biogeographic scenario for pikas in minor Great Basin mountain ranges adjacent to major cordillera wherein historical climate variability led to cycles of extirpation and re-colonization during alternating cool and warm centuries. Using this model to inform future dynamics for small ranges in biogeographic settings similar to the Bodie Mtns, CA, extirpation of pikas appears highly likely under directional warming trends projected for the next century, even while populations in extensive cordillera (e.g., Sierra Nevada, Rocky Mtns, Cascade Range) are likely to remain viable due to extensive, diverse, habitat and high connectivity.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Studies of predator-prey demographic responses and the physical drivers of such relationships are rare, yet essential for predicting future changes in the structure and dynamics of marine ecosystems. Here, we hypothesize that predator-prey relationships vary spatially in association with underlying physical ocean conditions, leading to observable changes in demographic rates, such as reproduction. To test this hypothesis, we quantified spatio-temporal variability in hydrographic conditions, krill, and forage fish to model predator (seabird) demographic responses over 18 years (1990-2007). We used principal component analysis and spatial correlation maps to assess coherence among ocean conditions, krill, and forage fish, and generalized additive models to quantify interannual variability in seabird breeding success relative to prey abundance. The first principal component of 4 hydrographic measurements yielded an index that partitioned "weak/warm upwelling" and "strong/cool upwelling" years. Partitioning of krill and forage fish time series among shelf and oceanic regions yielded spatially-explicit indicators of prey availability. Krill abundance within the oceanic region was remarkably consistent between years, whereas krill over the shelf showed marked interannual fluctuations in relation to ocean conditions. Anchovy abundance varied on the shelf, and was greater in years of strong stratification/weak upwelling and warmer temperatures. Spatio-temporal variability of juvenile forage fish covaried strongly with each other and with krill, but was weakly correlated with hydrographic conditions. Demographic responses between seabirds and prey availability revealed spatially-variable associations indicative of the dynamic nature of habitat-prey relationships. Quantification of spatially-explicit demographic responses, and their variability through time, demonstrates the possibility of delineating specific critical areas where the implementation of protective measures could maintain functions and productivity of central place foraging predators.

Description: Ecological Applications, Ahead of Print. Translocation experiments, in which researchers displace animals then monitor their movements to return home, are commonly used as tools to assess functional connectivity of fragmented landscapes. Such experiments are purported to have important advantages of being time efficient and standardizing 'motivation' to move across individuals. Yet, we lack tests of whether movement behavior of translocated birds reflects natural behavior of unmanipulated birds. We compared the routine movement behavior of a tropical hummingbird (Phaethornis guy) to that of experimentally translocated individuals. We tested for differences in site-selection patterns during movement at two spatial scales (point and path levels). We also compared movement rates between treatments. Behaviors documented during translocation experiments reflected those observed during routine movements. At the point level, both translocated and non-translocated birds showed similar levels of preference for mature tropical forest. At the path level, step selection functions showed both translocated and non-translocated hummingbirds avoiding movement across non-forested matrix and selecting streams as movement corridors. Movement rates were generally higher during translocation experiments. However, the negative influence of forest cover on movement rates was proportionately similar in translocation and routine movement treatments. We report the first evidence showing that movement behavior of birds during translocation experiments is similar to their natural movement behavior. Therefore, translocation experiments may be reliable tools to address effects of landscape structure on animal movement. We observed consistent selection of landscape elements between translocated and non-translocated birds, indicating that both routine and translocation movement studies lead to similar conclusions regarding the effect of landscape structure and forest composition on functional connectivity. Our observations that hummingbirds avoid non-forest matrix and select riparian corridors also provides a potential mechanism for pollen limitation in fragmented tropical forest.

Description: Ecological Applications, Ahead of Print. Climate change vulnerability assessments for species of conservation concern often use species distribution and ecological niche modeling to project changes in habitat. One of many assumptions of these approaches is that food web dependencies are consistent in time and environmental space. Species at higher trophic levels that rely on the availability of species at lower trophic levels as food may be sensitive to extinction cascades initiated by changes in the habitat of key food resources. Here we assess climate change vulnerability for Ursus arctos (grizzly bears) in the southern Canadian Rocky Mountains using projected changes to 17 of the most commonly consumed plant food items. We used presence-absence information from 7,088 field plots to estimate ecological niches and to project changes in future distributions of each species. Model projections indicated idiosyncratic responses among food items. Many food items persisted or even increased, although several species were found to be vulnerable based on declines or geographic shifts in suitable habitat. This included Hedysarum alpinum (alpine sweet vetch), a critical spring and autumn root-digging resource when little else is available. Potential habitat loss was also identified for three fruiting species of lower importance to bears: Empetrum nigrum (crowberry), Vaccinium scoparium (grouseberry) and Fragaria virginiana (strawberry). A general trend towards uphill migration of bear foods may result in higher vulnerability to bear populations at low elevations which are also those that are most likely to have human-bear conflict problems. Regardless, a wide diet breadth of grizzly bears, as well as wide environmental niches of most food items, make climate change a much lower threat to grizzly bears than other bear species such as polar bears and panda bears. We cannot exclude, however, future alterations in human behavior and land use resulting from climate change that may reduce survival rates.

Description: Ecological Applications, Ahead of Print. Efforts to test and improve terrestrial biosphere models (TBMs) using a variety of data sources have become increasingly common. However, geographically extensive forest inventories have been under-exploited in previous model-data fusion efforts. Inventory observations of forest growth, mortality, and biomass integrate processes across a range of time scales, including slow time-scale processes such as species turnover, that are likely to have important effects on ecosystem responses to environmental variation. However, the large number (thousands) of inventory plots precludes detailed measurements at each location, so that uncertainty in climate, soil properties, and other environmental drivers may be large. Errors in driver variables, if ignored, introduce bias into model-data fusion. We estimated errors in climate and soil drivers at U.S. Forest Inventory and Analysis (FIA) plots, and we explored the effects of these errors on model-data fusion with the Geophysical Fluid Dynamics Laboratory LM3V dynamic global vegetation model. When driver errors were ignored or assumed small at FIA plots, responses of biomass production in LM3V to precipitation and soil available water capacity appeared steeper than the corresponding responses estimated from FIA data. These differences became non-significant if driver errors at FIA plots were assumed large. Ignoring driver errors when optimizing LM3V parameter values yielded estimates for fine-root allocation that were larger than biometric estimates, which is consistent with the expected direction of bias. To explore if complications posed by driver errors could be circumvented by relying on intensive study sites where driver errors are small, we performed a power analysis. To accurately quantify the response of biomass production to spatial variation in mean annual precipitation within the eastern U.S. would require at least 40 intensive study sites, which is larger than the number of sites typically available for individual biomes in existing plot networks. Driver errors may be accommodated by several existing model-data fusion approaches, including hierarchical Bayesian methods and ensemble filtering methods; however, these methods are computationally expensive. We propose a new approach, in which the TBM functional response is fit directly to the driver-error-corrected functional response estimated from data, rather than to the raw observations.

Description: Ecological Applications, Ahead of Print. Despite intensive monitoring, temporary emigration from the sampling area can induce bias severe enough for managers to discard life-history parameter estimates toward the terminus of the times series (terminal bias). Under random temporary emigration unbiased parameters can be estimated with CJS models. However, unmodeled Markovian temporary emigration causes bias in parameter estimates and an unobservable state is required to model this type of emigration. The robust design is most flexible when modeling temporary emigration, and partial solutions to mitigate bias have been identified, nonetheless there are conditions were terminal bias prevails. Long-lived species with high adult survival and highly variable non-random temporary emigration present terminal bias in survival estimates, despite being modeled with the robust design and suggested constraints. Because this bias is due to uncertainty about the fate of individuals that are undetected toward the end of the time series, solutions should involve using additional information on survival status or location of these individuals at that time. Using simulation, we evaluated the performance of models that jointly analyze robust design data and an additional source of ancillary data (predictive covariate on temporary emigration, telemetry, dead recovery, or auxiliary resightings) in reducing terminal bias in survival estimates. The auxiliary resighting and predictive covariate models reduced terminal bias the most. Additional telemetry data was effective at reducing terminal bias only when individuals were tracked for a minimum of two years. High adult survival of long-lived species made the joint model with recovery data ineffective at reducing terminal bias because of small-sample bias. The naïve constraint model (last and penultimate temporary emigration parameters made equal), was the least efficient, though still able to reduce terminal bias when compared to an unconstrained model. Joint analysis of several sources of data improved parameter estimates and reduced terminal bias. Efforts to incorporate or acquire such data should be considered by researchers and wildlife managers, especially in the years leading up to status assessments of species of interest. Simulation modeling is a very cost effective method to explore the potential impacts of using different sources of data to produce high quality demographic data to inform management.

Description: Ecological Applications, Ahead of Print. Warmer and drier climate over the past few decades has brought larger fire sizes and increased annual area burned in forested ecosystems of western North America, and continued increases in annual area burned are expected due to climate change. As warming continues, fires may also increase in severity and produce larger contiguous patches of high severity. We use remotely sensed burn-severity data from 125 fires in the northern Cascade Range of Washington, USA, to explore relationships between fire size, severity, and the spatial pattern of severity. We examine relationships between climate and the annual area burned and the size of wildfires over a 25-year period. We test the hypothesis that increased fire size is commensurate with increased burn severity and increased spatial aggregation of high severity. We also ask how local ecological controls might modulate these relationships by comparing results over the whole study area (the northern Cascade Range) to those from four ecological subsections within it. We found significant positive relationships between climate and fire size, and between fire size and the proportion of high severity and spatial-pattern metrics that quantify the spatial aggregation of high-severity areas within fires, but the strength and significance of these relationships varied among the four subsections. In areas with more contiguous subalpine forests and less complex topography, the proportion of high severity and spatial aggregation of high severity were more strongly correlated with fire size. If fire sizes increase in a warming climate, changes in the extent, severity, and spatial pattern of fire regimes will likely be more pronounced in higher-severity fire regimes with less complex topography and more continuous fuels.

Description: Ecological Applications, Ahead of Print. Fremont cottonwood (Populus fremonti, Eckenwal.) is a foundation riparian tree species that drives community structure and ecosystem processes in southwestern U.S. ecosystems. Despite its ecological importance, little is known about the ecological and environmental processes that shape its genetic diversity, structure and landscape connectivity. Here, we combine molecular analyses of 82 populations including 1,312 individual trees dispersed over the species' geographical distribution. We reduced the dataset to 40 populations and 743 individuals to eliminate admixture with a sibling species, and used multi-variate restricted optimization and reciprocal causal modeling, to evaluate the effects of river network connectivity and climatic gradients on gene flow. Our results confirmed the following: First, gene flow of Fremont cottonwood is jointly controlled by the connectivity of the river network and gradients of seasonal precipitation. Second, gene flow is facilitated by mid-sized to large rivers, and is resisted by small streams and terrestrial uplands, with resistance to gene flow decreasing with river size. Third, genetic differentiation increases with cumulative differences in winter and spring precipitation. Our results, suggest that ongoing fragmentation of riparian habitats will lead to a loss of landscape level genetic connectivity, leading to increased inbreeding and the concomitant loss of genetic diversity in a foundation species. These genetic effects will cascade to a much larger community of organisms, some of which are threatened and endangered.

Description: Ecological Applications, Ahead of Print. Identifying determinants of the probability and intensity of infections is important for understanding the epidemiology of wildlife diseases, and for managing their impact on threatened species. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis, has decimated populations of some amphibians. However, recent studies have identified important environmental constraints on the disease, related to the pathogen's physiological tolerances. In this study, we identified several intrinsic and extrinsic determinants of the probability and intensity of chytrid infections for the threatened Growling Grass Frog (Litoria raniformis) in south-eastern Australia, and used mark-recapture to estimate the effect of chytrid infections on the probability of survival of these frogs. Water temperature and salinity had negative effects on both the probability and intensity of chytrid infections. We coupled models of the infection process with a model of the effect of chytrid infections on the probability of survival to assess variation in the impact of chytridiomycosis between wetlands with differing temperature and salinity profiles. Our results suggest that warm, saline wetlands may be refuges from chytridiomycosis for L. raniformis, and should be priorities for protection. Our results also suggest that management actions that increase water temperature (e.g. reducing canopy shading) and salinity (e.g. complementing inflows with groundwater) could be trialled to reduce the impacts of chytridiomycosis on this species. This and other recent studies highlight the value of research on environmental risk factors for chytridiomycosis.

Description: Ecological Applications, Ahead of Print. Terrestrial soil is a large reservoir of atmospherically deposited mercury (Hg). However, few studies have evaluated the accumulation of Hg in terrestrial ecosystems in the northeastern United States, a region which is sensitive to atmospheric Hg deposition. In this study, we characterize Hg and organic matter in soil profiles from 139 sampling sites for five sub-regions across the northeastern United States, and estimate atmospheric Hg deposition to these sites by combining numerical modeling with experimental data from the literature. We did not observe any significant relationships between current net atmospheric Hg deposition and soil Hg concentrations or pools, even though soils are a net sink for Hg inputs. Soil Hg appears to be preserved relative to organic carbon (OC) and/or nitrogen (N) in the soil matrix, as a significant negative relationship was observed between the ratios of Hg/OC and OC/N (r = 0.54, p 〈 0.0001) that shapes the horizonal distribution patterns. We estimated that atmospheric Hg deposition since 1850 (3.97 mg m-2) accounts for 102% of the Hg pool in the organic horizons (3.88 mg m-2) and 19% of the total soil Hg pool (21.32 mg m-2), except for the Southern New England (SNE) sub-region. The mean residence time for soil Hg was estimated to be 1,800 years, except SNE which was 800 years. These patterns suggest that in additional to atmospheric deposition, the accumulation of soil Hg is linked to the mineral diagenetic and soil development processes in the region.

Description: Ecological Applications, Ahead of Print. Predicting how climate change is likely to interact with myriad other stressors that threaten species of conservation concern is an essential challenge in aquatic ecosystems. This study provides a framework to accomplish this task in salmon-bearing streams of the northwestern United States, where land-use related reductions in riparian shading have caused changes in stream thermal regimes, and additional warming from projected climate change may result in significant losses of coldwater fish habitat over the next century. Predatory non-native smallmouth bass have also been introduced into many northwestern streams and their range is likely to expand as streams warm, presenting an additional challenge to the persistence of threatened Pacific salmon. The goal of this work was to forecast the interactive effects of climate change, riparian management, and non-native species on stream-rearing salmon, and to evaluate the capacity of restoration to mitigate these effects. We intersected downscaled global climate forecasts with a local-scale water temperature model to predict mid- and end-of-century temperatures in streams in the Columbia River basin; we compared one stream that is thermally impaired due to the loss of riparian vegetation and another that is cooler and has a largely intact riparian corridor. Using the forecasted stream temperatures in conjunction with fish-habitat models, we predicted how stream-rearing Chinook salmon and bass distributions would change as each stream warmed. In the highly modified stream, end-of-century warming may cause near total loss of Chinook salmon rearing habitat and a complete invasion of the upper watershed by bass. In the less modified stream, bass were thermally restricted from the upstream-most areas. In both systems, temperature increases resulted in higher predicted spatial overlap between stream-rearing Chinook salmon and potentially predatory bass in the early summer (2-4-fold increase) and greater abundance of bass. We found that riparian restoration could prevent the extirpation of Chinook salmon from the more altered stream, and could also restrict bass from occupying the upper 31 km of salmon rearing habitat. The proposed methodology and model predictions are critical for prioritizing climate-change adaptation strategies before salmonids are exposed to both warmer water and greater predation risk by non-native species.

