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At least 19 recordsLinked to original sources
USGS2011

On thinning of chains in MCMC

1. Markov chain Monte Carlo (MCMC) is a simulation technique that has revolutionised the analysis of ecological data, allowing the fitting of complex models in a Bayesian framework. Since 2001, there have been nearly 200 papers using MCMC in publications of the Ecological Society of America and the British Ecological Society, including more than 75 in the journal Ecology and 35 in the Journal of Applied Ecology . 2. We have noted that many authors routinely 'thin' their simulations, discarding all but every k th sampled value; of the studies we surveyed with details on MCMC implementation, 40% reported thinning. 3. Thinning is often unnecessary and always inefficient, reducing the precision with which features of the Markov chain are summarised. The inefficiency of thinning MCMC output has been known since the early 1990's, long before MCMC appeared in ecological publications. 4. We discuss the background and prevalence of thinning, illustrate its consequences, discuss circumstances when it might be regarded as a reasonable option and recommend against routine thinning of chains unless necessitated by computer memory limitations.

Methods in Ecology and Evolution↗
USGS2023

Reanalysis indicates little evidence of reduction in eagle mortality rate by automated curtailment of wind turbines

Unintended consequences of renewable energy development include collision-caused deaths of birds and bats. Energy companies may risk prosecution if protected species are among the casualties. Shutting down turbines during high collision-risk conditions could reduce mortality rates, and several companies are developing systems to identify such conditions. A recent peer-reviewed article published in the Journal of Applied Ecology reported a remarkable ‘82% (75%–89%) reduction in the fatality rate’ of eagles at a wind energy facility due to a device marketed as Identiflight®—remarkable because of the impressive effect size and the extremely high level of precision. We show that reported results stem from four major errors, which, when corrected, give an unremarkable estimate of 50% (−159%, 89%) reduction (or possible increase) in the fatality rate. The errors include the following: (i) Ignoring annual variation . They compare the average number of eagle fatalities over 4 years before activation of Identiflight® to the number in a single year after, ignoring annual variation in fatalities. (ii) Unfounded causal inference . Lack of replication (one treatment year at one site) is ignored, leading to unwarranted causal inference. (iii) Inflated effect size . Effect size is inflated by assuming (without providing evidence) that the difference in fatality relative to the mean at a neighbouring site would be exactly repeated at the treatment site. Furthermore, the observed difference in fatalities at the control site depends strongly on the arbitrarily chosen date distinguishing the ‘Before’ and ‘After’ periods, yielding unreliable results. (iv) Inconsistency of data . It is unclear why 7 of 42 reported eagle fatalities were not included in the data analyzed, potentially further inflating the estimated effect size. Synthesis and applications . The recent claim, published in the Journal of Applied Ecology, that ‘Eagle fatalities are reduced by automated curtailment of wind turbines’ is not supported by the data but stems from errors that led to strongly overstated effect size and precision, and unfounded inference. In theory, automated curtailment has obvious potential for reducing eagle fatalities, but several more years of data at several locations and appropriate statistical analyses will be required to evaluate its effectiveness and to inform management prescriptions involving this technology.

Journal of Applied Ecology↗
USGS2009

Forecasting the combined effects of urbanization and climate change on stream ecosystems: from impacts to management options

Streams collect runoff, heat, and sediment from their watersheds, making them highly vulnerable to anthropogenic disturbances such as urbanization and climate change. Forecasting the effects of these disturbances using process-based models is critical to identifying the form and magnitude of likely impacts. Here, we integrate a new biotic model with four previously developed physical models (downscaled climate projections, stream hydrology, geomorphology, and water temperature) to predict how stream fish growth and reproduction will most probably respond to shifts in climate and urbanization over the next several decades. The biotic submodel couples dynamics in fish populations and habitat suitability to predict fish assemblage composition, based on readily available biotic information (preferences for habitat, temperature, and food, and characteristics of spawning) and day-to-day variability in stream conditions. We illustrate the model using Piedmont headwater streams in the Chesapeake Bay watershed of the USA, projecting ten scenarios: Baseline (low urbanization; no on-going construction; and present-day climate); one Urbanization scenario (higher impervious surface, lower forest cover, significant construction activity); four future climate change scenarios [Hadley CM3 and Parallel Climate Models under medium-high (A2) and medium-low (B2) emissions scenarios]; and the same four climate change scenarios plus Urbanization. Urbanization alone depressed growth or reproduction of 8 of 39 species, while climate change alone depressed 22 to 29 species. Almost every recreationally important species (i.e. trouts, basses, sunfishes) and six of the ten currently most common species were predicted to be significantly stressed. The combined effect of climate change and urbanization on adult growth was sometimes large compared to the effect of either stressor alone. Thus, the model predicts considerable change in fish assemblage composition, including loss of diversity. Synthesis and applications . The interaction of climate change and urban growth may entail significant reconfiguring of headwater streams, including a loss of ecosystem structure and services, which will be more costly than climate change alone. On local scales, stakeholders cannot control climate drivers but they can mitigate stream impacts via careful land use. Therefore, to conserve stream ecosystems, we recommend that proactive measures be taken to insure against species loss or severe population declines. Delays will inevitably exacerbate the impacts of both climate change and urbanization on headwater systems.

