On the expected width function for topologically random channel networks
No abstract available.
Journal of Applied Probability↗
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Occupancy estimation and the closure assumption
1. Recent advances in occupancy estimation that adjust for imperfect detection have provided substantial improvements over traditional approaches and are receiving considerable use in applied ecology. To estimate and adjust for detectability, occupancy modelling requires multiple surveys at a site and requires the assumption of 'closure' between surveys, i.e. no changes in occupancy between surveys. Violations of this assumption could bias parameter estimates; however, little work has assessed model sensitivity to violations of this assumption or how commonly such violations occur in nature. 2. We apply a modelling procedure that can test for closure to two avian point-count data sets in Montana and New Hampshire, USA, that exemplify time-scales at which closure is often assumed. These data sets illustrate different sampling designs that allow testing for closure but are currently rarely employed in field investigations. Using a simulation study, we then evaluate the sensitivity of parameter estimates to changes in site occupancy and evaluate a power analysis developed for sampling designs that is aimed at limiting the likelihood of closure. 3. Application of our approach to point-count data indicates that habitats may frequently be open to changes in site occupancy at time-scales typical of many occupancy investigations, with 71% and 100% of species investigated in Montana and New Hampshire respectively, showing violation of closure across time periods of 3 weeks and 8 days respectively. 4. Simulations suggest that models assuming closure are sensitive to changes in occupancy. Power analyses further suggest that the modelling procedure we apply can effectively test for closure. 5. Synthesis and applications. Our demonstration that sites may be open to changes in site occupancy over time-scales typical of many occupancy investigations, combined with the sensitivity of models to violations of the closure assumption, highlights the importance of properly addressing the closure assumption in both sampling designs and analysis. Furthermore, inappropriately applying closed models could have negative consequences when monitoring rare or declining species for conservation and management decisions, because violations of closure typically lead to overestimates of the probability of occurrence.
Montana;New Hampshire↗
Survival estimation and the effects of dependency among animals
Survival models assume that fates of individuals are independent, yet the robustness of this assumption has been poorly quantified. We examine how empirically derived estimates of the variance of survival rates are affected by dependency in survival probability among individuals. We used Monte Carlo simulations to generate known amounts of dependency among pairs of individuals and analyzed these data with Kaplan-Meier and Cormack-Jolly-Seber models. Dependency significantly increased these empirical variances as compared to theoretically derived estimates of variance from the same populations. Using resighting data from 168 pairs of black brant, we used a resampling procedure and program RELEASE to estimate empirical and mean theoretical variances. We estimated that the relationship between paired individuals caused the empirical variance of the survival rate to be 155% larger than the empirical variance for unpaired individuals. Monte Carlo simulations and use of this resampling strategy can provide investigators with information on how robust their data are to this common assumption of independent survival probabilities.
Journal of Applied Statistics↗
Impacts of forest fragmentation on species richness: A hierarchical approach to community modelling
1. Species richness is often used as a tool for prioritizing conservation action. One method for predicting richness and other summaries of community structure is to develop species-specific models of occurrence probability based on habitat or landscape characteristics. However, this approach can be challenging for rare or elusive species for which survey data are often sparse. 2. Recent developments have allowed for improved inference about community structure based on species-specific models of occurrence probability, integrated within a hierarchical modelling framework. This framework offers advantages to inference about species richness over typical approaches by accounting for both species-level effects and the aggregated effects of landscape composition on a community as a whole, thus leading to increased precision in estimates of species richness by improving occupancy estimates for all species, including those that were observed infrequently. 3. We developed a hierarchical model to assess the community response of breeding birds in the Hudson River Valley, New York, to habitat fragmentation and analysed the model using a Bayesian approach. 4. The model was designed to estimate species-specific occurrence and the effects of fragment area and edge (as measured through the perimeter and the perimeter/area ratio, P/A), while accounting for imperfect detection of species. 5. We used the fitted model to make predictions of species richness within forest fragments of variable morphology. The model revealed that species richness of the observed bird community was maximized in small forest fragments with a high P/A. However, the number of forest interior species, a subset of the community with high conservation value, was maximized in large fragments with low P/A. 6. Synthesis and applications. Our results demonstrate the importance of understanding the responses of both individual, and groups of species, to environmental heterogeneity while illustrating the utility of hierarchical models for inference about species richness for conservation. This framework can be used to investigate the impacts of land-use change and fragmentation on species or assemblage richness, and to further understand trade-offs in species-specific occupancy probabilities associated with landscape variability.