Description: Ecological Applications, Volume 24, Issue 3, Page 528-538, April 2014. A unique high temporal frequency data set from an irrigated cotton–wheat rotation was used to test the agroecosystem model DayCent to simulate daily N2O emissions from subtropical vertisols under different irrigation intensities. DayCent was able to simulate the effect of different irrigation intensities on N2O fluxes and yield, although it tended to overestimate seasonal fluxes during the cotton season. DayCent accurately predicted soil moisture dynamics and the timing and magnitude of high fluxes associated with fertilizer additions and irrigation events. At the daily scale we found a good correlation of predicted vs. measured N2O fluxes (r2 = 0.52), confirming that DayCent can be used to test agricultural practices for mitigating N2O emission from irrigated cropping systems. A 25-year scenario analysis indicated that N2O losses from irrigated cotton–wheat rotations on black vertisols in Australia can be substantially reduced by an optimized fertilizer and irrigation management system (i.e., frequent irrigation, avoidance of excessive fertilizer application), while sustaining maximum yield potentials.

Description: Ecological Applications, Ahead of Print. Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e. cyanobacteria, lichens and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte) and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently-aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: 1) species with high resistance and resilience to grazing, 2) species with high resistance but low resilience, 3) species with low resistance but high resilience, and 4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

Description: Ecological Applications, Ahead of Print. Post-fire predictions of forest recovery under future climate change and management actions are necessary for forest managers to make decisions about treatments. We applied the Climate-Forest Vegetation Simulator (Climate-FVS), a new version of a widely used forest management model, to compare alternative climate and management scenarios in a severely burned multi-species forest of Arizona, U.S.A. The incorporation of seven combinations of General Circulation Models (GCM) and emissions scenarios altered long-term (100 years) predictions of future forest condition compared to a No Climate Change (NCC) scenario, which forecast a gradual increase to high levels of forest density and carbon stock. In contrast, emissions scenarios that included continued high greenhouse gas releases led to near-complete deforestation by 2111. GCM-emissions scenario combinations that were less severe reduced forest structure and carbon stock relative to NCC. Fuel reduction treatments that had been applied prior to the severe wildfire did have persistent effects, especially under NCC, but were overwhelmed by increasingly severe climate change. We tested six management strategies aimed at sustaining future forests: prescribed burning at 5, 10, or 20-year intervals, thinning 40% or 60% of stand basal area, and no-treatment. Severe climate change led to deforestation under all management regimes, but important differences emerged under the moderate scenarios: treatments that included regular prescribed burning fostered low density, wildfire-resistant forests composed of the naturally dominant species, ponderosa pine. Non-fire treatments under moderate climate change were forecast to become dense and susceptible to severe wildfire, with a shift to dominance by sprouting species. Current U.S. forest management requires modeling of future scenarios but does not mandate consideration of climate change effects. However, this study showed substantial differences in model outputs depending on climate and management actions. Managers should incorporate climate change into the process of analyzing the environmental effects of alternative actions.

Description: Ecological Applications, Ahead of Print. Digital repeat photography is becoming widely used for near surface remote sensing of vegetation. Canopy greenness, which has been used extensively for phenological applications, can be readily quantified from camera images. Important questions remain, however, as to whether the observed changes in canopy greenness are directly related to changes in leaf-level traits, changes in canopy structure, or some combination thereof. We investigated relationships between canopy greenness and various metrics of canopy structure and function, using five years (2008-2012) of automated digital imagery, ground observations of phenological transitions, leaf area index (LAI) measurements, and eddy-covariance estimates of gross ecosystem photosynthesis from the Harvard Forest, a temperate deciduous forest in the northeastern USA. Additionally, we sampled canopy sunlit leaves on a weekly basis throughout the growing season of 2011. We measured physiological and morphological traits including leaf size, mass (wet/dry), nitrogen content, chlorophyll fluorescence, and spectral reflectance, and characterized individual leaf color with flatbed scanner imagery. Our results show that observed spring and autumn phenological transition dates are well captured by information extracted from digital repeat photography. However, spring development of both LAI and the measured physiological and morphological traits are shown to lag behind spring increases in canopy greenness, which rises very quickly to its maximum value before leaves are even half their final size. Based on the hypothesis that changes in canopy greenness represent the aggregate effect of changes in both leaf-level properties (specifically, leaf color) and changes in canopy structure (specifically, LAI), we developed a two end-member mixing model. With just a single free parameter, the model was able to reproduce the observed seasonal trajectory of canopy greenness. This analysis shows that canopy greenness is relatively insensitive to changes in LAI at high LAI levels, which we further demonstrate by assessing the impact of an ice-storm on both LAI and canopy greenness. Our study provides new insights into the mechanisms driving seasonal changes in canopy greenness retrieved from digital camera imagery. The nonlinear relationship between canopy greenness and canopy LAI has important implications both for phenological research applications and for assessing responses of vegetation to disturbances.

Description: Ecological Applications, Ahead of Print. The degree to which recent bark beetle (Dendroctonus ponderosae) outbreaks may influence fire severity and post-fire tree regeneration is of heightened interest to resource managers throughout western North America, but empirical data on actual fire effects are lacking. Outcomes may depend on burning conditions (i.e., weather during fire), outbreak severity, or intervals between outbreaks and subsequent fire. We studied recent fires that burned through green-attack / red-stage (outbreaks 〈 3 yr before fire) and gray-stage (outbreaks 3-15 yr before fire) subalpine forests dominated by lodgepole pine (Pinus contorta var. latifolia) in Greater Yellowstone, Wyoming, USA, to determine if fire severity was linked to pre-fire beetle outbreak severity and whether these two disturbances produced compound ecological effects on post-fire tree regeneration. With field data from 143 post-fire plots that burned under different conditions, we assessed canopy and surface fire-severity, and post-fire tree seedling density against pre-fire outbreak severity. In the green-attack / red stage, several canopy fire-severity measures increased with pre-fire outbreak severity under moderate burning conditions. Under extreme conditions, few fire-severity measures were related to pre-fire outbreak severity, and effect sizes were of marginal biological significance. The percentage of tree stems and basal area killed by fire increased with more green-attack vs. red-stage trees (i.e., the earliest stages of outbreak). In the gray stage, by contrast, most fire-severity measures declined with increasing outbreak severity under moderate conditions, and fire severity was unrelated to outbreak severity under extreme burning conditions. Post-fire lodgepole pine seedling regeneration was unrelated to pre-fire outbreak severity in either post-outbreak stage, but increased with pre-fire serotiny. Results suggest bark beetle outbreaks can affect fire severity in subalpine forests under moderate burning conditions, but have little effect on fire severity under extreme burning conditions when most large wildfires occur in this system. Thus, beetle outbreak severity was moderately linked to fire severity, but the strength and direction of the linkage depended on both endogenous (outbreak stage) and exogenous (fire weather) factors. Closely-timed beetle outbreak and fire did not impart compound effects on tree regeneration, suggesting the presence of a canopy seedbank may enhance resilience to their combined effects.

Description: Ecological Applications, Ahead of Print. Ecological reserves provide important wildlife habitat in many landscapes, and the functional connectivity of reserves and other suitable habitat patches is crucial for the persistence and resilience of spatially structured populations. To maintain or increase connectivity at spatial scales larger than individual patches, conservation actions may focus on creating and maintaining reserves and/or influencing management on non-reserves. Using a graph-theoretic approach, we assessed the functional connectivity and spatial distribution of wetlands in the Rainwater Basin of Nebraska, U.S.A., an intensively cultivated agricultural matrix, at four assumed, but ecologically realistic, anuran dispersal distances. We compared connectivity in the current landscape to the historical landscape and putative future landscapes, and evaluated the importance of individual and aggregated reserve and non-reserve wetlands for maintaining connectivity. Connectivity was greatest in the historical landscape, where wetlands were also the most densely distributed. The construction of irrigation reuse pits for water storage has maintained connectivity in the current landscape by replacing destroyed wetlands, but these pits likely provide suboptimal habitat. Also, because there are fewer total wetlands (i.e., wetlands and irrigation reuse pits) in the current landscape than the historical landscape, and because the distribution of current wetlands is less clustered than that of historical wetlands, larger and longer-dispersing, sometimes non-native species may be favored over smaller, shorter-dispersing species of conservation concern. Because of their relatively low number, wetland reserves do not affect connectivity as greatly as non-reserve wetlands or irrigation reuse pits; however, they likely provide the highest-quality anuran habitat. To improve future levels of resilience in this wetland habitat network, management could focus on continuing to improve the conservation status of non-reserve wetlands, restoring wetlands at spatial scales that promote movements of shorter-dispersing species, and further scrutinizing irrigation reuse pit removal by considering effects on functional connectivity for anurans, an emblematic and threatened group of organisms. However, broader conservation plans will need to give consideration to other wetland-dependent species, incorporate invasive species management, and address additional challenges arising from global change in social-ecological systems like the Rainwater Basin.

Description: Ecological Applications, Ahead of Print. Ecosystem-based management of natural resources involves an explicit consideration of trade-offs among ecosystem services. In marine fisheries, there is the potential for a trade-off between the supporting role of small pelagic fish and cephalopods in food webs, and the provisioning service they play as a major target of fisheries. Because these species play central roles in food webs by providing a conduit of energy from small prey to upper trophic level predators, we hypothesized that trade-offs between these two ecosystem services could be predicted based on energetic properties of predator-prey linkages and food web structure. We compiled information from 27 marine food web models (Ecopath) that included either small pelagic fish or cephalopods, described predator-prey linkages involving these species, and developed a novel analytical framework to estimate how changes in yields of forage species would propagate through food webs and other fisheries. Consistent with expectations, diet overlap between predators and prey was generally low, and predator prey linkages tended to be asymmetric; contribution of these species to predator diets was, on average, larger than the contribution of individual predator stocks to prey mortality. The estimated trade-offs between yields of forage fish and predator species were highly variable when we assumed joint bottom-up and top-down control on predation. Roughly one-third of this variance was related to an interactive effect of fishing and predation intensity; strong trade-offs were predicted when fishing intensity on forage species is high and when predators account for a high proportion of total forage mortality. When trophic connections were presumed to be driven by bottom-up processes, trade-offs were more predictable but generally very small. Contrary to our expectations, trade-offs were not easily predicted from energetic properties, largely because predators of forage species exhibited a high degree of intra-guild predation and also consumed many of the same prey as forage species. Given the limited ability to a priori predict the food web implications of forage fisheries, we suggest that a precautionary risk-based approach be applied to decisions about acceptable biological removals of forage fish and biological targets used for their management.

Description: Ecological Applications, Ahead of Print. Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially-explicit, individual-based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement -- a function of water temperature, fluvial distance, and physical barriers -- might influence demogenetic connectivity and hence population vulnerability. We present demographic metrics (abundance, immigration, and change in abundance) and also genetic metrics (diversity, differentiation, and change in differentiation), and combine them into a single vulnerability index for identifying populations at risk of extirpation. We considered four realistic scenarios that illustrate the relative sensitivity of these metrics for early detection of reduced connectivity: (1) maximum resistance due to high water temperatures throughout the network, (2) minimum resistance due to low water temperatures throughout the network, (3) increased resistance at a tributary junction caused by a partial barrier, and (4) complete isolation of a tributary, leaving resident individuals only. We then apply this demogenetic framework using empirical data for a bull trout metapopulation in the upper Flathead River system, Canada and USA, to assess how current and predicted future stream warming may influence population vulnerability. Results suggest that warmer water temperatures and associated barriers to movement (e.g., low flows, de-watering) are predicted to fragment suitable habitat for migratory salmonids, resulting in the loss of genetic diversity and reduced sizes in certain vulnerable population. This demogenetic simulation framework, which is illustrated in a web-based interactive mapping prototype (http://ptolemy.dbs.umt.edu/pvm/), should be useful for evaluating population vulnerability in a wide variety of dendritic and fragmented riverscapes, helping to guide conservation and management efforts for freshwater species.

Description: Ecological Applications, Ahead of Print. Fire regimes of the Canadian boreal forest are driven by certain environmental factors that are highly variable from year to year (e.g., temperature, precipitation) and others that are relatively stable (e.g., land cover, topography). Studies examining the relative influence of these environmental drivers on fire activity suggest that models making explicit use of inter-annual variability appear to better capture years of climate extremes, whereas those using a temporal average of all available years highlight the importance of land-cover variables. It has been suggested that fire models built at different temporal resolutions may provide a complementary understanding of controls on fire regimes, but this claim has not been tested explicitly with parallel data and modelling approaches. We addressed this issue by building two models of area burned for the period 1980-2010 using 14 explanatory variables to describe ignitions, vegetation, climate, and topography. We built one model at an annual resolution, with climate and some land-cover variables being updated annually, and the other model using 31-year fire "climatology" based on averaged variables. Despite substantial differences in the variables' contributions to the two models, their predictions were broadly similar, which suggests coherence between the spatial patterns of annually varying climate extremes and long-term climate normals. Where the models' predictions diverged, discrepancies between the annual and averaged models could be attributed to specific explanatory variables. For instance, annually updating land cover allowed us to identify a possible negative feedback between flammable biomass and fire activity. These results show that building models at more than one temporal resolution affords a deeper understanding of controls on fire activity in boreal Canada than can be achieved by examining a single model. However, in terms of spatial predictions, the additional effort required to build annual models of fire activity may not always be warranted in this study area. From a management and policy standpoint, this key finding should boost confidence in models that incorporate climatic normals, thereby providing a stronger foundation on which to make decisions on adaptation and mitigation strategies for future fire activity.

Description: Ecological Applications, Ahead of Print. Fire is becoming a pervasive driver of environmental change in Amazonia and is expected to intensify, given projected reductions in precipitation and forest cover. Understanding of the influence of post-deforestation land cover change on fires in Amazonia is limited, even though fires in cleared lands constitute a threat for ecosystems, agriculture, and human health. We used MODIS satellite data to map burned areas annually between 2001 and 2010. We then combined these maps with land cover and climate information to understand the influence of land cover change in cleared lands and dry season severity on fire occurrence and spread in a focus area in the Peruvian Amazon. Fire occurrence, quantified as the probability of burning of individual 232m spatial resolution MODIS pixels was modeled as a function of the area of land cover types within each pixel, drought severity, and distance to roads. Fire spread, quantified as the number of pixels burned in 3x3 pixel windows around each focal burned pixel, was modeled as a function of land cover configuration and area, dry season severity, and distance to roads. We found that vegetation regrowth and oil palm expansion are significantly correlated with fire occurrence but that the magnitude and sign of the correlation depend on drought severity, successional stage of regrowing vegetation and oil palm age. Burning probability increased with the area of non-degraded pastures, fallow, and young oil palm and decreased with larger extents of degraded pastures, secondary forests and adult oil palm plantations. Drought severity had the strongest influence on fire occurrence overriding the effectiveness of secondary forests but not of adult plantations to reduce fire occurrence in severely dry years. Overall, irregular and scattered land cover patches reduced fire spread but irregular and dispersed fallows and secondary forests increased fire spread during dry years. Results underscore the importance of land cover management for reducing fire proliferation in this landscape. Incentives for promoting natural regeneration and perennial crops in cleared lands might help reduce fire risk if those areas are protected against burning in early stages of development and during severely dry years.