Journal of Applied Ecology↗
USGS2011

Restoration of the fire-grazing interaction in Artemisia filifolia shrubland of the Southern Great Plains, North America

1.  Patterns of landscape heterogeneity are crucial to the maintenance of biodiversity in shrublands and grasslands, yet management practices in these ecosystems typically seek to homogenize landscapes. Furthermore, there is limited understanding of how the interaction of ecological processes, such as fire and grazing, affects patterns of heterogeneity at different spatial scales. 2.  We conducted research in Artemisia filifolia (Asteraceae) shrublands located in the southern Great Plains of North America to determine the effect of restoring the fire–grazing interaction on vegetation structure. Data were collected for 3 years in replicated pastures grazed by cattle Bos taurus where the fire–grazing interaction had been restored (fire and grazing = treatment pastures) and in pastures that were grazed but remained unburned (grazing only, no fire = control pastures). The effect of the fire–grazing interaction on heterogeneity (variance) of vegetation structure was assessed at scales from 12·5 m 2 to 609 ha. 3.  Most measurements of vegetation structure within treatment pastures differed from control pastures for 1–3 years after being burned but were thereafter similar to the values found in unburned control pastures. 4.  Treatment pastures were characterized by a lower amount of total heterogeneity and a lower amount of heterogeneity through time. 5.  Heterogeneity of vegetation structure tended to decrease as the scale of measurement increased in both treatment and control pastures. There was deviation from this trend, however, in the treatment pastures that exhibited much higher heterogeneity at the patch scale (mean patch size = 202 ha) of measurement, the scale at which patch fires were conducted. 6. Synthesis and applications . Vegetation structure in A. filifolia shrublands of our study was readily altered by the fire–grazing interaction but also demonstrated substantial resilience to these effects. The fire–grazing interaction also changed the total amount of heterogeneity characterizing this system, the scale at which heterogeneity in this system was expressed and the amount of heterogeneity expressed through time. Land managers seeking to impose a shifting mosaic of heterogeneity on this vegetation type can do so by restoring the fire–grazing interaction with potential conservation benefits similar to what has been achieved in other ecosystems where historic cycles of disturbance and rest have been restored.

Oklahoma↗
USGS2009

Bird population density estimated from acoustic signals

Many animal species are detected primarily by sound. Although songs, calls and other sounds are often used for population assessment, as in bird point counts and hydrophone surveys of cetaceans, there are few rigorous methods for estimating population density from acoustic data. 2. The problem has several parts - distinguishing individuals, adjusting for individuals that are missed, and adjusting for the area sampled. Spatially explicit capture-recapture (SECR) is a statistical methodology that addresses jointly the second and third parts of the problem. We have extended SECR to use uncalibrated information from acoustic signals on the distance to each source. 3. We applied this extension of SECR to data from an acoustic survey of ovenbird Seiurus aurocapilla density in an eastern US deciduous forest with multiple four-microphone arrays. We modelled average power from spectrograms of ovenbird songs measured within a window of 0??7 s duration and frequencies between 4200 and 5200 Hz. 4. The resulting estimates of the density of singing males (0??19 ha -1 SE 0??03 ha -1 ) were consistent with estimates of the adult male population density from mist-netting (0??36 ha -1 SE 0??12 ha -1 ). The fitted model predicts sound attenuation of 0??11 dB m -1 (SE 0??01 dB m -1 ) in excess of losses from spherical spreading. 5.Synthesis and applications. Our method for estimating animal population density from acoustic signals fills a gap in the census methods available for visually cryptic but vocal taxa, including many species of bird and cetacean. The necessary equipment is simple and readily available; as few as two microphones may provide adequate estimates, given spatial replication. The method requires that individuals detected at the same place are acoustically distinguishable and all individuals vocalize during the recording interval, or that the per capita rate of vocalization is known. We believe these requirements can be met, with suitable field methods, for a significant number of songbird species. ?? 2009 British Ecological Society.