New York↗
N-mixture models for estimating population size from spatially replicated counts
Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, I describe a class of models (n-mixture models) which allow for estimation of population size from such data. The key idea is to view site-specific population sizes, n, as independent random variables distributed according to some mixing distribution (e.g., Poisson). Prior parameters are estimated from the marginal likelihood of the data, having integrated over the prior distribution for n. Carroll and Lombard (1985, Journal of American Statistical Association 80, 423-426) proposed a class of estimators based on mixing over a prior distribution for detection probability. Their estimator can be applied in limited settings, but is sensitive to prior parameter values that are fixed a priori. Spatial replication provides additional information regarding the parameters of the prior distribution on n that is exploited by the n-mixture models and which leads to reasonable estimates of abundance from sparse data. A simulation study demonstrates superior operating characteristics (bias, confidence interval coverage) of the n-mixture estimator compared to the Caroll and Lombard estimator. Both estimators are applied to point count data on six species of birds illustrating the sensitivity to choice of prior on p and substantially different estimates of abundance as a consequence.
Biometrics↗
Do breeding phase and detection distance influence the effective area surveyed for northern goshawks?
Broadcast surveys using conspecific calls are currently the most effective method for detecting northern goshawks (Accipiter gentilis) during the breeding season. These surveys typically use alarm calls during the nestling phase and juvenile food-begging calls during the fledgling-dependency phase. Because goshawks are most vocal during the courtship phase, we hypothesized that this phase would be an effective time to detect goshawks. Our objective was to improve current survey methodology by evaluating the probability of detecting goshawks at active nests in northern Minnesota in 3 breeding phases and at 4 broadcast distances and to determine the effective area surveyed per broadcast station. Unlike previous studies, we broadcast calls at only 1 distance per trial. This approach better quantifies (1) the relationship between distance and probability of detection, and (2) the effective area surveyed (EAS) per broadcast station. We conducted 99 broadcast trials at 14 active breeding areas. When pooled over all distances, detection rates were highest during the courtship (70%) and fledgling-dependency phases (68%). Detection rates were lowest during the nestling phase (28%), when there appeared to be higher variation in likelihood of detecting individuals. EAS per broadcast station was 39.8 ha during courtship and 24.8 ha during fledgling-dependency. Consequently, in northern Minnesota, broadcast stations may be spaced 712m and 562 m apart when conducting systematic surveys during courtship and fledgling-dependency, respectively. We could not calculate EAS for the nestling phase because probability of detection was not a simple function of distance from nest. Calculation of EAS could be applied to other areas where the probability of detection is a known function of distance.
Journal of Wildlife Management↗
Sources, sinks, and spatial ecology of cotton mice in longleaf pine stands undergoing restoration
The Fire and Fire Surrogate studya replicated, manipulative experimentsought the most economically and ecologically efficient way to restore the nation's fire-maintained ecosystems. As part of this study, we conducted a 3-year markrecapture study, comprising 105,000 trap-nights, to assess demographic responses of cotton mice (Peromyscus gossypinus) to Fire and Fire Surrogate treatments at the Gulf Coastal Plain site, where longleaf pine was the ecosystem to be restored. We compared competing models to evaluate restoration effects on variation in apparent survival and recruitment over time, space, and treatment, and incorporated measures of available source habitat for cotton mice with reverse-time modeling to infer immigration from outside the study area. The top-ranked survival model contained only variation over time, but the closely ranked 2nd and 3rd models included variation over space and treatment, respectively. The top 4 recruitment models all included effects for availability of source habitat and treatments. Burning appeared to degrade habitat quality for cotton mice, showing demographic characteristics of a sink, but treatments combining fire with thinning of trees or application of herbicide to the understory appeared to improve habitat quality, possibly creating sources. Bottomland hardwoods outside the study also acted as sources by providing immigrants to experimental units. Models suggested that population dynamics operated over multiple spatial scales. Treatments applied to 15-ha stands probably only caused local variation in vital rates within the larger population. ?? 2009 American Society of Mammalogists.
Journal of Mammalogy↗
A field test for differences in condition among trapped and shot mallards
We tested predictions from the condition bias hypothesis (Weatherland and Greenwood 1981) regarding the effects of sampling methods of body weights of mallards ( Anas platyrhynchos ) at White River National Wildlife Refuge (WRNWR), Arkansas, during 24 November-8 December 1985. Body weights of 84 mallards caught with unbaited rocket nets in a natural wetland were used as experimental controls and compared to the body weights of 70 mallards captured with baited rocket nets, 86 mallards captured with baited swim-in traps, and 130 mallards killed by hunters. We found no differences (P > 0.27) in body weight among sampling methods, but body condition (wt/wing length) of the birds killed by hunters was less (P < 0.02) than that of the controls. Power of the test statistics to reject the null hypothesis of equal body weights among sampling methods was > 0.75 for differences > 50 g. The condition bias hypothesis probably applies to ducks killed by hunters but not to trapping operations when substantial (> 20 at 1 time) numbers of birds are captured.