Description: Ecological Applications, Ahead of Print. Intraguild predators both feed on and compete with their intraguild prey. In theory, intraguild predators can therefore be very effective as biological control agents of intraguild prey species, especially in productive environments. We investigated this hypothesis using the mixotrophic chrysophyte Ochromonas as intraguild predator and the harmful cyanobacterium Microcystis aeruginosa as its prey. Ochromonas can grow photoautotrophically, but can also graze efficiently on Microcystis. Hence, it competes with its prey for inorganic resources. We developed a mathematical model and parameterized it for our experimental food web. The model predicts dominance of Microcystis at low nutrient loads, coexistence of both species at intermediate nutrient loads, and dominance of Ochromonas but a strong decrease of Microcystis with further nutrient enrichment. We tested these theoretical predictions in chemostat experiments supplied with three different nitrogen concentrations. Ochromonas initially suppressed the Microcystis abundance by 〉 97% compared to the Microcystis monocultures. Thereafter, however, Microcystis gradually recovered to ~20% of its monoculture abundance at low nitrogen loads, but to 50-60% at high nitrogen loads. Hence, Ochromonas largely lost control over the Microcystis population at high nitrogen loads. We explored several mechanisms that might explain this deviation from theoretical predictions, and found that intraspecific interference at high Ochromonas densities reduced their grazing rates on Microcystis. These results illustrate the potential of intraguild predation to control pest species, but also show that the effectiveness of their biological control can be reduced in productive environments.

Description: Ecological Applications, Ahead of Print. A novel strategy for suppressing disease transmission by Aedes aegypti, the main vector of dengue, uses releases of mosquitoes infected with the bacterium Wolbachia pipientis. Wolbachia are currently released to interfere with viral transmission, but there is also potential to use strains in mosquito suppression and elimination programs via the deleterious effects of the bacterium on the host. Mosquito suppression depends on target areas being relatively isolated to prevent reinvasion and on local climatic conditions. Here we explored the opportunity for suppression of Ae. aegypti in central Queensland, Australia, by using microsatellite data and simulations based on CIMSiM models of local weather conditions and breeding container data. Our results indicate that Wolbachia-induced extinctions in central Queensland are possible, although they may eventually be compromised by ongoing mosquito migration between towns until these sources are also suppressed. The results highlight a novel use of deleterious Wolbachia infections to achieve ecological as well as disease-related endpoints.

Description: Ecological Applications, Ahead of Print. The decreasing abundance of mature forests and their fragmentation have been identified as major threats for the preservation of biodiversity in managed landscapes. In this study, we developed a multi-level framework to coordinate forest harvestings so as to optimize the retention or restoration of large mature forest tracts in managed forests. We used mixed-integer programming for this optimization, and integrated realistic management assumptions regarding stand yields and operational harvest constraints. The model was parameterized for eastern Canadian boreal forests, where clearcutting is the main silvicultural system, and used to examine two hypotheses. First, we tested if mature forest tract targets had more negative impacts on wood supplies when implemented in landscapes that are very different from targeted conditions. Second, we tested the hypothesis that using more partial cuts can be useful to attenuate the negative impacts of mature forest targets on wood supplies. The results indicate that without the integration of an explicit mature forest tract target, forest management strategies lead to relatively high fragmentation levels. Forcing the retention or restoration of large mature forest tracts on 40% of the landscapes had negative impacts on wood supplies in all types of landscapes, but these impacts were less important in landscapes that were initially fragmented. This counter-intuitive result is explained by the presence in the models of an operational constraint that forbids diffuse patterns of harvestings, which are more costly. Once this constraint is applied, the residual impact of the mature forest tract target is low. The results also indicate that partial cuts are of very limited use to attenuate the impacts of mature forest tract targets on wood supplies in highly fragmented landscapes. Partial cuts are somewhat more useful in landscapes that are less fragmented, but they have to be well coordinated with clearcut schedules in order to contribute efficiently to conservation objectives. This modelling framework could easily be adapted and parameterized to test hypotheses or to optimize restoration schedules in landscapes where issues such as forest fragmentation and the abundance of mature or old-growth forests are a concern.

Description: Ecological Applications, Ahead of Print. Cellulose δ18O and δD can provide insights on climates and hydrological cycling in the distant past and how these factors differ spatially. However, most studies of plant cellulose have used only one isotope, most commonly δ18O, resulting in difficulties partitioning variation in δ18O of precipitation versus evaporative conditions that affect leaf water isotopic enrichment. Moreover, observations of pronounced diurnal differences from conventional steady-state model predictions of leaf water isotopic fractionation have cast some doubt on single isotope modeling approaches for separating precipitation and evaporation drivers of cellulose δ18O or δD. We explore a dual isotope approach akin to the concept of deuterium-excess (d), to establish deuterium deviations from the global meteoric water line in leaf water (Δdl) as driven by relative humidity (RH). To demonstrate this concept, we survey studies of leaf water δ18O and δD in hardwood versus conifer trees. We then apply the concept to cellulose δ18O and δD using a mechanistic model of cellulose δ18O and δD to reconstruct deuterium deviations from the global meteoric water line (Δdc) in Quercus macrocarpa, Q. robur and Pseudotsuga menziesii. For each species Δdc showed strong correlations with RH across sites. Δdc agreed well with steady state predictions for Q. macrocarpa while for Q. robur the relationship with RH was steeper than expected. The slope of Δdc versus RH of P. menziesii was also close to steady state predictions, but Δdc were more enriched than predicted. This is in agreement with our leaf water survey showing conifer Δdl was more enriched than predicted. Our data reveal that applications of this method should be appropriate for reconstructing RH from cellulose δ18O and δD after accounting for differences between hardwoods and conifers. Hence, Δdc should be useful for understanding variability in RH associated with past climatic cycles, across regional climates, or across complex terrain where climate modeling is challenging. Furthermore, Δdc and inferred RH values should help in constraining variation in source water δ18O.

Description: Ecological Applications, Ahead of Print. The size, shape, and connectivity of water bodies (lakes, ponds, and wetlands) can have important effects on ecological communities and ecosystem processes, but how these characteristics are influenced by land use and land cover change over broad spatial scales is not known. Intensive alteration of water bodies during urban development, including construction, burial, drainage, and reshaping, may select for certain morphometric characteristics and influence the types of water bodies present in cities. We used a database of over 1 million water bodies in 100 cities across the conterminous United States to compare the size distributions, connectivity (as intersection with surface flow lines), and shape (as measured by shoreline development factor) of water bodies in different land cover classes. Water bodies in all urban land covers were dominated by lakes and ponds, while reservoirs and wetlands comprised only a small fraction of the sample. In urban land covers, as compared to surrounding undeveloped land, water body size distributions converged on moderate sizes, shapes toward less tortuous shorelines, and the number and area of water bodies that intersected surface flow lines (i.e. streams and rivers). Potential mechanisms responsible for changing the characteristics of urban water bodies include: preferential removal, physical reshaping or addition of water bodies, and selection of locations for development. The relative contributions of each mechanism likely changes as cities grow. The larger size and reduced surface connectivity of urban water bodies may affect the role of internal dynamics and sensitivity to catchment processes. More broadly, these results illustrate the complex nature of urban watersheds and highlight the need to develop a conceptual framework for urban water bodies.

Description: Ecological Applications, Ahead of Print. In the context of the reduction of greenhouse gas emissions caused by deforestation and forest degradation (the REDD+ program), optical very high resolution (VHR) satellite images provide an opportunity to characterize forest canopy structure and to quantify aboveground biomass (AGB) at less expense than methods based on airborne remote sensing data. Among the methods for processing these VHR images, Fourier textural ordination (FOTO) presents a good potential to detect forest canopy structural heterogeneity and therefore to predict AGB variations. Notably, the method does not saturate at intermediate AGB values as do pixelwise processing of available space borne optical and radar signals. However, a regional scale application requires to overcome two difficulties: (i) instrumental effects due to variations in sun-scene-sensor geometry or sensor-specific responses that preclude the use of wide arrays of images acquired under heterogeneous conditions and (ii) forest structural diversity including monodominant or open canopy forests, which are of particular importance in Central Africa. In this study, we demonstrate the feasibility of a rigorous regional study of canopy texture by harmonizing FOTO indices of images acquired from two different sensors (Geoeye-1 and QuickBird-2) and different sun-scene-sensor geometries and by calibrating a piecewise biomass inversion model using 26 inventory plots (1 ha) sampled across very heterogeneous forest types. A good agreement was found between observed and predicted AGB (RSE=15%; R²=0.85; p-value

Description: Ecological Applications, Ahead of Print. Variable retention harvesting (VRH) is an approach for sustaining complex structure in managed forests. A criticism of VRH is that ecological benefits may come at a cost of reduced growth of regeneration, due to competition with residual trees. However, the spatial pattern of retention, i.e., dispersed or aggregated, in VRH systems can be manipulated to minimize suppression of regeneration, and resource limitation to regeneration might be mitigated by reduction of woody shrubs. Continued growth of the residual cohort will compensate for growth reduction of regeneration, although this may differ with retention pattern. We examined above-ground whole-stand biomass growth of trees in a VRH experiment in Pinus resinosa forest in Minnesota, USA. Treatments included dispersed retention, aggregated retention, and an uncut control, as well as a shrub treatment (reduced density or ambient). We addressed the following hypotheses: 1) biomass growth of a cohort of planted pine seedlings will be highest with aggregated rather than dispersed retention; 2) biomass growth of the planted seedlings will increase with shrub reduction; and 3) biomass growth of the residual overstory will be higher with dispersed rather than aggregated retention. Above-ground biomass growth of the planted pines ranged from 0.4 kg ha-1 yr-1 in the overstory control-ambient shrub treatment to 23 kg ha-1 yr-1 in the aggregated retention-shrub reduction treatment. The difference between the control and the retention treatments was significant (p 100% increase) with shrub reduction (p=0.001), supporting our second hypothesis. Biomass growth of residual trees ranged from 2404 kg ha-1 yr-1 in the uncut control-ambient shrub treatment to 1043 kg ha-1 yr-1 in the aggregated retention-shrub reduction treatment. Differences were significant between the control and retention treatments (p=0.003), and marginally higher with dispersed versus aggregated retention (p=0.09), lending support to our third hypothesis. Our results suggest that managers have flexibility in application of VRH and can expect similar stand-level biomass growth of planted regeneration regardless of retention pattern, but somewhat higher stand-level biomass growth of retained trees with dispersed retention.

Description: Ecological Applications, Ahead of Print. Biodiversity conservation in rangeland environments is often addressed by removing livestock, but inconsistent responses by biota mean that the efficacy of this form of management is hotly debated. Reasons for this inconsistency include the usually short duration and small spatial scale of manipulations compared to the area of grazing properties, as well as divergent responses amongst biota. In low-productivity arid environments, the pulse-reserve dynamic also complicates the outcome of manipulations. Here, we test and extend these ideas in a heterogeneous desert environment in central Australia that consists of small patches of open woodland (gidgee) in a grassland (spinifex) matrix. Taking advantage of a controlled property-scale removal of cattle, and a rain event that stimulated productivity, we firstly quantify differences in the vegetation and small vertebrates of these two habitats, and then track the diversity, composition and abundance of these biota for 6-19 months post-rain. We predicted that the two habitats would differ in the structure, composition and reproductive output of their constituent plant species. We predicted also that the effects of cattle removal would interact with these habitat differences, with the abundance, richness and diversity of small mammals and reptiles differing across habitats and grazing treatments. As anticipated, plant species composition in woodland was distinct from that in grassland and varied over time. The effects of cattle-removal were habitat-specific: plant composition responded to de-stocking in woodland but not in grassland; flowers were more abundant, and palatable plant cover also was greater following cessation of grazing pressure. The responses of small mammals but not reptiles showed some accord with our predictions, varying over time but inconsistently with treatment, and perhaps reflected high variability in capture success. We conclude that the timing and length of sampling are important when evaluating the responses of biota to livestock removal, as is the inclusion of all key habitats in the sampling regime.

Description: Ecological Applications, Ahead of Print. Over-harvest and landscape change are two of the greatest threats to marine ecosystems. Over-harvest may directly affect key population regulation mechanisms (e.g., density dependence), with the magnitude of the effects being further influenced by changes in landscape structure and associated resource availability. Because resource availability and conspecific density often co-vary within the natural landscape, manipulative experiments are needed to understand how changes in these two drivers may affect density dependence in wild populations. We used a common, shoaling, coral reef fish (white grunt, Haemulon plumierii) as our model species, and manipulated fish densities and landscape context of artificial reef habitats to assess the effects of each on fish condition. We found evidence of inverse density dependence, where individual condition was positively related to conspecific density; landscape context had little effect. Mean grunt condition on natural patch reefs was similar to that for our low grunt density treatment artificial reefs, possibly due to differences in fish densities or landscape context. These findings suggest that over-harvest may have detrimental effects on wild populations that extend beyond mere reductions in population size, especially for group-living species.

Description: Ecological Applications, Ahead of Print. Studies on the interactive responses to multiple simultaneously acting stressors have focused on individual or population-level responses in laboratory microcosms, while field-based studies on community-level responses are rare. We examined the influence of a natural (non-anthropogenic acidity) vs. human-induced stress (land drainage) and their interaction on species richness and spatial turnover (β-diversity) of stream diatom, bryophyte and benthic invertebrate communities. Our four stream categories were: circumneutral reference, circumneutral impacted, naturally acidic and naturally acidic impacted streams. We expected the most sensitive species to be only present in the circumneutral reference streams. Therefore, species richness should be highest in these streams and lowest in the naturally acidic streams additionally stressed by forest drainage. Alternatively, communities in acidic streams may consist of the most tolerant taxa that are unaffected by further stressors, species richness in these streams remaining unaffected by drainage. We also expected spatial turnover to be highest in the circumneutral near-pristine streams and lowest in the drainage-impacted acidic streams. In all three taxonomic groups, α-diversity was lower in the naturally acidic than circumneutral streams. The additional impact of the anthropogenic stress on species richness varied between groups, having no effect on diatoms, antagonistic effect on bryophytes, and additive effect on invertebrates. We also found differences in how each stressor modified β-diversity of each taxonomic group. For diatoms, β-diversity showed an overall tendency to decrease with increasing stress level while bryophyte β-diversity responded mainly to forest drainage. Benthic invertebrate β-diversity did not differ between treatments. Our results suggest that non-additive effects among stressors need special attention to improve the understanding and management of multifactor responses in streams. Our results also argue for the primacy of a multi-taxon approach to environmental impact detection, and for the inclusion of a wide array of ecological responses, particularly community turnover, in bioassessment programs to detect responses that may go unnoticed by conventional richness-based measures.