Journal of Applied Ecology↗
USGS2008

Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys

1. Species richness is the most widely used biodiversity metric, but cannot be observed directly as, typically, some species are overlooked. Imperfect detectability must therefore be accounted for to obtain unbiased species-richness estimates. When richness is assessed at multiple sites, two approaches can be used to estimate species richness: either estimating for each site separately, or pooling all samples. The first approach produces imprecise estimates, while the second loses site-specific information. 2. In contrast, a hierarchical Bayes (HB) multispecies site-occupancy model benefits from the combination of information across sites without losing site-specific information and also yields occupancy estimates for each species. The heart of the model is an estimate of the incompletely observed presence-absence matrix, a centrepiece of biogeography and monitoring studies. We illustrate the model using Swiss breeding bird survey data, and compare its estimates with the widely used jackknife species-richness estimator and raw species counts. 3. Two independent observers each conducted three surveys in 26 1-km(2) quadrats, and detected 27-56 (total 103) species. The average estimated proportion of species detected after three surveys was 0.87 under the HB model. Jackknife estimates were less precise (less repeatable between observers) than raw counts, but HB estimates were as repeatable as raw counts. The combination of information in the HB model thus resulted in species-richness estimates presumably at least as unbiased as previous approaches that correct for detectability, but without costs in precision relative to uncorrected, biased species counts. 4. Total species richness in the entire region sampled was estimated at 113.1 (CI 106-123); species detectability ranged from 0.08 to 0.99, illustrating very heterogeneous species detectability; and species occupancy was 0.06-0.96. Even after six surveys, absolute bias in observed occupancy was estimated at up to 0.40. 5. Synthesis and applications. The HB model for species-richness estimation combines information across sites and enjoys more precise, and presumably less biased, estimates than previous approaches. It also yields estimates of several measures of community size and composition. Covariates for occupancy and detectability can be included. We believe it has considerable potential for monitoring programmes as well as in biogeography and community ecology.

Journal of Applied Ecology↗
USGS2010

Modelling detection probabilities to evaluate management and control tools for an invasive species

For most ecologists, detection probability (p) is a nuisance variable that must be modelled to estimate the state variable of interest (i.e. survival, abundance, or occupancy). However, in the realm of invasive species control, the rate of detection and removal is the rate-limiting step for management of this pervasive environmental problem. For strategic planning of an eradication (removal of every individual), one must identify the least likely individual to be removed, and determine the probability of removing it. To evaluate visual searching as a control tool for populations of the invasive brown treesnake Boiga irregularis, we designed a mark-recapture study to evaluate detection probability as a function of time, gender, size, body condition, recent detection history, residency status, searcher team and environmental covariates. We evaluated these factors using 654 captures resulting from visual detections of 117 snakes residing in a 5-ha semi-forested enclosure on Guam, fenced to prevent immigration and emigration of snakes but not their prey. Visual detection probability was low overall (= 0??07 per occasion) but reached 0??18 under optimal circumstances. Our results supported sex-specific differences in detectability that were a quadratic function of size, with both small and large females having lower detection probabilities than males of those sizes. There was strong evidence for individual periodic changes in detectability of a few days duration, roughly doubling detection probability (comparing peak to non-elevated detections). Snakes in poor body condition had estimated mean detection probabilities greater than snakes with high body condition. Search teams with high average detection rates exhibited detection probabilities about twice that of search teams with low average detection rates. Surveys conducted with bright moonlight and strong wind gusts exhibited moderately decreased probabilities of detecting snakes. Synthesis and applications. By emphasizing and modelling detection probabilities, we now know: (i) that eradication of this species by searching is possible, (ii) how much searching effort would be required, (iii) under what environmental conditions searching would be most efficient, and (iv) several factors that are likely to modulate this quantification when searching is applied to new areas. The same approach can be use for evaluation of any control technology or population monitoring programme. ?? 2009 The Authors. Journal compilation ?? 2009 British Ecological Society.

