Experimental investigation of false positive errors in auditory species occurrence surveys

False positive errors are a significant component of many ecological data sets, which in combination with false negative errors, can lead to severe biases in conclusions about ecological systems. We present results of a field experiment where observers recorded observations for known combinations of electronically broadcast calling anurans under conditions mimicking field surveys to determine species occurrence. Our objectives were to characterize false positive error probabilities for auditory methods based on a large number of observers, to determine if targeted instruction could be used to reduce false positive error rates, and to establish useful predictors of among-observer and among-species differences in error rates. We recruited 31 observers, ranging in abilities from novice to expert, who recorded detections for 12 species during 180 calling trials (66,960 total observations). All observers made multiple false positive errors, and on average 8.1% of recorded detections in the experiment were false positive errors. Additional instruction had only minor effects on error rates. After instruction, false positive error probabilities decreased by 16% for treatment individuals compared to controls with broad confidence interval overlap of 0 (95% CI:--46 to 30%). This coincided with an increase in false negative errors due to the treatment (26%;--3 to 61%). Differences among observers in false positive and in false negative error rates were best predicted by scores from an online test and a self-assessment of observer ability completed prior to the field experiment. In contrast, years of experience conducting call surveys was a weak predictor of error rates. False positive errors were also more common for species that were played more frequently but were not related to the dominant spectral frequency of the call. Our results corroborate other work that demonstrates false positives are a significant component of species occurrence data collected by auditory methods. Instructing observers to only report detections they are completely certain are correct is not sufficient to eliminate errors. As a result, analytical methods that account for false positive errors will be needed, and independent testing of observer ability is a useful predictor for among-observer variation in observation error rates.     

Using multilevel spatial models to understand salamander site occupancy patterns after wildfire

Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of variation in the response that may occur when there are dependence structures such as smaller sampling units that are nested within larger sampling units. We used multilevel Bayesian occupancy modeling to handle dependence structures and to partition sources of variation in occupancy of sites by terrestrial salamanders (family Plethodontidae) within and surrounding an earlier wildfire in western Oregon, USA. Comparison of model fit favored a spatial N-mixture model that accounted for variation in salamander abundance over models that were based on binary detection/non-detection data. Though catch per unit effort was higher in burned areas than unburned, there was strong support that this pattern was due to a higher probability of capture for individuals in burned plots. Within the burn, the odds of capturing an individual given it was present were 2.06 times the odds outside the burn, reflecting reduced complexity of ground cover in the burn. Ther was weak support that true occupancy was lower within the burned area. While the odds of occupancy in the burn were 0.49 times the odds outside the burn among the five species, the magnitude of variation attributed to the burn was small in comparison to variation attributed to other landscape variables and to unexplained, spatially autocorrelated random variation. While ordinary occupancy models may separate the biological pattern of interest from variation in detection probability when all sources of variation are known, the addition of random effects structures for unexplained sources of variation in occupancy and detection probability may often more appropriately represent levels of uncertainty.     

Non-parametric MLE for Poisson species abundance models allowing for heterogeneity between species

The proper management of an ecological population is greatly aided by solid information about its species' abundances. For the general heterogeneous Poisson species abundance setting, we develop the non-parametric mle for the entire probability model, namely for the total number N of species and the generating distribution F for the expected values of the species' abundances. Solid estimation of the entire probability model allows us to develop generator-based measures of ecological diversity and evenness which have inferences over similar regions. Also, our methods produce a solid goodness-of-fit test for our model as well as a likelihood ratio test to examine if there is heterogeneity in the expected values of the species' abundances. These estimates and tests are examined, in detail, in the paper. In particular, we apply our methods to important data from the National Breeding Bird Survey and discuss how our methods can also be easily applied to sweep net sampling data. To further examine our methods, we provide simulations for several illustrative situations.     