Description: Ecological Applications, Ahead of Print. The American pika (Ochotona princeps) has become a species of concern for its sensitivity to warm temperatures and potential vulnerability to global warming. We explored the value of radiocarbon dating of fecal pellets to address questions of population persistence and timing of site extirpation. Carbon was extracted from pellets collected at 43 locations in the western Great Basin, USA, including 3 known occupied sites and 40 sites of uncertain status at range margins or where previous studies indicated the species is vulnerable. We resolved calibrated dates with high precision (within several years), most of which fell in the period of the mid-late 20th century "bomb curve." The two-sided nature of the bomb curve renders "far-" and "near-side" dates of equal probability, which are separated by 1-4 decades. We document methods for narrowing resolution to one age range, including stratigraphic analysis of vegetation collected from pika haypiles. No evidence was found for biases in atmospheric 14C levels due to fossil-derived or industrial CO2 contamination. Radiocarbon dating indicated that pellets can persist for 〉59 years; known-occupied sites resolved contemporary dates. Using combined evidence from field observations and radiocarbon-dating, and the Bodie Mountains (Mtns) as an example, we propose a historical biogeographic scenario for pikas in minor Great Basin mountain ranges adjacent to major cordillera wherein historical climate variability led to cycles of extirpation and re-colonization during alternating cool and warm centuries. Using this model to inform future dynamics for small ranges in biogeographic settings similar to the Bodie Mtns, CA, extirpation of pikas appears highly likely under directional warming trends projected for the next century, even while populations in extensive cordillera (e.g., Sierra Nevada, Rocky Mtns, Cascade Range) are likely to remain viable due to extensive, diverse, habitat and high connectivity.

Description: Ecological Applications, Ahead of Print. Studies of predator-prey demographic responses and the physical drivers of such relationships are rare, yet essential for predicting future changes in the structure and dynamics of marine ecosystems. Here, we hypothesize that predator-prey relationships vary spatially in association with underlying physical ocean conditions, leading to observable changes in demographic rates, such as reproduction. To test this hypothesis, we quantified spatio-temporal variability in hydrographic conditions, krill, and forage fish to model predator (seabird) demographic responses over 18 years (1990-2007). We used principal component analysis and spatial correlation maps to assess coherence among ocean conditions, krill, and forage fish, and generalized additive models to quantify interannual variability in seabird breeding success relative to prey abundance. The first principal component of 4 hydrographic measurements yielded an index that partitioned "weak/warm upwelling" and "strong/cool upwelling" years. Partitioning of krill and forage fish time series among shelf and oceanic regions yielded spatially-explicit indicators of prey availability. Krill abundance within the oceanic region was remarkably consistent between years, whereas krill over the shelf showed marked interannual fluctuations in relation to ocean conditions. Anchovy abundance varied on the shelf, and was greater in years of strong stratification/weak upwelling and warmer temperatures. Spatio-temporal variability of juvenile forage fish covaried strongly with each other and with krill, but was weakly correlated with hydrographic conditions. Demographic responses between seabirds and prey availability revealed spatially-variable associations indicative of the dynamic nature of habitat-prey relationships. Quantification of spatially-explicit demographic responses, and their variability through time, demonstrates the possibility of delineating specific critical areas where the implementation of protective measures could maintain functions and productivity of central place foraging predators.

Description: Ecological Applications, Volume 24, Issue 3, Page 518-527, April 2014. Mangroves are recognized to possess a variety of ecosystem services including high rates of carbon sequestration and storage. Deforestation and conversion of these ecosystems continue to be high and have been predicted to result in significant carbon emissions to the atmosphere. Yet few studies have quantified the carbon stocks or losses associated with conversion of these ecosystems. In this study we quantified the ecosystem carbon stocks of three common mangrove types of the Caribbean as well as those of abandoned shrimp ponds in areas formerly occupied by mangrove—a common land-use conversion of mangroves throughout the world. In the mangroves of the Montecristi Province in Northwest Dominican Republic we found C stocks ranged from 706 to 1131 Mg/ha. The medium-statured mangroves (3–10 m in height) had the highest C stocks while the tall (〉10 m) mangroves had the lowest ecosystem carbon storage. Carbon stocks of the low mangrove (shrub) type (

Description: Ecological Applications, Volume 24, Issue 3, Page 539-547, April 2014. Diazotrophic cyanobacteria are capable of fixing atmospheric N2 to satisfy their physiological nitrogen requirements. This process can result in the transfer of substantial amounts of “new” diazotrophic nitrogen (ND) to aquatic ecosystems during blooms of these taxa. Using in situ measurements of plankton natural abundance stable isotope composition and a combination of underway and fixed site survey data, the total ND flux into the Gippsland Lakes estuary (Australia) was estimated during a summer bloom of the diazotrophic cyanobacterium Nodularia spumigena. Over the course of the bloom, ND increased in the upper water column of the estuary from 33% ± 17% (mean ± SD) to 73% ± 13% of the standing pool of total particulate N. A conservative estimate of total ND flux (146 Mg) equates to an estimated 177% of the summer total N load and 22% of the annual total N load to the estuary. Combining natural abundance stable isotope measurements with relatively simple fixed and underway survey designs can provide a cost-effective approach for monitoring the ND flux into estuary or lacustrine environments. This approach relies on an isotopic differential between the diazotrophic and the non-diazotrophic components of the plankton community; it may not be appropriate in ecosystems that experience low-level blooms or blooms of intermittent N-fixing cyanobacteria. Large-scale blooms of diazotrophic cyanobacteria are considered uncommon in estuaries, yet it is clear that these blooms can represent major sources of new N to estuarine ecosystems when and where they occur.

Description: Ecological Applications, Ahead of Print. Conservation practitioners, faced with managing multiple threats to biodiversity and limited funding, must prioritize investment in different management actions. From an economic perspective, it is routine practice to invest where the highest rate of return is expected. This return-on-investment (ROI) thinking can also benefit species conservation, and researchers are developing sophisticated approaches to support decision-making for cost-effective conservation. However, applied use of these approaches is limited. Managers may be wary of 'black-box' algorithms or complex methods that are difficult to explain to funding agencies. As an alternative, we demonstrate the use of a basic ROI analysis for determining where to invest in cost-effective management to address threats to species. This method can be applied using basic geographic information system and spread sheet calculations. We illustrate the approach in a management-action prioritization for a biodiverse region of eastern Australia. We use ROI to prioritize management actions for two threats to a suite of threatened species: habitat degradation by cattle grazing and predation by invasive red foxes (Vulpes vulpes). We show how decisions based on cost-effective threat management depend upon how expected benefits to species are defined and how benefits and costs co-vary. By considering a combination of species richness, restricted habitats, species vulnerability, and costs of management actions, small investments can result in greater expected benefit compared with management decisions that consider only species richness. Furthermore, a landscape management strategy that implements multiple actions is more efficient than managing only for one threat or more traditional approaches that don't consider ROI. Our approach provides transparent and logical decision-support for prioritizing different actions intended to abate threats associated with multiple species; it is of use when managers need a justifiable and repeatable approach to investment.

Description: Ecological Applications, Ahead of Print. Widespread fire suppression and thinning have altered the structure and composition of many western U.S. forests making them more susceptible to the synergy of large-scale drought and fire events. We examine how these changes affect carbon storage and stability compared to historic fire-adapted conditions. We modeled carbon dynamics under possible drought and fire conditions over a 300 year simulation period in two mixed-conifer conditions common in the western U.S.: 1) pine-dominated with an active fire regime and 2) fir-dominated, fire suppressed forests. Fir-dominated stands, with higher live and dead wood density, had much lower carbon stability as drought and fire frequency increased compared to pine-dominated forest. Carbon instability results from species (i.e., fir's greater susceptibility to drought and fire) and stand (i.e., high density of smaller trees) conditions that develop in the absence of active management. Our modeling suggests restoring historic species composition and active fire regimes can significantly increase carbon stability in fire-suppressed, mixed-conifer forests. Long-term management of forest carbon should consider the relative resilience of stand structure and composition to possible increases in disturbance frequency and intensity under changing climate.

Description: Ecological Applications, Ahead of Print. Protected areas are a cornerstone for biodiversity, but they also provide amenities that attract housing development on inholdings and adjacent private lands. We explored how this development affects biodiversity within and near protected areas among six ecological regions throughout the United States. We quantified the effect of housing density within, at the boundary, and outside protected areas, and natural land cover within protected areas, on the proportional abundance and proportional richness of three avian guilds within protected areas. We developed three guilds from the North American Breeding Bird Survey, which included Species of Greatest Conservation Need, land cover affiliates (e.g., forest breeders), and synanthropic species associated with urban environments. We gathered housing density data for the year 2000 from the U.S. Census Bureau, and centered the bird data on this year. We obtained land cover data from the 2001 National Land Cover Database, and we used single- and multiple-variable analyses to address our research question. In all regions, housing density within protected areas was positively associated with the proportional abundance or proportional richness of synanthropes, and negatively associated with the proportional abundance or proportional richness of Species of Greatest Conservation Need. These relationships were strongest in the eastern-forested regions and the central grasslands, where more than 70% and 45%, respectively, of the variation in the proportional abundance of synanthropes and Species of Greatest Conservation Need were explained by housing within protected areas. Furthermore, in most regions, housing density outside protected areas was positively associated with the proportional abundance or proportional richness of synanthropes and negatively associated with the proportional abundance of land cover affiliates and Species of Greatest Conservation Need within protected areas. However, these effects were weaker than housing within protected areas. Natural land cover was high with little variability within protected areas and consequently was less influential than housing density within or outside protected areas explaining the proportional abundance or proportional richness of the avian guilds. Our results indicate that housing development within, at the boundary, and outside protected areas impacts avian community structure within protected areas throughout the United States.

Description: Ecological Applications, Ahead of Print. Understanding space use of free-living endangered animals is key to inform management decisions for conservation planning. Like most scavengers, vultures have evolved under a context of unpredictability of food resources (i.e. exploiting scattered carcasses that are intermittently available). However, the role of predictable sources of food in shaping spatial ecology of vultures has seldom been studied in detail. Here, we quantify the home range of the Egyptian vulture (Neophron percnopterus), a long-lived raptor which has experienced severe population decline throughout its range and is qualified as endangered worldwide. To this end six adults were tracked by satellite telemetry in Spain during the breeding season, from 2007 to 2012, recording 10360 GPS locations. Using Resource Utilization Functions, we assessed the topology of the Utilization Distribution, a three-dimensional measure that shows the probability of finding an animal within the home range. Our results showed how food availability and principally, how food predictability, determines ranging behaviour of this species. Egyptian vultures showed consistent site fidelity across years, measured as the two and three-dimensional overlap in their home ranges. Space use varied considerably within the home range and remarkably, places located far from nesting sites were used more frequently than some areas located closer. Therefore, traditional conservation measures based on establishing restrictive rules within a fixed radius around nesting sites could be biologically meaningless if other areas within the home range are not protected too. Finally, our results emphasize the importance of anthropogenic predictable sources of food (mainly vulture restaurants) in shaping the space use of scavengers, which is in agreement with recent findings. Hence, measures aimed at ensuring food availability are essential to preserve this endangered vulture, especially in the present context of limiting carrion dumping in the field due to sanitary regulations according to European legislation.

Description: Ecological Applications, Ahead of Print. A better understanding of how individuals respond to variation in habitat quality while moving through heterogeneous habitats is needed to predict ecological phenomena at larger scales, such as local population and metapopulation dynamics. We sought to identify how fine-scale habitat quality affects the decisions of juvenile pond-breeding salamanders (Ambystoma maculatum and A. annulatum) to cease dispersive movements away from their natal pond, select a refuge, and settle. Because of the acute susceptibility of juvenile amphibians to evaporative water loss in terrestrial habitats we predicted that they possess mechanisms for adjusting their behavior in response to variations in fine-scale habitat quality. We used experimental field enclosures to isolate the effects of habitat quality on settling behavior and employed generalized linear mixed models to examine how manipulations in canopy cover (closed or open) and microhabitat (control, compacted soils, high coarse woody debris, high burrow density), along with environmental variables (rainfall and air temperature) affect the individual's probability of settling. Our results indicated that A. maculatum and A. annulatum had a 10% and 30% decreased probability of settling in open-canopy clearcut habitat, respectively, compared to closed-canopy forest habitat. In addition, A. annulatum were 24% less likely to settle in compacted soil treatments. Although the settlement probability of A. annulatum did not depend on refuge availability, A. maculatum were 18% and 25% more likely to settle under conditions of high burrow density and high coarse woody debris, respectively. These findings make a unique contribution to our understanding of amphibian movement ecology by demonstrating how the interplay of external factors and individual behavior produce observed patterns of movement and habitat selection.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Variable retention harvesting (VRH) is an approach for sustaining complex structure in managed forests. A criticism of VRH is that ecological benefits may come at a cost of reduced growth of regeneration, due to competition with residual trees. However, the spatial pattern of retention, i.e., dispersed or aggregated, in VRH systems can be manipulated to minimize suppression of regeneration, and resource limitation to regeneration might be mitigated by reduction of woody shrubs. Continued growth of the residual cohort will compensate for growth reduction of regeneration, although this may differ with retention pattern. We examined above-ground whole-stand biomass growth of trees in a VRH experiment in Pinus resinosa forest in Minnesota, USA. Treatments included dispersed retention, aggregated retention, and an uncut control, as well as a shrub treatment (reduced density or ambient). We addressed the following hypotheses: 1) biomass growth of a cohort of planted pine seedlings will be highest with aggregated rather than dispersed retention; 2) biomass growth of the planted seedlings will increase with shrub reduction; and 3) biomass growth of the residual overstory will be higher with dispersed rather than aggregated retention. Above-ground biomass growth of the planted pines ranged from 0.4 kg ha-1 yr-1 in the overstory control-ambient shrub treatment to 23 kg ha-1 yr-1 in the aggregated retention-shrub reduction treatment. The difference between the control and the retention treatments was significant (p 100% increase) with shrub reduction (p=0.001), supporting our second hypothesis. Biomass growth of residual trees ranged from 2404 kg ha-1 yr-1 in the uncut control-ambient shrub treatment to 1043 kg ha-1 yr-1 in the aggregated retention-shrub reduction treatment. Differences were significant between the control and retention treatments (p=0.003), and marginally higher with dispersed versus aggregated retention (p=0.09), lending support to our third hypothesis. Our results suggest that managers have flexibility in application of VRH and can expect similar stand-level biomass growth of planted regeneration regardless of retention pattern, but somewhat higher stand-level biomass growth of retained trees with dispersed retention.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. In the context of the reduction of greenhouse gas emissions caused by deforestation and forest degradation (the REDD+ program), optical very high resolution (VHR) satellite images provide an opportunity to characterize forest canopy structure and to quantify aboveground biomass (AGB) at less expense than methods based on airborne remote sensing data. Among the methods for processing these VHR images, Fourier textural ordination (FOTO) presents a good potential to detect forest canopy structural heterogeneity and therefore to predict AGB variations. Notably, the method does not saturate at intermediate AGB values as do pixelwise processing of available space borne optical and radar signals. However, a regional scale application requires to overcome two difficulties: (i) instrumental effects due to variations in sun-scene-sensor geometry or sensor-specific responses that preclude the use of wide arrays of images acquired under heterogeneous conditions and (ii) forest structural diversity including monodominant or open canopy forests, which are of particular importance in Central Africa. In this study, we demonstrate the feasibility of a rigorous regional study of canopy texture by harmonizing FOTO indices of images acquired from two different sensors (Geoeye-1 and QuickBird-2) and different sun-scene-sensor geometries and by calibrating a piecewise biomass inversion model using 26 inventory plots (1 ha) sampled across very heterogeneous forest types. A good agreement was found between observed and predicted AGB (RSE=15%; R²=0.85; p-value