Journal of Applied Ecology↗
USGS2010

Quantifying restoration success and recovery in a metal-polluted stream: A 17-year assessment of physicochemical and biological responses

Evaluating the effectiveness of stream restoration is often challenging because of the lack of pre-treatment data, narrow focus on physicochemical measures and insufficient post-restoration monitoring. Even when these fundamental elements are present, quantifying restoration success is difficult because of the challenges associated with distinguishing treatment effects from seasonal variation, episodic events and long-term climatic changes.2. We report results of one of the most comprehensive and continuous records of physical, chemical and biological data available to assess restoration success for a stream ecosystem in North America. Over a 17 year period we measured seasonal and annual changes in metal concentrations, physicochemical characteristics, macroinvertebrate communities, and brown trout Salmo trutta populations in the Arkansas River, a metal-contaminated stream in Colorado, USA.3. Although we observed significant improvements in water quality after treatment, the effectiveness of restoration varied temporally, spatially and among biological response variables. The fastest recovery was observed at stations where restoration eliminated point sources of metal contamination. Recovery of macroinvertebrates was significantly delayed at some stations because of residual sediment contamination and because extreme seasonal and episodic variation in metal concentrations prevented recolonization by sensitive species. Synthesis and applications. Because recovery trajectories after the removal of a stressor are often complex or nonlinear, long-term studies are necessary to assess restoration success within the context of episodic events and changes in regional climate. The observed variation in recovery among chemical and biological endpoints highlights the importance of developing objective criteria to assess restoration success. Although the rapid response of macroinvertebrates to reduced metal concentrations is encouraging, we have previously demonstrated that benthic communities from the Arkansas River remained susceptible to other novel anthropogenic stressors. We suggest that the resistance or resilience of benthic macroinvertebrate communities to novel stressors may be effective indicators of restoration success that can account for the non-additive (e.g. synergistic) nature of compound perturbations. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

Journal of Applied Ecology↗
USGS2010

Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance

Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

Journal of Applied Ecology↗
USGS2021

Biodiversity effects on grape quality depend on variety and management intensity

Interactions between plants can be beneficial, detrimental or neutral. In agricultural systems, competition between crop and spontaneous vegetation is a major concern. We evaluated the relative support for three non-exclusive ecological hypotheses about interactions between crop and spontaneous plants based on competition, complementarity or facilitation. The study was conducted in Swiss vineyards with different vegetation management intensities. In all, 33 vineyards planted with two different grape varieties were studied over 3 years to determine whether low-intensity vegetation management might provide benefits for grape quality parameters. Management intensity varied with the degree of control of spontaneous inter-row vegetation. Features of spontaneous vegetation measured included total cover, total species richness and abundance of nitrogen-fixing plants. Grape quality parameters of known importance to wine making (yeast assimilable nitrogen, sugars, tartaric acid and malic acid) were determined by Fourier-transform infrared spectroscopy (FTIR). Using structural equation modelling, we evaluated hypotheses about the multivariate responses of grape quality parameters as well as the direct and indirect (plant-mediated) effects of management. Observed effects of management differed between grape varieties. Management intensity and abundance of N-fixing plants significantly influenced grape quality parameters while total richness of spontaneous plants did not have detectable effects. Abundance of N-fixing plants was enhanced by low-intensity management resulting in increased N content in the red grape variety Pinot noir , potentially enhancing grape quality, while measured soil N content did not explain the increase. Synthesis and applications . Our study shows that crop quality can be enhanced by spontaneous plants, in this case by the abundance of a key functional group (N-fixers), most likely through plant–plant or plant–microbe facilitation. However, beneficial interactions may have a high specificity in terms of facilitation partners and may have contrasting effects at low taxonomic resolutions such as crop varieties. Generally, increasing plant biodiversity in agricultural systems may increase competition with crops. Thus, the identification of suitable interaction partners and a careful balance between crop variety and spontaneous plant species may be necessary to utilize beneficial interactions and to reduce the trade-off between agricultural production and biodiversity to achieve a sustainable ecological benefit in agricultural systems.