General methods for sensitivity analysis of equilibrium dynamics in patch occupancy models

Sensitivity analysis is a useful tool for the study of ecological models that has many potential applications for patch occupancy modeling. Drawing from the rich foundation of existing methods for Markov chain models, I demonstrate new methods for sensitivity analysis of the equilibrium state dynamics of occupancy models. Estimates from three previous studies are used to illustrate the utility of the sensitivity calculations: a joint occupancy model for a prey species, its predators, and habitat used by both; occurrence dynamics from a well-known metapopulation study of three butterfly species; and Golden Eagle occupancy and reproductive dynamics. I show how to deal efficiently with multistate models and how to calculate sensitivities involving derived state variables and lower-level parameters. In addition, I extend methods to incorporate environmental variation by allowing for spatial and temporal variability in transition probabilities. The approach used here is concise and general and can fully account for environmental variability in transition parameters. The methods can be used to improve inferences in occupancy studies by quantifying the effects of underlying parameters, aiding prediction of future system states, and identifying priorities for sampling effort.     

Using interview surveys and multispecies occupancy models to inform vertebrate conservation

Species distribution data are an essential biodiversity variable requiring robust monitoring to inform wildlife conservation. Yet, such data remain inherently sparse because of the logistical challenges of monitoring biodiversity across broad geographic extents. Surveys of people knowledgeable about the occurrence of wildlife provide an opportunity to evaluate species distributions and the ecology of wildlife communities across large spatial scales. We analyzed detection histories of 30 vertebrate species across the Western Ghats biodiversity hotspot in India, obtained from a large-scale interview survey of 2318 people who live and work in the forests of this region. We developed a multispecies occupancy model that simultaneously corrected for false-negative (non-detection) and false-positive (misidentification) errors that interview surveys can be prone to. Using this model, we integrated data across species in composite analyses of the responses of functional species groups (based on disturbance tolerance, diet, and body mass traits) to spatial variation in environmental variables, protection, and anthropogenic pressures. We observed a positive association between forest cover and the occurrence of species with low tolerance of human disturbance. Protected areas were associated with higher occurrence for species across different functional groups compared with unprotected lands. We also observed the occurrence of species with low disturbance tolerance, herbivores, and large-bodied species was negatively associated with developmental pressures, such as human settlements, energy production and mining, and demographic pressures, such as biological resource extraction. For the conservation of threatened vertebrates, our work underscores the importance of maintaining forest cover and reducing deforestation within and outside protected areas, respectively. In addition, mitigating a suite of pervasive human pressures is also crucial for wildlife conservation in one of the world's most densely populated biodiversity hotspots.     

Forest production model for upland black spruce stands—Optimal site occupancy levels for maximizing net production

The objective of this study was to develop a forest production model for determining optimal density management regimes for upland black spruce (Picea mariana (Mill.) B.S.P.) stands based on the maximization of net production. This objective was attained via the development of an allometrically extended stand density management diagram (SDMD), which was used to describe the mass dynamics of biotic and abiotic tree components by initial density regime, site quality and fine root turnover rate. Specifically, periderm, stem, branch, foliage and abiotic crown masses were estimated employing multivariate allometric regression functions based on data derived from 125 destructively sampled trees. Below-ground mass estimates were obtained using generalized allometric relationships derived from the literature. Abiotic masses included three basic components: (1) allometrically estimated retained woody debris consisting of abiotic crown structures that remained attached to the main stem; (2) fine woody debris arising from needle loss, root turnover, and abscission of modular components; (3) coarse woody debris arising from trees which incurred mortality through self-thinning. The algorithmic version of the model (1) simultaneously calculates periodic annual net production estimates (Mg/ha/year) by 10-year intervals over 100-year rotation lengths for eight initial density conditions, (2) given (1), determines the occupancy level for which net production is maximized for each stage of development (decade interval), and (3) given (2), determines the optimal size–density trajectory within the context of a SDMD. Additionally, results derived from multiple model simulations employing a range of initial densities (1500, 1650,…, 16,350 stems/ha), site indices (9, 10,…, 15 m) and fine root turnover rates (0.2, 0.3,…,0.8 proportion/year), indicated that black spruce productivity was maximized when site occupancies were maintained slightly below the zone of imminent competition mortality. Instructions for acquiring an executable version of the model through the Internet are also included.     