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Wood borers and bark beetles are among the most serious forest pests worldwide. Many such species have become successful invaders, often causing substantial, costly damages to forests. Here we design and evaluate the cost-efficiency of a trap-based surveillance program for early detection of wood borers and bark beetles at risk of establishing in New Zealand. Though costly, a surveillance program could lead to earlier detection of newly established forest pests, thereby increasing the likelihood of successful eradication and reducing control costs and damages from future invasions. We develop a mechanistic bioeconomic model that relates surveillance intensity (i.e., trap density) and invasion size to probabilities of detection and control; it captures the dynamics of invasive species establishment, spread, and damages to urban and plantation forests. We employ the model to design surveillance programs that provide the greatest net present benefits. Our findings suggest that implementing a surveillance trapping program for invasive wood borers and bark beetles would provide positive net benefits under all scenarios considered. The economically optimal trapping strategy calls for a very high investment in surveillance: about 10,000 traps in each year of the 30-year surveillance program, at a present value cost of US$54 million. This strategy provides a 39% reduction in costs compared with no surveillance, corresponding to an expected net present benefit of approximately US$300 million. Although surveillance may provide the greatest net benefits when implemented at relatively high levels, our findings also show that even low levels of surveillance are worthwhile: the economic benefits from surveillance more than offset the rising costs associated with increasing trapping density. Our results also show that the cost-efficiency of surveillance varies across target regions because of differences in pest introduction and damage accumulation rates across locales, with greater surveillance warranted in areas closer to at-risk high-value resources and in areas that receive more imported goods that serve as an invasion pathway.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. To ensure viable species populations in fragmented landscapes, individuals must be able to move between suitable habitat patches. Despite the increased interest in biodiversity assessment in urban environments the ecological relevance of habitat connectivity in highly fragmented landscapes remains largely unknown. The first step to understanding the role of habitat connectivity in urban ecology is the challenging task of assessing connectivity in the complex patchwork of contrasting habitats, which is found in cities. We developed a data-based framework, minimizing the use of subjective assumptions, to assess habitat connectivity, which consists of the following sequential steps: 1) identification of habitat preference based on empirical habitat-use data, 2) derivation of habitat resistance surfaces evaluating various transformation functions, 3) modeling of different connectivity maps with electrical circuit theory (Circuitscape), a method considering all possible pathways across the landscape simultaneously, 4) identification of the best connectivity map with information-theoretic model selection. We applied this analytical framework to assess habitat connectivity of the European hedgehog Erinaceus europaeus, a model species for ground-dwelling animals, in the city of Zurich, Switzerland, using GPS track points from 40 individuals. The best model revealed spatially explicit connectivity 'pinch points', as well as multiple habitat connections. Cross validation indicated the general validity of the selected connectivity model. The results show that both habitat connectivity and habitat quality affect the movement of urban hedgehogs (relative importance of the two variables 19.2% and 80.8%, respectively), and are thus both relevant for predicting urban animal movements. Our study demonstrates that even in the complex habitat patchwork of cities habitat connectivity plays a major role for ground-dwelling animal movement. Data-based habitat connectivity maps can thus serve as an important tool for city planners to identify habitat corridors and plan appropriate management and conservation measures for urban animals. The analytical framework we describe to model such connectivity maps is generally applicable to different types of habitat-use data and can be adapted to the movement scale of the focal species. It also allows evaluation of the impact of future landscape changes or management scenarios on habitat connectivity in urban landscapes.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Deploying well-adapted and ecologically appropriate plant materials is a core component of successful restoration projects. We have developed generalized provisional seed zones that can be applied to any plant species in the United States to help guide seed movement. These seed zones are based on the intersection of high resolution climatic data for winter minimum temperature and aridity (as measured by annual heat:moisture index), each classified into discrete bands. This results in the delineation of 64 provisional seed zones for the continental United States. These zones represent areas of relative climatic similarity, and movement of seed within these zones should help to minimize maladaptation. Superimposing Omernik's level III ecoregions over these seed zones distinguishes areas that are similar climatically yet different ecologically. A quantitative comparison of provisional seed zones with level III ecoregions and provisional seed zones within ecoregions for three species showed that provisional seed zone within ecoregion often explained the greatest proportion of variation in a suite of traits potentially related to plant fitness. These provisional seed zones can be considered a starting point for guidelines for seed transfer, and should be utilized in conjunction with appropriate species-specific information as well as local knowledge of microsite differences.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Ecosystem-based management of natural resources involves an explicit consideration of trade-offs among ecosystem services. In marine fisheries, there is the potential for a trade-off between the supporting role of small pelagic fish and cephalopods in food webs, and the provisioning service they play as a major target of fisheries. Because these species play central roles in food webs by providing a conduit of energy from small prey to upper trophic level predators, we hypothesized that trade-offs between these two ecosystem services could be predicted based on energetic properties of predator-prey linkages and food web structure. We compiled information from 27 marine food web models (Ecopath) that included either small pelagic fish or cephalopods, described predator-prey linkages involving these species, and developed a novel analytical framework to estimate how changes in yields of forage species would propagate through food webs and other fisheries. Consistent with expectations, diet overlap between predators and prey was generally low, and predator prey linkages tended to be asymmetric; contribution of these species to predator diets was, on average, larger than the contribution of individual predator stocks to prey mortality. The estimated trade-offs between yields of forage fish and predator species were highly variable when we assumed joint bottom-up and top-down control on predation. Roughly one-third of this variance was related to an interactive effect of fishing and predation intensity; strong trade-offs were predicted when fishing intensity on forage species is high and when predators account for a high proportion of total forage mortality. When trophic connections were presumed to be driven by bottom-up processes, trade-offs were more predictable but generally very small. Contrary to our expectations, trade-offs were not easily predicted from energetic properties, largely because predators of forage species exhibited a high degree of intra-guild predation and also consumed many of the same prey as forage species. Given the limited ability to a priori predict the food web implications of forage fisheries, we suggest that a precautionary risk-based approach be applied to decisions about acceptable biological removals of forage fish and biological targets used for their management.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Twentieth century land management has altered the structure and composition of mixed-conifer forests and decreased their resilience to fire, drought, and insects in many parts of the Interior West. These forests occur across a wide range of environmental settings and historical disturbance regimes so their response to land management is likely to vary across landscapes and among ecoregions. However, this variation has not been well characterized and hampers the development of appropriate management and restoration plans. We identified mixed-conifer types in central Oregon based on historical structure and composition and successional trajectories following recent changes in lands use, and evaluated how they types were distributed across environmental gradients. We used field data from 171 sites sampled across a range of environmental settings in two subregions: the eastern Cascades and Ochoco Mountains. We identified four forest types in the eastern Cascades and four analogous types with lower densities in the Ochoco Mountains. All types historically contained ponderosa pine, but differ in the historical and modern proportions of shade-tolerant versus intolerant tree species. The Persistent Ponderosa Pine and Recent Douglas-fir types occupied relatively hot-dry environments compared to Recent Grand Fir and Persistent Shade Tolerant sites, which occupied warm-moist and cold-wet environments, respectively. Twentieth-century selective harvesting halved the density of large trees, with some variation among forest types. In contrast, the density of small trees doubled or tripled early in the 20th century, likely due to land-use change and a relatively cool-wet climate. Contrary to the common perception that dry ponderosa pine forests are the most highly departed from historical conditions, we found a greater departure in the modern composition of small trees in warm-moist environments than in either hot-dry or cold-wet environments. Furthermore, shade tolerants began infilling earlier in cold-wet than in hot-dry environments and also in topographically shaded sites in the Ochoco Mountains. Our new classification could be used to prioritize management that seeks to restore structure and composition or create resilience in mixed-conifer forests of the region.

Description: Ecological Applications, Volume 24, Issue 3, Page 457-466, April 2014. Coastal ecologists and managers have frequently used nitrogen stable isotopes (δ15N) to trace and monitor sources of anthropogenic nitrogen (N) in coastal ecosystems. However, the interpretation of δ15N data can often be challenging, as the isotope values fractionate substantially due to preferential retention and uptake by biota. There is a growing body of evidence that carbon isotopes may be a useful alternative indicator for eutrophication, as they may be sensitive to changes in primary production that result from anthropogenic nutrient inputs. We provide three examples of systems where δ13C values sensitively track phytoplankton production. First, earlier (1980s) mesocosm work established positive relationships between δ13C and dissolved inorganic nitrogen and dissolved silica concentrations. Consistent with these findings, a contemporary mesocosm experiment designed to replicate a temperate intertidal salt marsh environment also demonstrated that the system receiving supplementary nutrient additions had higher nutrient concentrations, higher chlorophyll concentrations, and higher δ13C values. This trend was particularly pronounced during the growing season, with differences less evident during senescence. And finally, these results were replicated in the open waters of Narragansett Bay, Rhode Island, USA, during a spring phytoplankton bloom. These three examples, taken together with the pre-existing body of literature, suggest that, at least in autotrophic, phytoplankton-dominated systems, δ13C values can be a useful and sensitive indicator of eutrophication.

Description: Ecological Applications, Volume 24, Issue 3, Page 503-517, April 2014. Even when no baseline data are available, the impacts of 150 years of livestock grazing on natural grasslands can be assessed using a combined approach of grazing manipulation and regional-scale assessment of the flora. Here, we demonstrate the efficacy of this method across 18 sites in the semidesert Mitchell grasslands of northeastern Australia. Fifteen-year-old exclosures (ungrazed and macropod grazed) revealed that the dominant perennial grasses in the genus Astrebla do not respond negatively to grazing disturbance typical of commercial pastoralism. Neutral, positive, intermediate, and negative responses to grazing disturbance were recorded amongst plant species with no single life-form group associated with any response type. Only one exotic species, Cenchrus ciliaris, was recorded at low frequency. The strongest negative response was from a native annual grass, Chionachne hubbardiana, an example of a species that is highly sensitive to grazing disturbance. Herbarium records revealed only scant evidence that species with a negative response to grazing have declined through the period of commercial pastoralism. A regional analysis identified 14 from a total of 433 plant species in the regional flora that may be rare and potentially threatened by grazing disturbance. However, a targeted survey precluded grazing as a cause of decline for seven of these based on low palatability and positive responses to grazing and other disturbance. Our findings suggest that livestock grazing of semidesert grasslands with a short evolutionary history of ungulate grazing has altered plant composition, but has not caused declines in the dominant perennial grasses or in species richness as predicted by the preceding literature. The biggest impact of commercial pastoralism is the spread of woody leguminous trees that can transform grassland to thorny shrubland. The conservation of plant biodiversity is largely compatible with commercial pastoralism provided these woody weeds are controlled, but reserves strategically positioned within water remote areas are necessary to protect grazing-sensitive species. This study demonstrates that a combination of experimental studies and regional surveys can be used to understand anthropogenic impacts on natural ecosystems where reference habitat is not available.

Description: Ecological Applications, Volume 24, Issue 3, Page 548-559, April 2014. Recent research indicates increasing openness among conservation experts toward a set of previously controversial proposals for biodiversity protection. These include actions such as assisted migration, and the application of climate-change-informed triage principles for decision-making (e.g., forgoing attention to target species deemed no longer viable). Little is known however, about the levels of expert agreement across different conservation adaptation actions, or the preferences that may come to shape policy recommendations. In this paper, we report findings from a web-based survey of biodiversity experts that assessed: (1) perceived risks of climate change (and other drivers) to biodiversity, (2) relative importance of different conservation goals, (3) levels of agreement/disagreement with the potential necessity of unconventional-taboo actions and approaches including affective evaluations of these, (4) preferences regarding the most important adaptation action for biodiversity, and (5) perceived barriers and strategic considerations regarding implementing adaptation initiatives. We found widespread agreement with a set of previously contentious approaches and actions, including the need for frameworks for prioritization and decision-making that take expected losses and emerging novel ecosystems into consideration. Simultaneously, this survey found enduring preferences for conventional actions (such as protected areas) as the most important policy action, and negative affective responses toward more interventionist proposals. We argue that expert views are converging on agreement across a set of taboo components in ways that differ from earlier published positions, and that these views are tempered by preferences for existing conventional actions and discomfort toward interventionist options. We discuss these findings in the context of anticipating some of the likely contours of future conservation debates. Lastly, we underscore the critical need for interdisciplinary, comparative, place-based adaptation research.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. Over-harvest and landscape change are two of the greatest threats to marine ecosystems. Over-harvest may directly affect key population regulation mechanisms (e.g., density dependence), with the magnitude of the effects being further influenced by changes in landscape structure and associated resource availability. Because resource availability and conspecific density often co-vary within the natural landscape, manipulative experiments are needed to understand how changes in these two drivers may affect density dependence in wild populations. We used a common, shoaling, coral reef fish (white grunt, Haemulon plumierii) as our model species, and manipulated fish densities and landscape context of artificial reef habitats to assess the effects of each on fish condition. We found evidence of inverse density dependence, where individual condition was positively related to conspecific density; landscape context had little effect. Mean grunt condition on natural patch reefs was similar to that for our low grunt density treatment artificial reefs, possibly due to differences in fish densities or landscape context. These findings suggest that over-harvest may have detrimental effects on wild populations that extend beyond mere reductions in population size, especially for group-living species.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print. The morphological and biochemical properties of plant canopies are strong predictors of photosynthetic capacity and nutrient cycling. Remote sensing research at the leaf and canopy scales has demonstrated the ability to characterize the biochemical status of vegetation canopies using reflectance spectroscopy, including at the leaf level and canopy level from air- and space-borne imaging spectrometers. We developed a set of accurate and precise spectroscopic calibrations for the determination of leaf chemistry (contents of nitrogen, carbon, and fiber constituents), morphology (leaf mass per area, Marea), and isotopic composition (δ15N) of temperate and boreal tree species using spectra of dried and ground leaf material. The dataset consisted of leaves from both broadleaf and conifer species and displayed a wide range in values, determined with standard analytical approaches: 0.7 - 4.4% for nitrogen (Nmass), 42 - 54% for carbon (Cmass), 17 - 58% for fiber (ADF), 7 - 44% for lignin (ADL), 3 - 31 for cellulose, 17 - 265 g m-2 for Marea, and -9.4 to 0.8‰ for δ15N. The calibrations were developed using a partial least-squares regression (PLSR) modeling approach combined with a novel uncertainty analysis. Our PLSR models yielded model calibration (independent validation) R2 and RMSE values, respectively, of 0.98 (0.97) and 0.10% (0.13%) for Nmass, R2= 0.77 (0.73%) and RMSE= 0.88% (0.95%) for Cmass, R2= 0.89 (0.84) and RMSE= 2.8% (3.4%) for ADF, R2= 0.77 (0.69) and RMSE= 2.4% (3.9%) for ADL, R2= 0.77 (0.72) and RMSE= 1.4% (1.9%) for leaf cellulose, R2= 0.62 (0.60) and RMSE= 0.91‰ (1.5‰) for δ15N, and R2= 0.88 (0.87) with RMSE= 17.2 g m-2 (22.8 g m-2) for Marea. This study demonstrates the potential for rapid, and accurate estimation of key foliar traits of forest canopies that are important for ecological research and modeling activities, with a single calibration equation valid over a wide range of northern temperate and boreal species and leaf physiognomies. The results provide the basis to characterize important variability between and within species, and across ecological gradients using a rapid, cost-effective, easily replicated method.