Canton of Valais↗
USGS2006

Correlates of biological soil crust abundance across a continuum of spatial scales: Support for a hierarchical conceptual model

1. Desertification negatively impacts a large proportion of the global human population and > 30% of the terrestrial land surface. Better methods are needed to detect areas that are at risk of desertification and to ameliorate desertified areas. Biological soil crusts are an important soil lichen-moss-microbial community that can be used toward these goals, as (i) bioindicators of desertification damage and (ii) promoters of soil stability and fertility. 2. We identified environmental factors that correlate with soil crust occurrence on the landscape and might be manipulated to assist recovery of soil crusts in degraded areas. We conducted three studies on the Colorado Plateau, USA, to investigate the hypotheses that soil fertility [particularly phosphorus (P), manganese (Mn) and zinc (Zn)] and/or moisture limit soil crust lichens and mosses at four spatial scales. 3. In support of the soil fertility hypothesis, we found that lichen-moss crusts were positively correlated with several nutrients [Mn, Zn, potassium (K) and magnesium (Mg) were most consistent] at three of four spatial scales ranging from 3.5 cm2 in area to c. 800 km2. In contrast, P was negatively correlated with lichen-moss crusts at three scales. 4. Community composition varied with micro-aspect on ridges in the soil crust. Three micro-aspects [north-north-west (NNW), east-north-east (ENE) and TOP] supported greater lichen and moss cover than the warmer, windward and more xeric micro-aspects [west-south-west (WSW) and south-south-east (SSE)]. This pattern was poorly related to soil fertility; rather, it was consistent with the moisture limitation hypothesis. 5. Synthesis and application. Use of crusts as desertification bioindicators requires knowledge of a site's potential for crust cover in the absence of desertification. We present a multi-scale model of crust potential as a function of site properties. Future quantitative studies can use this model to guide sampling efforts. Also, our results suggest new directions in restoration research: enhancement of moisture residence time and fertilization with key nutrients (Mn, Zn, K and Mg). Re-establishment of soil crusts in desertified lands will help regain lost soil stability and fertility, and facilitate plant re-establishment. ?? 2006 British Ecological Society.

Journal of Applied Ecology↗
USGS2007

Assessments of habitat preferences and quality depend on spatial scale and metrics of fitness

1. Identifying the habitat features that influence habitat selection and enhance fitness is critical for effective management. Ecological theory predicts that habitat choices should be adaptive, such that fitness is enhanced in preferred habitats. However, studies often report mismatches between habitat preferences and fitness consequences across a wide variety of taxa based on a single spatial scale and/or a single fitness component. 2. We examined whether habitat preferences of a declining shrub steppe songbird, the Brewer's sparrow Spizella breweri, were adaptive when multiple reproductive fitness components and spatial scales (landscape, territory and nest patch) were considered. 3. We found that birds settled earlier and in higher densities, together suggesting preference, in landscapes with greater shrub cover and height. Yet nest success was not higher in these landscapes; nest success was primarily determined by nest predation rates. Thus landscape preferences did not match nest predation risk. Instead, nestling mass and the number of nesting attempts per pair increased in preferred landscapes, raising the possibility that landscapes were chosen on the basis of food availability rather than safe nest sites. 4. At smaller spatial scales (territory and nest patch), birds preferred different habitat features (i.e. density of potential nest shrubs) that reduced nest predation risk and allowed greater season-long reproductive success. 5. Synthesis and applications. Habitat preferences reflect the integration of multiple environmental factors across multiple spatial scales, and individuals may have more than one option for optimizing fitness via habitat selection strategies. Assessments of habitat quality for management prescriptions should ideally include analysis of diverse fitness consequences across multiple ecologically relevant spatial scales. ?? 2007 The Authors.