Correct and false olfactory orientation of homing pigeons as depending on geographical relationships between release site and home site

Summary Pigeons from two German home sites were released at a site near Mantua in northern Italy. The home sites, Andechs and Würzburg, are 303 and 508 km north of the release site, respectively. Not only the initial bearings but still more the distributions of recoveries after a longer flight distance (median 65 km) were very different in pigeons from these two lofts. While the majority of the Wurzburg birds were found north of the release site, almost all birds from Andechs were found south of it (Fig. 1). Pigeons from both lofts, if made anosmic by sectioning the olfactory nerves, showed no average tendency towards change of latitude. These findings strongly suggest that both correct and false positional information were deduced by the birds from olfactory inputs. A coherent (though very hypothetical) interpretation of these and earlier results is based on regularly varying proportions of chemical tract compounds in the atmospheric boundary layer over the Alps and adjacent regions (Fig. 4).     

Waterborne chemical compounds in tropical macroalgae: positive and negative cues for larval settlement

Settlement sites of marine invertebrate larvae are frequently influenced by positive or negative cues, many of which are chemical in nature. Following from the observation that many shallow-water, Hawai'ian marine macroalgae are free of fouling by sessile invertebrates, we predicted that the algae are chemically protected and dependent on either surface-bound or continuously released soluble compounds to deter settling invertebrate larvae. To address the importance of waterborne algal compounds, we experimentally determined whether larvae of two of Hawai'i's dominant hard-surface fouling organisms, the polychaete tube worm Hydroides elegans and the bryozoan Bugula neritina, would settle in the presence of waters conditioned by 12 species of common Hawai'ian macroalgae (representing the Phaeophyta, Chlorophyta, Rhodophyta and Cyanophyta). The results included a full spectrum of biological responses by each larval species to waterborne algal compounds. Larval responses to conditioned water were consistent for each algal species, but the outcomes were not predictable based on the taxonomic relationships of the algae. For example, among the species of Phaeophyta examined, different conditioned waters were: (1) toxic, (2) inhibited settlement, (3) simulated settlement, or (4) had no effect, compared to larvae in control dishes containing filtered seawater. Additionally, larval responses to aged (24 h) conditioned waters could not be predicted from the results of assays run with conditioned waters utilized immediately after preparation. Finally, settlement by larvae of one species did not predict outcomes of tests for the other species. Four of 12 shallow-reef Hawai'ian macroalgae tested released compounds into surrounding waters that immediately killed or inhibited settlement by both H. elegans and B. neritina (toxic: Dictyota sandvicensis; inhibitory: Halimeda discoidea, Sphacelaria tribuloides, Ulva reticulata); the remaining 8 algal species prevented settlement by one of these fouling organisms but for the other had no effect or, in some cases, even stimulated settlement     

Landscape history, fragmentation, and patch occupancy: models for a forest bird with limited dispersal.

We developed and tested patch occupancy models for an endemic understory bird with limited dispersal ability, the Chucao Tapaculo (Scelorchilus rubecula), in two South American temperate rain forest landscapes that differed in levels and duration of forest loss. We assessed cover changes since 1961 in each landscape and surveyed patches for Chucao Tapaculo occupancy. We then developed incidence-based predictive models independently for each landscape and tested each model reciprocally in the alternative study area. We thereby assessed the domain of model applicability and identified those predictor variables with general effects and those that varied between the two landscapes. The two models were consistent regarding variable selection, and predictive accuracy of each model was high in the landscape where training data were collected. However, the models differed substantially in the magnitudes of effects related to patch size, with larger unoccupied patches observed in the landscape with the more advanced stage of fragmentation. Due to this discrepancy, each model performed poorly when applied to the alternative landscape, potentially reflecting the contrasting stages of habitat loss. Although it was impossible to dissociate effects of level and duration of forest loss, we viewed the landscapes as representing two extremes along a continuum of fragmentation, providing insights into potential trajectories for portions of the biome where deforestation is occurring. Further, our data suggest that static equilibrium models developed from distribution patterns in recently fragmented landscapes may overestimate persistence when used as a forecasting tool, or when extrapolated to alternative landscapes where fragmentation is more advanced. Thus, we suggest that landscapes used as standards for model building should be selected with caution. We recommend that distribution patterns be obtained from landscapes where fragmentation is advanced, preferably with histories of fragmentation long enough that time-delayed extinctions already would have occurred.     