Description: Ecological Applications, Ahead of Print. There are several remote-sensing tools readily available for the study of nocturnally flying animals (e.g., migrating birds); each possessing unique measurement biases. We used three tools, 1) weather surveillance radar, 2) thermal-infrared camera, and 3) acoustic recorder to measure temporal and spatial patterns of nocturnal traffic estimates of flying animals during the spring and fall of 2011 and 2012 in Lewes, DE. Our objective was to compare measures among different technologies to better understand their animal detection biases. For radar and thermal imaging, the greatest observed traffic rate tended to occur at or shortly after evening twilight, while for the acoustic recorder peak bird flight-calling activity was observed just prior to morning twilight. Comparing traffic rates during the night for all seasons, we found that mean nightly correlations between acoustics and the other two tools were weakly correlated (thermal-infrared camera-acoustics, r= 0.004 ± 0.04 SE, n= 100 nights; radar-acoustics, r= 0.14 ± 0.04 SE, n= 101 nights), but highly variable on an individual nightly basis (range= -0.84 to 0.92, range= -0.73 to 0.94). The mean nightly correlations between radar and thermal-infrared camera traffic rates during the night were more strongly positively correlated (r= 0.39 ± 0.04 SE, n= 125 nights), but also highly variable for individual nights (range = -0.76 to 0.98). Through comparison with radar data among numerous height intervals, we determined that flying animal height above the ground influenced thermal imaging positively and flight call detections negatively. Moreover, thermal imaging detections decreased with the presence of cloud cover and increased with mean ground flight speed of animals while acoustic detections showed no relationship with cloud cover presence but did decrease with increased flight speed. We found sampling methods to be positively correlated when comparing mean nightly traffic rates across nights. The strength of these correlations generally increased throughout the night, peaking 2-3 hours before morning twilight. Given the convergence of measures by different tools at this time, we suggest researchers consider sampling flight activity in the hours before morning twilight when differences due to detection biases among sampling tools appear to be minimized.

Description: Many wind-power facilities in the United States have established effective monitoring programs to determine turbine-caused fatality rates of birds and bats. But estimating the number of fatalities of rare species poses special difficulties. The loss of even small numbers of individuals may adversely affect fragile populations, but typically, few (if any) carcasses are observed during monitoring. If monitoring design results in only a small proportion of carcasses detected, then finding zero carcasses may give little assurance that the number of actual fatalities was small. Fatality monitoring at wind-power facilities commonly involves conducting experiments to estimate the probability (g) an individual will be observed, accounting for the possibilities that it falls in an unsearched area, is scavenged prior to detection, or remains undetected even when present. When g

Description: The strength and prevalence of trophic cascades, defined as positive, indirect effects of natural enemies (predatory and parasitic arthropods) on plants, is highly variable in agroecosystems. This variation may in part be due to the spatial or landscape context in which these trophic cascades occur. In 2011 and 2012, we conducted a natural-enemy exclusion experiment in soybean fields along a gradient of landscape composition across southern Wisconsin and Michigan. We used structural equation modeling to ask (1) whether natural enemies influence biocontrol of soybean aphids (SBA) and soybean yield and (2) whether landscape effects on natural enemies influence the strength of the trophic cascades. We found that natural enemies (NE) suppressed aphid populations in both years of our study and, in 2011, the yield of soybean plants exposed to natural enemies was 37% higher than the yield of plants with aphid populations protected from natural enemies. The strength of the trophic cascade was also influenced by landscape context. We found that landscapes with a higher proportion of soybean and higher diversity habitats resulted in more NE, fewer aphids, and in some cases a trend toward greater soybean yield. These results indicate that landscape context is important for understanding spatial variability in biocontrol and yield, but other factors, such as environmental variability and compensatory growth, might overwhelm the beneficial effects of biocontrol on crop yield. # doi:10.1890/14-0570.1

Description: Woodpeckers and other primary cavity excavators (PCEs) are important worldwide for excavating cavities in trees, and a large number of studies have examined their nesting preferences. However, quantitative measures of wood hardness have been omitted from most studies, and ecologists have focused on the effects of external tree- and habitat-level features on nesting. Moreover, information is lacking on the role of wood hardness in limiting nesting opportunities for this important guild. Here, we used an information theoretic approach to examine the role of wood hardness in multi-scale nest-site selection, and in limiting nesting opportunities for six species of North American PCEs. We found that interior wood hardness at nests (n = 259) differed from that at random sites, and all six species of PCE had nests with significantly softer interior wood than random trees (F(1,517) = 106.15, P 〈 0.0001). Accordingly, interior wood hardness was the most influential factor in our models of nest-site selection at both spatial scales that we examined - in the selection of trees within territories and in the selection of nest locations on trees. Moreover, regardless of hypothesized excavation abilities, all the species in our study appeared constrained by interior wood hardness, and only 4-14% of random sites were actually suitable for nesting. Our findings suggest that past studies that did not measure wood hardness counted many sites as available to PCEs when they were actually unsuitable, potentially biasing results. Moreover, by not accounting for nest-site limitations in PCEs, managers may overestimate the amount of suitable habitat. We therefore urge ecologists to incorporate quantitative measures of wood hardness into PCE nest-site selection studies, and to consider the limitations faced by avian cavity excavators in forest management decisions. # doi:10.1890/14-1042.1

Description: Grasslands are inherently dynamic in space and time evolving with frequent disturbance from fire and herbivores. As a consequence of human actions, many remaining grasslands have become homogenous which has led to reduced ecosystem function, biodiversity loss, and decreased ecological services. Previous research has shown that restoring inherent heterogeneity to grasslands can increase avian diversity, but the amount of heterogeneity (i.e., number of patches or fire return interval) and the impact on avian community stability have yet to be investigated. We used a unique landscape level design to examine avian response to interacting fire and grazing across multiple experimental landscapes that represented a gradient of fire and grazing dependent heterogeneity. We used seven landscapes (430-980 ha; x ? = 627) with varying levels of patchiness ranging from annually burned (one single patch) with spring only fires to a four year fire-return-interval with spring and summer fires (eight patches). This design created a range of heterogeneity as a result of pyric herbivory, an ecological process in which fire and grazing are allowed to interact in space and time. We found that greater heterogeneity across experimental landscapes resulted in increased avian diversity and stability over time. An index of bird community change, quantified as the sum of the range of detrended correspondence analysis axis site scores, was nearly four times greater in the most homogenous experimental landscape when compared to the most heterogeneous experimental landscape. Species responses were consistently positively associated with increased heterogeneity at the landscape scale and within experimental landscape responses were most often related to litter cover, litter accumulation, and vegetation height. We conclude that increased fire and grazing dependent heterogeneity can result in high variability in the bird community at finer, transect scales but increased diversity and stability at broad landscape scales. We recommend future management efforts in rangelands focus on restored disturbance processes to increase heterogeneity and improve grassland bird conservation. # doi:10.1890/14-1067.1

Description: Understanding the relative effects of climate, harvest, and density dependence on population dynamics is critical for guiding sound population management, especially for ungulates in arid and semi-arid environments experiencing climate change. To address these issues for bison in southern Utah, we applied a Bayesian state-space model to a 72-year time series of abundance counts. While accounting for known harvest (as well as live removal) from the population, we found that the bison population in southern Utah exhibited strong potential to grow from low density (?0 = 0.26; Bayesian credible interval based on 95% of the highest posterior density: BCI = 0.19 to 0.33), and weak but statistically significant density dependence (?1 = -0.02, BCI = -0.04 to -0.004). Early spring temperatures also had strong positive effects on population growth (?febaprtemp1 = 0.09, BCI = 0.04 to 0.14), much more so than precipitation and other temperature-related variables (model weight 〉 3 times more than that for other climate variables). Although we hypothesized that harvest is the primary driving force of bison population dynamics in southern Utah, our elasticity analysis indicated that changes in early spring temperature could have a greater 'relative effect' on equilibrium abundance than either harvest or the strength of density dependence. Our findings highlight the utility of incorporating elasticity analyses into state-space population models, and the need to include climatic processes in wildlife management policies and planning. # doi:10.1890/14-0932.1

Description: Agricultural expansion continues to drive forest loss in species-rich tropical systems and often disrupts movement and distributions of organisms. The ability of species to occupy and move through altered habitats likely depends on the level of contrast between natural forest and surrounding land uses. Connectivity models, such as circuit theory models, are widely used in conservation biology, and their primary input consists of resistance surfaces representing movement costs associated with landscape features. Cost values are most frequently determined by 'expert opinion' which may not capture relevant levels of contrast among features. Here, we developed resistance surfaces using experiments that represent different local mechanisms hypothesized to affect connectivity for two neotropical amphibian species. Response ratios were calculated to translate experimental results to cost values used in connectivity modeling. We used relative abundance data in three land-cover types to generate resistance surfaces for evaluating independent support of models derived from experiments. Finally, we analyzed agreement among movement pathways predicted for each species and among three commonly-used connectivity measures, Euclidean, least cost, and resistance distances. Experiments showed that extreme microclimates associated with altered habitats significantly increased desiccation and mortality risk for both species. Resistances estimated from microclimate experiments were concordant with those from survey data for both species. For one focal species, resistance estimates derived from predator encounter rates were also highly correlated with abundance-derived resistances. There was generally low agreement among the three alternative distance measures, which underscores the importance of choosing connectivity models that are most appropriate for the study objectives. Overall, similarity among linkages modeled for each species was high, but decreased with declining forest cover. Our results highlight the value of experiments for drawing inferences about processes in resistance modeling as well as the need to consider model differences and species-specific responses when developing strategies to maintain connectivity. # doi:10.1890/14-0833.1

Description: A mechanistic model is developed to predict mid-summer bottom water dissolved oxygen (BWDO) concentration and hypoxic area on the Louisiana shelf of the northern Gulf of Mexico (1985-2011). Because of its parsimonious formulation, the model possesses many of the benefits of simpler, more empirical models, in that it is computationally efficient and can rigorously account for uncertainty through Bayesian inference. At the same time, the model incorporates important biophysical processes such that its parameterization can be informed by field-measured biological and physical rates. The model is used to explore how freshwater flow, nutrient load, benthic oxygen demand, and wind velocity affect hypoxia on western and eastern sections of the shelf, delineated by the Atchafalaya River outfall. The model explains over 70% of the variability in BWDO on both shelf sections, and outperforms linear regression models developed from the same input variables. Model results suggest that physical factors (i.e., wind and flow) control a larger portion of the year-to-year variability in hypoxia than previously thought, especially on the western shelf; though seasonal nutrient loads remain an important driver of hypoxia, as well. Unlike several previous Gulf hypoxia modeling studies, results do not indicate a temporal shift in the system's propensity for hypoxia formation (i.e., no regime change). Results do indicate that benthic oxygen demand is a substantial BWDO sink, and a better understanding of the long-term dynamics of this sink is required to better predict how the size of the hypoxic zone will respond to proposed reductions in nutrient loading. # doi:10.1890/13-2257.1

Description: Stable isotopes are valuable tools for partitioning the components contributing to ecological processes of interest, such as animal diets and trophic interactions, plant resource use, ecosystem gas fluxes, streamflow, and many more. Stable isotope data are often analyzed with simple linear mixing (SLM) models to partition the contributions of different sources, but SLM models cannot incorporate a mechanistic understanding of the underlying processes and do not accommodate additional data associated with these processes (e.g., environmental covariates, flux data, gut contents). Thus, SLM models lack predictive ability. We describe a process-based mixing (PBM) model approach for integrating stable isotopes, other data sources, and process models to partition different sources or process components. This is accomplished via a hierarchical Bayesian framework that quantifies multiple sources of uncertainty and enables the incorporation of process models and prior information to help constrain the source-specific proportional contributions, thereby potentially avoiding identifiability issues that plague SLM models applied to "too many" sources. We discuss the application of the PBM model framework to three diverse examples: temporal and spatial partitioning of streamflow, estimation of plant rooting profiles and water uptake profiles (or water sources) with extension to partitioning soil and ecosystem CO2 fluxes, and reconstructing animal diets. These examples illustrate the advantages of the PBM modeling approach, which facilitates incorporation of ecological theory and diverse sources of information into the mixing model framework, thus enabling one to partitioning key processes components across time and space. # doi:10.1890/12-1970.1

Description: White-nose Syndrome (WNS) is an emerging infectious disease that has resulted in severe declines of its hibernating bat hosts in North America. The ongoing epidemic of White-nose Syndrome is a multi-scale phenomenon because it causes hibernaculum-level extirpations, while simultaneously spreading over larger spatial scales. Here, we investigate a neglected topic in ecological epidemiology- how local pathogen-driven extirpations impact large-scale pathogen spread. Previous studies have identified risk factors for propagation of WNS over hibernaculum and landscape scales but none of these have tested the hypothesis that separation of spatial scales and disease-induced mortality at the hibernaculum level might slow or halt its spread. To test this hypothesis, we developed a mechanistic multi-scale model parameterized using White-nose Syndrome county and site incidence data that connects hibernaculum-level Susceptible-Infectious-Removed (SIR) epidemiology to the county-scale contagion process. Our key result is that hibernaculum-level extirpations will not inhibit county-scale spread of WNS. We show that over 80% of counties of the contiguous USA are likely to become infected before the current epidemic is over and that geometry of habitat connectivity is such that host refuges are exceedingly rare. The macro-scale spatiotemporal infection pattern that emerges from local SIR epidemiological processes falls within a narrow spectrum of possible outcomes, suggesting that recolonization, rescue effects and multi-host complexities at local scales are not important to forward propagation of WNS at large spatial scales. If effective control measures are not implemented, precipitous declines in bat populations are likely, particularly in cave-dense regions that constitute the main geographic corridors of the USA -a serious concern for bat conservation. # doi:10.1890/14-0417.1