Journal of Applied Ecology↗
USGS2009

Patterns and determinants of mammal species occurrence in India

Many Indian mammals face range contraction and extinction, but assessments of their population status are hindered by the lack of reliable distribution data and range maps. 2. We estimated the current geographical ranges of 20 species of large mammals by applying occupancy models to data from country-wide expert. We modelled species in relation to ecological and social covariates (protected areas, landscape characteristics and human influences) based on a priori hypotheses about plausible determinants of mammalian distribution patterns. 3. We demonstrated that failure to incorporate detection probability in distribution survey methods underestimated habitat occupancy for all species. 4. Protected areas were important for the distribution of 16 species. However, for many species much of their current range remains unprotected. The availability of evergreen forests was important for the occurrence of 14 species, temperate forests for six species, deciduous forests for 15 species and higher altitude habitats for two species. Low human population density was critical for the occurrence of five species, while culturally based tolerance was important for the occurrence of nine other species. 5. Rhino Rhinoceros unicornis, gaur Bos gaurus and elephant Elephas maximus showed the most restricted ranges among herbivores, and sun bear Helarctos malayanus, brown bear Ursus arctos and tiger Panthera tigris were most restricted among carnivores. While cultural tolerance has helped the survival of some mammals, legal protection has been critically associated with occurrence of most species. 6. Synthesis and applications. Extent of range is an important determinant of species conservation status. Understanding the relationship of species occurrence with ecological and socio-cultural covariates is important for identification and management of key conservation areas. The combination of occupancy models with field data from country-wide experts enables reliable estimation of species range and habitat associations for conservation at regional scales. ?? 2009 British Ecological Society.

Journal of Applied Ecology↗
USGS2017

Examining the occupancy–density relationship for a low-density carnivore

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

Journal of Applied Ecology↗
USGS2003

Effects of increased soil nitrogen on the dominance of alien annual plants in the Mojave Desert

1. Deserts are one of the least invaded ecosystems by plants, possibly due to naturally low levels of soil nitrogen. Increased levels of soil nitrogen caused by atmospheric nitrogen deposition may increase the dominance of invasive alien plants and decrease the diversity of plant communities in desert regions, as it has in other ecosystems. Deserts should be particularly susceptible to even small increases in soil nitrogen levels because the ratio of increased nitrogen to plant biomass is higher compared with most other ecosystems. 2. The hypothesis that increased soil nitrogen will lead to increased dominance by alien plants and decreased plant species diversity was tested in field experiments using nitrogen additions at three sites in the in the Mojave Desert of western North America. 3. Responses of alien and native annual plants to soil nitrogen additions were measured in terms of density, biomass and species richness. Effects of nitrogen additions were evaluated during 2 years of contrasting rainfall and annual plant productivity. The rate of nitrogen addition was similar to published rates of atmospheric nitrogen deposition in urban areas adjacent to the Mojave Desert (3·2 g N m −2 year −1 ). The dominant alien species included the grasses Bromus madritensis ssp. rubens and Schismus spp. ( S. arabicus and S. barbatus ) and the forb Erodium cicutarium . 4. Soil nitrogen addition increased the density and biomass of alien annual plants during both years, but decreased density, biomass and species richness of native species only during the year of highest annual plant productivity. The negative response of natives may have been due to increased competitive stress for soil water and other nutrients caused by the increased productivity of aliens. 5. The effects of nitrogen additions were significant at both ends of a natural nutrient gradient, beneath creosote bush Larrea tridentata canopies and in the interspaces between them, although responses varied among individual alien species. The positive effects of nitrogen addition were highest in the beneath-canopy for B. rubens and in interspaces for Schismus spp. and E. cicutarium . 6. The results indicated that increased levels of soil nitrogen from atmospheric nitrogen deposition or from other sources could increase the dominance of alien annual plants and possibly promote the invasion of new species in desert regions. Increased dominance by alien annuals may decrease the diversity of native annual plants, and increased biomass of alien annual grasses may also increase the frequency of fire. 7. Although nitrogen deposition cannot be controlled by local land managers, the managers need to understand its potential effects on plant communities and ecosystem properties, in particular how these effects may interact with land-use activities that can be managed at the local scale. These interactions are currently unknown, and hinder the ability of managers to make appropriate land-use decisions related to nitrogen deposition in desert ecosystems. 8. Synthesis and applications. The effects of nitrogen deposition on invasive alien plants should be considered when deciding where to locate new conservation areas, and in evaluating the full scope of ecological effects of new projects that would increase nitrogen deposition rates.