Shifts in positive and negative plant interactions along a grazing intensity gradient

Isolating the single effects and net balance of negative and positive species effects in complex interaction networks is a necessary step for understanding community dynamics. Facilitation and competition have both been found to operate in harsh environments, but their relative strength may be predicted to change along gradients of herbivory. Moreover, facilitation effects through habitat amelioration and protection from herbivory may act together determining the outcome of neighborhood plant-plant interactions. We tested the hypothesis that grazing pressure alters the balance of positive and negative interactions between palatable and unpalatable species by increasing the strength of positive indirect effects mediated by associational resistance to herbivory. We conducted a two-year factorial experiment in which distance (i.e., spatial association) from the nearest unpalatable neighbor (Stipa speciosa) and root competition were manipulated for two palatable grasses (Poa ligularis and Bromus pictus), at three levels of sheep grazing (none, moderate, and high) in a Patagonian steppe community. We found that grazing shifted the effect of Stipa on both palatable grasses, from negative (competition) in the absence of grazing to positive (facilitation) under increasing herbivore pressure. In ungrazed sites, belowground competition was the dominant interaction, as shown by a significant reduction in performance of palatable grasses transplanted near to Stipa tussocks. In grazed sites, biomass of palatable plants was greater near than far from Stipa regardless of competition treatment. Proximity to Stipa reduced the amount of herbivory suffered by palatable grasses, an indirect effect that was stronger under moderate than under intense grazing. Our results demonstrate that facilitation, resulting mainly from protection against herbivory, is the overriding effect produced by unpalatable neighbors on palatable grasses in this rangeland community. This finding challenges the common view that abiotic stress amelioration should be the predominant type of facilitation in arid environments and highlights the role of herbivory in modulating complex neighborhood plant interactions in grazing systems.     

Use of stochastic patch occupancy models in the California red-legged frog for Bayesian inference regarding past events and future persistence

Assessing causes of population decline is critically important to management of threatened species. Stochastic patch occupancy models (SPOMs) are popular tools for examining spatial and temporal dynamics of populations when presence–absence data in multiple habitat patches are available. We developed a Bayesian Markov chain method that extends existing SPOMs by focusing on past environmental changes that may have altered occupancy patterns prior to the beginning of data collection. Using occupancy data from 3 creeks, we applied the method to assess 2 hypothesized causes of population decline—in situ die-off and residual impact of past source population loss—in the California red-legged frog. Despite having no data for the 20–30 years between the hypothetical event leading to population decline and the first data collected, we were able to discriminate among hypotheses, finding evidence that in situ die-off increased in 2 of the creeks. Although the creeks had comparable numbers of occupied segments, owing to different extinction–colonization dynamics, our model predicted an 8-fold difference in persistence probabilities of their populations to 2030. Adding a source population led to a greater predicted persistence probability than did decreasing the in situ die-off, emphasizing that reversing the deleterious impacts of a disturbance may not be the most efficient management strategy. We expect our method will be useful for studying dynamics and evaluating management strategies of many species.     

Grassland establishment under varying resource availability: a test of positive and negative feedback