Description: Conserving a declining species that is facing many threats including overlap of its habitats with energy extraction activities depends upon identifying and prioritizing the value of the habitats that remain. In addition, habitat quality is often compromised when source habitats are lost or fragmented due to anthropogenic development. Our objective was to build an ecological model to classify and map habitat quality in terms of source or sink dynamics for greater sage-grouse (Centrocercus urophasianus) in the Atlantic Rim Project Area (ARPA), a developing coalbed natural gas field in south-central Wyoming. We used occurrence and survival modeling to evaluate relationships between environmental and anthropogenic variables at multiple spatial scales and for all female summer life-stages including nesting, brood-rearing, and non-brooding females. For each life-stage we created resource selection functions (RSFs). We weighted the RSFs and combined them to form a female summer occurrence map. We modeled survival also as a function of spatial variables for nest, brood, and adult female summer survival. Our survival models were mapped as survival probability functions individually and then combined with fixed vital rates in a fitness metric model that when mapped predicted habitat productivity (productivity map). Our results demonstrate a suite of environmental and anthropogenic variables at multiple scales that were predictive of occurrence and survival. We created a source-sink map by overlaying our female summer occurrence map and productivity map to predict habitats contributing to population surpluses (source habitats) or deficits (sink habitat) and low-occurrence habitats on the landscape. The source-sink map predicted that of the sage-grouse habitat within the ARPA, 30% was primary source, 29% was secondary source, 4% was primary sink, 6% was secondary sink, and 31% was low-occurrence. Our results provide evidence that energy development and avoidance of energy infrastructure was likely reducing the amount of source habitat within the ARPA landscape. Our source-sink map provides managers with a means of prioritizing habitats for conservation planning based on source and sink dynamics. The spatial identification of high value (i.e., primary source) as well as suboptimal (i.e., primary sink) habitats allows for informed energy development to minimize effects on local wildlife populations. # doi:10.1890/13-1152.1

Description: We calibrated the Multiple Element Limitation (MEL) model to Alaskan arctic tundra to simulate recovery of thermal erosion features (TEFs) caused by permafrost thaw and mass wasting. TEFs could significantly alter regional carbon (C) and nutrient budgets because permafrost soils contain large stocks of soil organic matter (SOM) and TEFs are expected to become more frequent as the climate warms. We simulated recovery following TEF stabilization and did not address initial, short-term losses of C and nutrients during TEF formation. To capture the variability among and within TEFs, we modeled a range of post-stabilization conditions by varying the initial size of SOM stocks and nutrient supply rates. Simulations indicate that nitrogen (N) losses after the TEF stabilizes are small, but phosphorus (P) losses continue. Vegetation biomass recovered 90% of its undisturbed C, N, and P stocks in 100 years using nutrients mineralized from SOM. Because of low litter inputs but continued decomposition, younger SOM continued to be lost for 10 years after the TEF began to recover, but recovered to about 84% of its undisturbed amount in 100 years. The older recalcitrant SOM in mineral soil continued to be lost throughout the 100-year simulation. Simulations suggest that biomass recovery depended on the amount of SOM remaining after disturbance. Recovery was initially limited by the photosynthetic capacity of vegetation, but became co-limited by N and P once a plant canopy developed. Biomass and SOM recovery was enhanced by increasing nutrient supplies, but the magnitude, source, and controls on these supplies are poorly understood. Faster mineralization of nutrients from SOM (e.g., by warming) enhanced vegetation recovery but delayed recovery of SOM. Taken together, these results suggest that although vegetation and surface SOM on TEFs recovered quickly (25 and 100 years respectively), the recovery of deep, mineral soil SOM took centuries and represented a major ecosystem C loss. # doi:10.1890/14-1323.1

Description: Fisheries bycatch is a global threat to marine megafauna. Environmental laws require bycatch assessment for protected species, but this is difficult when bycatch is rare. Low bycatch rates combined with low observer coverage may lead to biased, imprecise estimates when using standard ratio estimators. Bayesian model-based approaches incorporate uncertainty, produce less volatile estimates, and enable probabilistic evaluation of estimates relative to management thresholds. Here, we demonstrate a pragmatic decision-making process that uses Bayesian model-based inferences to estimate the probability of exceeding management thresholds for bycatch in fisheries with

Description: The non-lethal effects of wildlife tourism can threaten the conservation status of targeted animal populations. In turn, such resource depletion can compromise the economic viability of the industry. Therefore, wildlife tourism exploits resources that can become common-pool and that should be managed accordingly. We used a simulation approach to test whether different management regimes (tax, tax and subsidy, cap, cap-and-trade) could provide socio-ecologically sustainable solutions. Such schemes are sensitive to errors in estimated management targets. We determined the sensitivity of each scenario to various realistic uncertainties in management implementation and in our knowledge of the population. Scenarios where time quotas were enforced using a tax and subsidy approach, or they were traded between operators were more likely to be sustainable. Importantly, sustainability could be achieved even when operators were assumed to make simple rational economic decisions. We suggest that a combination of the two regimes might offer a robust solution, especially on a small spatial scale and under the control of a self-organized, operator-level institution. Our simulation platform could be parameterized to mimic local conditions and provide a test-bed for experimenting different governance solutions in specific case-studies. # doi:10.1890/14-0986.1

Description: Wild pollinators, bees in particular, may greatly contribute to crop pollination and provide a safety-net against declines in commercial pollinators. However, the identity, life history traits and environmental sensitivities of main crop pollinator species have received limited attention. These are crucial for predicting pollination services of different communities and for developing management practices that enhance crop pollinators. We sampled wild bees in three crop systems (almond, confection sunflower and seed watermelon) in a mosaic Israeli Mediterranean landscape. Bees were sampled in field/orchard edges and interiors, and in semi-natural scrub surrounding the fields/orchards. We also analysed land cover at 50?2500 m radii around fields/orchards. We used this data to distinguish crop- from non-crop pollinators based on a set of life history traits (nesting, lecty, sociality, body size) linked to habitat preference and crop visitation. Bee abundance and species richness decreased from the surrounding semi-natural habitat to the field/orchard interior, especially across the semi-natural?field edge ecotone. Thus, although rich bee communities were found near fields, only small fractions crossed the ecotone and visited crop flowers in substantial numbers. The bee assemblage in agricultural fields/orchards and on crop flowers was dominated by ground-nesting bees of the tribe Halictini, which tend to nest within fields. Bees' habitat preferences were determined mainly by nesting guild, whereas crop visitation was determined mainly by sociality. Lecty and body size also affected both measures. The percentage of surrounding semi-natural habitat at 250?2500 m radii had a positive effect on wild bee diversity in field edges, for all bee guilds, while at 50?100 m radii, only above-ground nesters were positively affected. In sum, we found that crop- and non-crop pollinators are distinguished by behavioral and morphological traits. Hence, analysis of life-history traits of bee communities can help assess the pollination services they are likely to provide (when taking into account single-visit pollination efficiency). The ecotone between agricultural fields and surrounding habitats is a major barrier that filters many bee species, particularly with regard to their nesting requirements. Thus greater attention should be given to management practices that encourage pollinators to live and nest, and not only forage, within fields. # doi:10.1890/14-0910.1

Description: Past studies have shown that tropical forest regeneration on degraded farmlands is initially limited by lack of seed dispersal, but few studies have tracked changes in abundance and composition of seed rain past the first few years after land abandonment. We measured seed rain for 12 months in ten 6-9-year old restoration sites and five mature, reference forests in southern Costa Rica in order to learn: (1) if seed rain limitation persists past the first few years of regeneration; (2) how restoration treatments influence seed community structure and composition; and (3) whether seed rain limitation is contingent on landscape context. Each restoration site contained three 0.25-ha treatment plots: (1) a naturally-regenerating control, (2) tree islands, and (3) a mixed-species tree plantation. Sites spanned a deforestation gradient with 9-89% forest area within 500 m around the treatment plots. Contrary to previous studies, we found that tree seeds were abundant and ubiquitous across all treatment plots (mean ± se: 585.1 ± 142.0 seeds m-2 y-1), indicating that lack of seed rain ceased to limit forest regeneration within the first decade of recovery. Pioneer trees and shrubs comprised the vast majority of seeds, but compositional differences between restoration sites and reference forests were driven by rarer, large-seeded species. Large, animal-dispersed tree seeds were more abundant in tree islands (4.6 ± 2.9 seeds m-2 y-1) and plantations (5.8 ± 3.0 seeds m-2 y-1) than control plots (0.2 ± 0.1 seeds m-2 y-1), contributing to greater tree species richness in actively-restored plots. Planted tree species accounted for

Description: Habitat suitability, dispersal potential, and fragmentation influence the distribution of stream fishes; however, their relative influence and interacting effects on species distributions are poorly understood, which may result in uncertain outcomes of river rehabilitation and conservation. Using empirical data describing 17 relatively common stream fishes, we combine (i) species habitat suitability models (MaxEnt) with a (ii) species dispersal model (FIDIMO) and a (iii) worst-case scenario of the influence of river fragmentation on dispersal. Using generalized linear mixed models, we aimed to uncover the role of these factors for explaining the probability of presence. Simulations over nine years allowed for assessing the relative importance of dispersal over time for structuring species occurrences versus the importance of habitat suitability. Models combining all three structuring factors performed consistently better in predicting the spatial occurrence patterns than models including only single factors. Our results confirmed that distribution patterns of stream fishes are jointly controlled by species dispersal and habitat suitability. An increase of 0.1 habitat suitability probability more than doubled the odds of species occurrence; an increase of 0.1 dispersal probability yielded a 14-fold increase of the odds of species occurrence. Temporal simulations revealed that over short time frames (1-2 years) dispersal from nearby source populations is four times more important than habitat suitability for species presence. However, over longer time periods, the importance of habitat suitability increases relative to the importance of dispersal. Surprisingly, fragmentation by migration barriers did not appear as significant driver of occurrence patterns. Concluding, these findings demonstrate the importance of the spatial arrangement of suitable habitats and potential source populations as well as their relative position in relation to barriers. We emphasize considering the direction of connections within river networks and the dispersal abilities of fishes, as well as providing (access to) new, suitable habitat for successful river rehabilitation. # doi:10.1890/14-0422.1

Description: In intensive farmland habitats, pollination of wild flowers and crops may be threatened by the widespread decline of pollinators. The honey bee decline, in particular, appears to result from the combination of multiple stresses, including diseases, pathogens, and pesticides. The reduction of semi-natural habitats is also suspected to entail floral resource scarcity for bees. Yet, the seasonal dynamics and composition of the honey bee diet remains poorly documented to date. In this study we studied the seasonal contribution of mass-flowering crops (rapeseed and sunflower) versus other floral resources, as well as the influence of nutritional quality and landscape composition on pollen diet composition over five consecutive years. From April to October, the mass of pollen and nectar collected by honey bees followed a bimodal seasonal trend, marked by two months of low food supply period between the two oilseed crops mass-flowerings (May for rapeseed and July for sunflower). Bees collected nectar mainly from crops while pollen came from a wide diversity of herbaceous and woody plant species, from semi-natural habitats or weeds in crops. Weed species constituted the bulk of the honey bee diet between the mass flowering crop periods (up to 40%) and are therefore suspected to play a critical role at this time period. The pollen diet composition was related to the nutritional value of the collected pollen and by the local landscape composition. Our study highlights (i) a food supply depletion period of both pollen and nectar resources during late spring, contemporaneously with the demographic peak of honey bee populations, (ii) a high botanical richness of pollen diet, mostly proceeding from trees and weeds, and (iii) a pollen diet composition influenced by the local landscape composition. Our results therefore support the Agri-Environmental Schemes intended to promote honey bees and beekeeping sustainability through the enhancement of flower availability in agricultural landscapes. # doi:10.1890/14-1011.1

Description: Resilience of ecological communities to perturbation is important in the face of increased global change from anthropogenic stressors. Monitoring is required to detect the impact of, and recovery from, perturbations, and before-after-control-impact (BACI) analysis provides a powerful framework in this regard. However, species in a community are not observed with perfect detection, and occupancy analysis is required to correct for imperfect detectability of species. We present a Bayesian community occupancy before-after-control-impact (CO-BACI) framework to monitor ecological community response to perturbation when constituent species are imperfectly detected. We test the power of the model to detect changes in community composition following an acute perturbation with simulation. We then apply the model to a study of the impact of a large hurricane on the forest bird community of Sweden, using data from the national bird survey scheme. Although simulation shows the model can detect changes in community occupancy following an acute perturbation, application to a Swedish forest bird community following a major hurricane detected no change in community occupancy despite widespread forest loss. Birds with landscape occupancy less than 50% required correcting for detectability. We conclude that CO-BACI analysis is a useful tool which can incorporate rare species in analyses and detect occupancy changes in ecological communities following perturbation, but because it does not include abundance some impacts may be overlooked. # doi:10.1890/14-0645.1

Description: Ecosystem-based management of natural resources involves an explicit consideration of trade-offs among ecosystem services. In marine fisheries, there is the potential for a trade-off between the supporting role of small pelagic fish and cephalopods in food webs, and the provisioning service they play as a major target of fisheries. Because these species play central roles in food webs by providing a conduit of energy from small prey to upper trophic level predators, we hypothesized that trade-offs between these two ecosystem services could be predicted based on energetic properties of predator?prey linkages and food-web structure. We compiled information from 27 marine food-web models (all within the Ecopath framework) that included either small pelagic fish or cephalopods, described predator?prey linkages involving these species, and developed a novel analytical framework to estimate how changes in yields of forage species would propagate through food webs and other fisheries. Consistent with expectations, diet overlap between predators and prey was generally low, and predator?prey linkages tended to be asymmetric; contribution of these species to predator diets was, on average, larger than the contribution of individual predator stocks to prey mortality. The estimated trade-offs between yields of forage fish and predator species were highly variable when we assumed joint bottom-up and top-down control on predation. Roughly one-third of this variance was related to an interactive effect of fishing and predation intensity; strong trade-offs were predicted when fishing intensity on forage species is high and when predators account for a high proportion of total forage mortality. When trophic connections were presumed to be driven by bottom-up processes, trade-offs were more predictable, but generally very small. Contrary to our expectations, trade-offs were not easily predicted from energetic properties, largely because predators of forage species exhibited a high degree of intra-guild predation, and also consumed many of the same prey as forage species. Given the limited ability to a priori predict the food-web implications of forage fisheries, we suggest that a precautionary risk-based approach be applied to decisions about acceptable biological removals of forage fish and biological targets used for their management. # doi:10.1890/13-1403.1