Journal of Applied Ecology↗
USGS2013

Taming wildlife disease: bridging the gap between science and management

1.Parasites and pathogens of wildlife can threaten biodiversity, infect humans and domestic animals, and cause significant economic losses, providing incentives to manage wildlife diseases. Recent insights from disease ecology have helped transform our understanding of infectious disease dynamics and yielded new strategies to better manage wildlife diseases. Simultaneously, wildlife disease management (WDM) presents opportunities for large-scale empirical tests of disease ecology theory in diverse natural systems. 2.To assess whether the potential complementarity between WDM and disease ecology theory has been realized, we evaluate the extent to which specific concepts in disease ecology theory have been explicitly applied in peer-reviewed WDM literature. 3.While only half of WDM articles published in the past decade incorporated disease ecology theory, theory has been incorporated with increasing frequency over the past 40 years. Contrary to expectations, articles authored by academics were no more likely to apply disease ecology theory, but articles that explain unsuccessful management often do so in terms of theory. 4.Some theoretical concepts such as density-dependent transmission have been commonly applied, whereas emerging concepts such as pathogen evolutionary responses to management, biodiversity–disease relationships and within-host parasite interactions have not yet been fully integrated as management considerations. 5.Synthesis and applications. Theory-based disease management can meet the needs of both academics and managers by testing disease ecology theory and improving disease interventions. Theoretical concepts that have received limited attention to date in wildlife disease management could provide a basis for improving management and advancing disease ecology in the future.

Journal of Applied Ecology↗
USGS2026

Optimizing camera-trap survey designs for multi-species density estimation using spatial capture–recapture models

Conservation efforts are increasingly required to move beyond single-species perspectives and towards community-level inferences. Obtaining reliable multispecies population size estimates poses practical challenges as analytical tools and design recommendations are primarily focused on single species. Density estimation using spatial capture–recapture methods requires deploying detectors (e.g. camera-traps) with spacing proportional to the space use of the focal species. Given that the design itself is species-specific, sampling can be inefficient for species with larger ranges than the focal species due to restricted spatial coverage and insufficient for species with smaller ranges because fewer recaptures are generated. To address this practical issue, we developed a two-stage optimization approach to generate camera-trap survey designs that are appropriate for estimating density of a suite of individually identifiable species that vary in home range sizes. Our approach applies an algorithm to first optimize placement of a subset of detectors for large and vagile species based on maximizing spatial coverage, followed by a second optimization for the remaining cameras based on maximizing spatial recaptures for smaller and less mobile species. We empirically tested our approach using six individually identifiable carnivore species with varying home range sizes in the Munywana Conservancy, South Africa. Our design included 60 camera locations optimized for leopards ( Panthera pardus ) and 40 cameras optimized for small-bodied, less-mobile carnivores. Our design optimization procedure generated designs characterized by a distribution of inter-trap distances, based on ecological parameters, and resulted in plausible density estimates for all species. The two-stage approach resulted in moderate precision gains for larger ranging species and, importantly, substantial gains for smaller ranging species. Simulations demonstrated improved precision of spatially explicit capture–recapture (SCR) parameter estimates for all species compared to standard grid-based designs, driven not solely by increased sampling but also by the optimized spatial configuration. Synthesis and applications . We developed and tested a new camera-trap survey design method for estimating population densities for multiple co-occurring species with differing spatial ecologies. By streamlining multispecies population monitoring, our approach reduces costs associated with species-specific programmes and broadens opportunities for community ecology and conservation research based on explicit demographic parameters.

Munyawana Conservancy↗
USGS2015

Management applications of discontinuity theory

Human impacts on the environment are multifaceted and can occur across distinct spatiotemporal scales. Ecological responses to environmental change are therefore difficult to predict, and entail large degrees of uncertainty. Such uncertainty requires robust tools for management to sustain ecosystem goods and services and maintain resilient ecosystems. We propose an approach based on discontinuity theory that accounts for patterns and processes at distinct spatial and temporal scales, an inherent property of ecological systems. Discontinuity theory has not been applied in natural resource management and could therefore improve ecosystem management because it explicitly accounts for ecological complexity. Synthesis and applications . We highlight the application of discontinuity approaches for meeting management goals. Specifically, discontinuity approaches have significant potential to measure and thus understand the resilience of ecosystems, to objectively identify critical scales of space and time in ecological systems at which human impact might be most severe, to provide warning indicators of regime change, to help predict and understand biological invasions and extinctions and to focus monitoring efforts. Discontinuity theory can complement current approaches, providing a broader paradigm for ecological management and conservation.

Journal of Applied Ecology↗