The traditional logic of carbon (C) and nitrogen (N) interactions in ecosystems predicts further increases or decreases in productivity (positive feedback) in response to high and low fertility in the soil, respectively; but the potential for development of feedback in ecosystems recovering from disturbance is less well understood. Furthermore, this logic has been challenged in grassland ecosystems where frequent fires or grazing may reduce the contribution of aboveground litter inputs to soil organic matter pools and nutrient supply for plant growth, relative to forest ecosystems. Further, if increases in plant productivity increase soil C content more than soil N content, negative feedback may result from increased microbial demand for N making less available for plant growth. We used a field experiment to test for feedback in an establishing grassland by comparing aboveground net primary productivity (ANPP) and belowground pools and fluxes of C and N in soil with enriched, ambient, and reduced N availability. For eight years annual N enrichment increased ANPP, root N, and root tissue quality, but root C:N ratios remained well above the threshold for net mineralization of N. There was no evidence that N enrichment increased root biomass, soil C or N accrual rates, or storage of C in total, microbial, or mineralizable pools within this time frame. However, the net nitrogen mineralization potential (NMP) rate was greater following eight years of N enrichment, and we attributed this to N saturation of the microbial biomass. Grassland developing under experimentally imposed N limitation through C addition to the soil exhibited ANPP, root biomass and quality, and net NMP rate similar to the ambient soil. Similarity in productivity and roots in the reduced and ambient N treatments was attributed to the potentially high nitrogen-use efficiency (NUE) of the dominant C4 grasses, and increasing cover of legumes over time in the C-amended soil. Thus, in a developing ecosystem, positive feedback between soil N supply and plant productivity may promote enhanced long-term N availability and override progressive N limitation as C accrues in plant and soil pools. However, experimentally imposed reduction in N availability did not feed back to reduce ANPP, possibly due to shifts in NUE and functional group composition.     

Desert pastoralists’ negative and positive effects on rare wildlife in the Gobi

In arid regions of the developing world, pastoralists and livestock commonly inhabit protected areas, resulting in human–wildlife conflict. Conflict is inextricably linked to the ecological processes shaping relationships between pastoralists and native herbivores and carnivores. To elucidate relationships underpinning human–wildlife conflict, we synthesized 15 years of ecological and ethnographic data from Ikh Nart Nature Reserve in Mongolia's Gobi steppe. The density of argali (Ovis ammon), the world's largest wild sheep, at Ikh Nart was among the highest in Mongolia, yet livestock were >90% of ungulate biomass and dogs >90% of large‐carnivore biomass. For argali, pastoral activities decreased food availability, increased mortality from dog predation, and potentially increased disease risk. Isotope analyses indicated that livestock accounted for >50% of the diet of the majority of gray wolves (Canis lupus) and up to 90% of diet in 25% of sampled wolves (n = 8). Livestock composed at least 96% of ungulate prey in the single wolf pack for which we collected species‐specific prey data. Interviews with pastoralists indicated that wolves annually killed 1–4% of Ikh Nart's livestock, and pastoralists killed wolves in retribution. Pastoralists reduced wolf survival by killing them, but their livestock were an abundant food source for wolves. Consequently, wolf density appeared to be largely decoupled from argali density, and pastoralists had indirect effects on argali that could be negative if pastoralists increased wolf density (apparent competition) or positive if pastoralists decreased wolf predation (apparent facilitation). Ikh Nart's argali population was stable despite these threats, but livestock are increasingly dominant numerically and functionally relative to argali. To support both native wildlife and pastoral livelihoods, we suggest training dogs to not kill argali, community insurance against livestock losses to wolves, reintroducing key native prey species to hotspots of human–wolf conflict, and developing incentives for pastoralists to reduce livestock density.     

Untangling positive and negative biotic interactions: views from above and below ground in a forest ecosystem

In ecological communities, the outcome of plant-plant interactions represents the net effect of positive and negative interactions occurring above and below ground. Untangling these complex relationships can provide a better understanding of mechanisms that underlie plant-plant interactions and enhance our ability to predict population, community, and ecosystem effects of biotic interactions. In forested ecosystems, tree seedlings interact with established vegetation, but the mechanisms and outcomes of these interactions are not well understood. To explore such mechanisms, we manipulated above- and belowground interactions among tree seedlings, shrubs, and trees and monitored seedling survival and growth of six species (Pinus banksiana, Betula papyrifera, P. resinosa, Quercus rubra, P. strobus, and Acer rubrum) in mature pine-dominated forest in northern Minnesota, USA. The forest had a moderately open canopy and sandy soils. Understory manipulations were implemented in the forest interior and in large gaps and included removal of shrubs (no interactions), tieback of shrubs (belowground), removal of shrubs with addition of shade (aboveground), and unmanipulated shrubs (both below- and aboveground). We found that shrubs either suppressed or facilitated seedling survival and growth depending on the seedling species, source of interaction (e.g., above- or belowground), and ecological context (e.g., gap or forest interior). In general, shrubs strongly influenced survival and growth in gaps, with more modest effects in the forest interior. In gaps, the presence of shrub roots markedly decreased seedling growth and survival, supporting the idea that belowground competition may be more important in dry, nutrient-poor sites. Shrub shade effects were neutral for three species and facilitative for the other three. Facilitation was more likely for shade-tolerant species. In the forest interior, shrub shade negatively affected seedling survival for the most shade-intolerant species. For several species the net effect of shrubs masked the existence of both positive and negative interactions above and below ground. Our results highlight the complexity of plant-plant interactions, demonstrate that outcomes of these interactions vary with the nature of resource limitation and the ecophysiology of the species involved, and suggest that ecological theory that rests on particular notions of plant-plant interactions (e.g., competition) should consider simultaneous positive and negative interactions occurring above and below ground.     