Description: Strong global demand for tropical timber and agricultural products has driven large-scale logging and subsequent conversion of tropical forests. Given that the majority of tropical landscapes have been or will likely be logged, the protection of biodiversity within tropical forests thus depends on whether species can persist in these economically exploited lands, and if species cannot persist, whether we can protect enough primary forest from logging and conversion. However, our knowledge of the impact of logging and conversion on biodiversity is limited to a few taxa, often sampled in different locations with complex land-use histories, hampering attempts to plan cost-effective conservation strategies and to draw conclusions across taxa. Spanning a land-use gradient of primary forest, once- and twice-logged forests, and oil palm plantations, we used traditional sampling and DNA metabarcoding to compile an extensive data set in Sabah, Malaysian Borneo for nine vertebrate and invertebrate taxa to quantify the biological impacts of logging and oil palm, develop cost-effective methods of protecting biodiversity, and examine whether there is congruence in response among taxa. Logged forests retained high species richness, including, on average, 70% of species found in primary forest. In contrast, conversion to oil palm dramatically reduces species richness, with significantly fewer primary-forest species than found on logged forest transects for seven taxa. Using a systematic conservation planning analysis, we show that efficient protection of primary-forest species is achieved with land portfolios that include a large proportion of logged-forest plots. Protecting logged forests is thus a cost-effective method of protecting an ecologically and taxonomically diverse range of species, particularly when conservation budgets are limited. Six indicator groups (birds, leaf-litter ants, beetles, aerial hymenopterans, flies, and true bugs) proved to be consistently good predictors of the response of the other taxa to logging and oil palm. Our results confidently establish the high conservation value of logged forests and the low value of oil palm. Cross-taxon congruence in responses to disturbance also suggests that the practice of focusing on key indicator taxa yields important information of general biodiversity in studies of logging and oil palm. # doi:10.1890/14-0010.1

Description: The dissolution of anthropogenically emitted excess carbon dioxide lowers the pH of the world's ocean water. The larvae of mass spawning marine fishes may be particularly vulnerable to such ocean acidification (OA), yet the generality of earlier results is unclear. Here we show the detrimental effects of OA on the development of a commercially important fish species, the Atlantic herring (Clupea harengus). Larvae were reared at three levels of CO2: today (0.0385 kPa), end of next century (0.183 kPa), and a coastal upwelling scenario (0.426 kPa), under near-natural conditions in large outdoor tanks. Exposure to elevated CO2 levels resulted in stunted growth and development, decreased condition, and severe tissue damage in many organs, with the degree of damage increasing with CO2 concentration. This complements earlier studies of OA on Atlantic cod larvae that revealed similar organ damage but at increased growth rates and no effect on condition. # doi:10.1890/13-0297.1

Description: Species distributions are responding rapidly to global change. While correlative studies of local extinction have been vital to understanding the ecological impacts of global change, more mechanistic lines of inquiry are needed for enhanced forecasting. The current study assesses whether the predictors of local extinction also explain population density for a species apparently impacted by climate change. We tested a suite of climatic and habitat metrics as predictors of American pika (Ochotona princeps) relative population density in the Southern Rocky Mountains, USA. Population density was indexed as the density of pika latrine sites. Negative binomial regression and AICc showed that the best predictors of pika latrine density were patch area followed by two measures of vegetation quality: the diversity and relative cover of forbs. In contrast with previous studies of habitat occupancy in the Southern Rockies, climatic factors were not among the top predictors of latrine density. Populations may be buffered from decline and ultimately from extirpation at sites with high-quality vegetation. Conversely, populations at highest risk for declining density and extirpation are likely to be those in sites with poor-quality vegetation. # doi:10.1890/13-1072.1

Description: Tropical forests play a vital role in the global carbon cycle, but the amount of carbon they contain and its spatial distribution remain uncertain. Recent studies suggest that once tree height is accounted for in biomass calculations, in addition to diameter and wood density, carbon stock estimates are reduced in many areas. However, it is possible that larger crown sizes might offset the reduction in biomass estimates in some forests where tree heights are lower because even comparatively short trees develop large, well-lit crowns in or above the forest canopy. While current allometric models and theory focus on diameter, wood density, and height, the influence of crown size and structure has not been well studied. To test the extent to which accounting for crown parameters can improve biomass estimates, we harvested and weighed 51 trees (11?169 cm diameter) in southwestern Amazonia where no direct biomass measurements have been made. The trees in our study had nearly half of total aboveground biomass in the branches (44% ± 2% [mean ± SE]), demonstrating the importance of accounting for tree crowns. Consistent with our predictions, key pantropical equations that include height, but do not account for crown dimensions, underestimated the sum total biomass of all 51 trees by 11% to 14%, primarily due to substantial underestimates of many of the largest trees. In our models, including crown radius greatly improves performance and reduces error, especially for the largest trees. In addition, over the full data set, crown radius explained more variation in aboveground biomass (10.5%) than height (6.0%). Crown form is also important: Trees with a monopodial architectural type are estimated to have 21?44% less mass than trees with other growth patterns. Our analysis suggests that accounting for crown allometry would substantially improve the accuracy of tropical estimates of tree biomass and its distribution in primary and degraded forests. # doi:10.1890/13-0070.1

Description: Microtopographic variation is ubiquitous throughout lowland Amazonia, and it may impart patterns of species richness and abundance, and perhaps community compositional changes. To date, no studies have determined the degree to which lowland microtopography influences forest canopy diversity. We developed the first high-resolution maps of forest canopy diversity in Amazonia, focusing on four landscapes on two river systems in Peru. Spectroscopic images were acquired using the Carnegie Airborne Observatory combined with a new method based on spectral species to map α- and ?-diversity. We analyzed spatial patterns in diversity with respect to floodplain and terrace (terra firme) surfaces and in upriver and downriver locations with contrasting landscape morphologies. We found slightly lower average α-diversity in floodplains, but with greater variance than in terrace communities caused by the floodplain mix of swamp forests, anoxic low-diversity ecosystems, and high-diversity areas. ?-diversity estimated with the Bray-Curtis dissimilarity (BC) was strongly related to microtopography, with floodplains showing higher internal compositional dissimilarity than terraces. Throughout all landscapes, remotely mapped BC within terrace environments ranged from 0.25 to 0.43, but these values increased 30?77% on floodplains. Upriver landscapes characterized by higher terraces showed more distinct community turnover than did their downstream counterparts. We conclude that microtopography strongly influences ?-diversity throughout the study landscapes, but terrain is weakly associated with variation in α-diversity. We uncover the importance of microtopography in determining species composition in lowland Amazonia and highlight the value of imaging spectroscopy for biodiversity research and conservation. # doi:10.1890/13-1896.1

Description: Species invasions have a range of negative effects on recipient ecosystems, and many occur at a scale and magnitude that preclude complete eradication. When complete extirpation is unlikely with available management resources, an effective strategy may be to suppress invasive populations below levels predicted to cause undesirable ecological change. We illustrated this approach by developing and testing targets for the control of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) on Western Atlantic coral reefs. We first developed a size-structured simulation model of predation by lionfish on native fish communities, which we used to predict threshold densities of lionfish beyond which native fish biomass should decline. We then tested our predictions by experimentally manipulating lionfish densities above or below reef-specific thresholds, and monitoring the consequences for native fish populations on 24 Bahamian patch reefs over 18 months. We found that reducing lionfish below predicted threshold densities effectively protected native fish community biomass from predation-induced declines. Reductions in density of 25?92%, depending on the reef, were required to suppress lionfish below levels predicted to overconsume prey. On reefs where lionfish were kept below threshold densities, native prey fish biomass increased by 50?70%. Gains in small ( 15 cm total length), including ecologically important grazers and economically important fisheries species, had increased by 10?65% by the end of the experiment. Crucially, similar gains in prey fish biomass were realized on reefs subjected to partial and full removal of lionfish, but partial removals took 30% less time to implement. By contrast, the biomass of small native fishes declined by 〉50% on all reefs with lionfish densities exceeding reef-specific thresholds. Large inter-reef variation in the biomass of prey fishes at the outset of the study, which influences the threshold density of lionfish, means that we could not identify a single rule of thumb for guiding control efforts. However, our model provides a method for setting reef-specific targets for population control using local monitoring data. Our work is the first to demonstrate that for ongoing invasions, suppressing invaders below densities that cause environmental harm can have a similar effect, in terms of protecting the native ecosystem on a local scale, to achieving complete eradication. # doi:10.1890/13-0979.1

Description: A general understanding of grazing effects on plant diversity in drylands is still missing, despite an extensive theoretical background. Cross-biome syntheses are hindered by the fact that the outcomes of disturbance studies are strongly affected by the choice of diversity measures, and the spatial and temporal scales of measurements. The aim of this study is to overcome these weaknesses by applying a wide range of diversity measures to a data set derived from identical sampling in three distinct ecosystems. We analyzed three fence-line contrasts (heavier vs. lighter grazing intensity), representing different degrees of aridity (from arid to semiarid) and precipitation regimes (summer rain vs. winter rain) in southern Africa. We tested the impact of grazing intensity on multiple aspects of plant diversity (species and functional group level, richness and evenness components, alpha and beta diversity, and composition) at two spatial scales, and for both 5-yr means and interannual variability. Heavier grazing reduced total plant cover and substantially altered the species and functional composition at all sites. However, a significant decrease in species alpha diversity was detected at only one of the three sites. By contrast, alpha diversity of plant functional groups responded consistently across ecosystems and scales, with a significant decrease at heavier grazing intensity. The cover-based measures of functional group diversity responded more sensitively and more consistently than functional group richness. Beta diversity of species and functional types increased under heavier grazing, showing that at larger scales, the heterogeneity of the community composition and the functional structure were increased. Heavier grazing mostly increased interannual variability of alpha diversity, while effects on beta diversity and cover were inconsistent. Our results suggest that species diversity alone may not adequately reflect the shifts in vegetation structure that occur in response to increased grazing intensity in the dryland biomes of southern Africa. Compositional and structural changes of the vegetation are better reflected by trait-based diversity measures. In particular, measures of plant functional diversity that include evenness represent a promising tool to detect and quantify disturbance effects on ecosystems. # doi:10.1890/13-0377.1

Description: Oyster reefs have declined globally. Interest in their restoration has motivated research into oyster-mediated ecosystem services including effects on biodiversity, filtration, and nitrogen (N) cycling. Recent evidence suggests oysters may promote denitrification, or anaerobic respiration of nitrate (NO3?) into di-nitrogen gas, via benthic deposition of carbon (C) and N-rich biodeposits. However, the mechanisms whereby biodeposits promote N transformations prerequisite to denitrification (e.g., mineralization and nitrification) are unclear. Previous research has also not measured oysters' influence on N cycling in urbanized areas. In May 2010 we deployed eastern oysters (Crassostrea virginica) in mesh cages above sand-filled boxes at four sites across a nutrient gradient in Jamaica Bay, New York City (New York, USA). Oysters were arranged at four densities: 0, 40, 85, and 150 oysters/m2. For 17 months we measured water-column nutrients and chlorophyll a, every two weeks to monthly. Every two months we measured sediment ash-free dry mass (AFDM), exchangeable ammonium (NH4+), ammonification, nitrification, denitrification potential (DNP), and NO3? and C limitation of DNP. Oysters increased sediment AFDM at three of four sites, with the greatest increase at high density. Oysters did not affect any N pools or transformations. However, variation among sites and dates illustrated environmental drivers of C and N biogeochemistry in this urban estuary. Overall, nitrification was positively related to net ammonification, water column NH4+, and sediment NH4+, but was not correlated with DNP. Denitrification was consistently and strongly NO3? limited, while C was not limiting or secondarily limiting. Therefore, the oyster-mediated increase in AFDM did not affect DNP because C was not its primary driver. Also, because DNP was unrelated to nitrification, it is unlikely that biodeposit N was converted to NO3? for use as a denitrification substrate. Predicting times or sites where denitrification is driven by the C and N species originating from oyster biodeposits remains a challenge under eutrophic conditions. Towards this goal, we synthesized our conclusions with literature predictions in a conceptual model for pathways whereby oysters might influence C and N dynamics differently in oligotrophic relative to eutrophic ecosystems. # doi:10.1890/12-1798.1

Description: Determining appropriate actions to create or maintain landscapes resilient to climate change is challenging because of uncertainty associated with potential effects of climate change and their interactions with land management. We used a set of climate-informed state-and-transition models to explore the effects of management and natural disturbances on vegetation composition and structure under different future climates. Models were run for dry forests of central Oregon under a fire suppression scenario (i.e., no management other than the continued suppression of wildfires) and an active management scenario characterized by light to moderate thinning from below and some prescribed fire, planting, and salvage logging. Without climate change, area in dry province forest types remained constant. With climate change, dry mixed-conifer forests increased in area (by an average of 21?26% by 2100), and moist mixed-conifer forests decreased in area (by an average of 36?60% by 2100), under both management scenarios. Average area in dry mixed-conifer forests varied little by management scenario, but potential decreases in the moist mixed-conifer forest were lower with active management. With changing climate in the dry province of central Oregon, our results suggest the likelihood of sustaining current levels of dense, moist mixed-conifer forests with large-diameter, old trees is low (less than a 10% chance) irrespective of management scenario; an opposite trend was observed under no climate change simulations. However, results also suggest active management within the dry and moist mixed-conifer forests that creates less dense forest conditions can increase the persistence of larger-diameter, older trees across the landscape. Owing to projected increases in wildfire, our results also suggest future distributions of tree structures will differ from the present. Overall, our projections indicate proactive management can increase forest resilience and sustain some societal values, particularly in drier forest types. However, opportunities to create more disturbance-adapted systems are finite, all values likely cannot be sustained at current levels, and levels of resilience success will likely vary by dry province forest type. Land managers planning for a future without climate change may be assuming a future that is unlikely to exist. # doi:10.1890/13-1653.1

Description: Mounting evidence now shows that fishing activity modifies both heritable life-history traits and ecological processes in harvested populations. However, ecological and evolutionary changes are intimately linked and can occur on the same time scale, and few studies have investigated their combined effect on fish population dynamics. Here, we contrast two population subunits of a harvested fish species in the Northeast Atlantic, the European hake (Merluccius merluccius), in the light of the emerging field of evolutionary demography, which considers the interacting processes between ecology and evolution. The two subunits experienced similar age/size truncation due to size-selective fishing, but displayed differences in key ecological processes (recruitment success) and phenotypic characteristics (maturation schedule). We investigate how temporal variation in maturation and recruitment success interactively shape the population dynamics of the two subunits. We document that the two subunits of European hake displayed different responses to fishing in maturation schedules, possibly because of the different level of adaptive phenotypic plasticity. Our results also suggest that high phenotypic plasticity can dampen the effects of fisheries-induced demographic truncation on population dynamics, whereas a population subunit characterized by low phenotypic plasticity may suffer from additive effects of ecological and life-history responses. Similar fishing pressure may thus trigger contrasting interactions between life history variation and ecological processes within the same population. The presented findings improve our understanding of how fishing impacts eco-evolutionary dynamics, which is a keystone for a more comprehensive management of harvested species. # doi:10.1890/12-1777.1