Critical analysis of turbulence models for simulating positive surge waves in open channels in a RANS-VOF setup

Environmental Fluid Mechanics - The study presents a systematic assessment of 2D RANS-VOF simulation of positive surge wave propagation in open channels using three widely used turbulence models:...     

Adjusting age and stage distributions for misclassification errors

Ecologists often use samples from the age or stage structure of a population to make inferences about population-level processes and to parameterize matrix models. Typically, researchers make a simplifying assumption that age and stage classes are determined without error, when in fact some level of misclassification often can be expected. If unaccounted for, misclassification will lead to overly optimistic levels of precision and can cause biased estimates of age or stage structure. Although several studies have used information from known-age individuals to quantify errors in age or stage distribution, the problem of estimating the age or stage structure in face of such errors has received comparably little attention. In this paper, we describe a general statistical framework for estimating the true stage distribution of a sample when misclassification rates can be estimated. The estimation process requires auxiliary information on misclassification rates, such as data from individuals of known age. We analyze age-structured harvest records from black bears in Pennsylvania to illustrate how incorporating misclassification errors leads to changes in point estimates and provides a measure of precision.     

Colonization and extinction in dynamic habitats: an occupancy approach for a Great Plains stream fish assemblage

Despite the importance of habitat in determining species distribution and persistence, habitat dynamics are rarely modeled in studies of metapopulations. We used an integrated habitat-occupancy model to simultaneously quantify habitat change, site fidelity, and local colonization and extinction rates for larvae of a suite of Great Plains stream fishes in the Arikaree River, eastern Colorado, USA, across three years. Sites were located along a gradient of flow intermittency and groundwater connectivity. Hydrology varied across years: the first and third being relatively wet and the second dry. Despite hydrologic variation, our results indicated that site suitability was random from one year to the next. Occupancy probabilities were also independent of previous habitat and occupancy state for most species, indicating little site fidelity. Climate and groundwater connectivity were important drivers of local extinction and colonization, but the importance of groundwater differed between periods. Across species, site extinction probabilities were highest during the transition from wet to dry conditions (range: 0.52-0.98), and the effect of groundwater was apparent with higher extinction probabilities for sites not fed by groundwater. Colonization probabilities during this period were relatively low for both previously dry sites (range: 0.02-0.38) and previously wet sites (range: 0.02-0.43). In contrast, no sites dried or remained dry during the transition from dry to wet conditions, yielding lower but still substantial extinction probabilities (range: 0.16-0.63) and higher colonization probabilities (range: 0.06-0.86), with little difference among sites with and without groundwater. This approach of jointly modeling both habitat change and species occupancy will likely be useful to incorporate effects of dynamic habitat on metapopulation processes and to better inform appropriate conservation actions.     

Estimation and testing for covariance-spectral spatial-temporal models

Environmental and Ecological Statistics - In this paper we explore a covariance-spectral modelling strategy for spatial-temporal processes which involves a spectral approach for time but a...     

Estimation and inference for upper hinge regression models

Environmental and Ecological Statistics - We introduce a new type of threshold regression models called upper hinge models. Under this type of threshold models, there only exists an association...