Arkansas↗
The aqueous photolysis of α-pinene in solution with humic acid
Terpenes are produced abundantly by environmental processes but are found in very low concentrations in natural waters. Aqueous photolysis of solutions containing α-pinene, a representative terpene, in the presence of humic acid resulted in degradation of the pinene. Comparison of this reaction to photolysis of α-pinene in the presence of methylene blue leads to the conclusion that the reactive pathway for the abiotic degradation of α-pinene is due to reaction with singlet oxygen produced by irradiation of the humic material. The initial product of single oxygen and α-pinene is a hydroperoxide. Since humic materials are prevalent in most natural waters, this mechanism of photodecomposition for α-pinene probably also applies to other terpenes in surface waters and may be reasonably considered to contribute to their low environmental concentration.
Journal of Contaminant Hydrology↗
The changes in species composition mediate direct effects of climate change on future fire regimes of boreal forests in northeastern China
Direct effects of climate change (i.e. temperature rise, changes in seasonal precipitation, wind patterns and atmospheric stability) affect fire regimes of boreal forests by altering fire behaviour, fire seasons and fuel moisture. Climate change also alters species composition and fuel characteristics, which subsequently alter fire regimes. However, indirect effects of climate change are often simplified or neglected in the direct climate–fire relationship models and dynamic global vegetation models. This may result in high uncertainties associated with existing projections of fire regimes for climate change scenarios. Moreover, few studies have examined fire regime predictions beyond the 21st century, and consequently, how the fire regimes of boreal forests would respond to climate change at the long term (>100 years) are not clear. We develop a coupled modelling framework integrating direct and indirect effects of climate change to predict fire occurrence probability and burned area for boreal forests in northeastern China. We applied repeated measures ANOVA to quantify direct and indirect effects of climate change on fire regimes in the short (0–50 years), medium (60–100 years) and long term (150–200 years). Results showed that for the 21st century, direct effects of climate change are likely to exert a stronger influence on fire regimes than indirect effects. However, increases in fire occurrence probability and burned area will accelerate the transition of boreal forests to temperate forests in the period 2100–2200, and thereby reduce fire occurrence probability and burned area. This suggests that vegetation change will mediate direct effects of climate change on fire regimes of boreal forests at the long term. Synthesis and applications . Vegetation change will mediate direct effects of climate change on fire regimes of boreal forests at the long term. This finding suggested that policymakers may consider adaptive management by planting deciduous species to reduce fire occurrence probability and resistant management by reducing competition to promote boreal species under changing climate conditions.
Journal of Applied Ecology↗
Flow development and entrainment in turbulent particle-laden jets
Explosive eruptions expel volcanic gases and particles at high pressures and velocities. Within this multiphase fluid, small ash particles affect the flow dynamics, impacting mixing, entrainment, turbulence, and aggregation. To examine the role of turbulent particle behavior, we conducted an analogue experiment using a particle-laden jet. We used compressed air as the carrier fluid, considering turbulent conditions at Reynolds numbers from approximately 5,000 to 20,000. Two different particles were examined: 14-μm diameter solid nickel spheres and 13-μm diameter hollow glass spheres. These resulted in Stokes numbers between 1 and 35 based on the convective scale. The particle mass percentage in the mixture is varied from 0.3% to more than 20%. Based on a 1-D volcanic plume model, these Stokes numbers and mass loadings corresponded to millimeter-scale particle diameters at heights of 4–8 km above the vent during large, sustained eruptions. Through particle image velocimetry, we measured the mean flow behavior and the turbulence statistics in the near-exit region, primarily focusing on the dispersed phase. We show that the flow behavior is dominated by the particle inertia, with high Stokes numbers reducing the entrainment by more than 40%. When applied to volcanic plumes, these results suggest that high-density particles can greatly increase the probability of column collapse.
Journal of Geophysical Research: Atmospheres↗
Multi-scale occupancy estimation and modelling using multiple detection methods
Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method. We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site. We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber . For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species. Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock's robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.
Journal of Applied Ecology↗
Modeling the effect of toe clipping on treefrog survival: Beyond the return rate
Some studies have described a negative effect of toe clipping on return rates of marked anurans, but the return rate is limited in that it does not account for heterogeneity of capture probabilities. We used open population mark-recapture models to estimate both apparent survival ( ϕ ) and the recapture probability ( p ) of two treefrog species individually marked by clipping 2–4 toes. We used information-theoretic model selection to examine the effect of toe clipping on survival while accounting for variation in capture probability. The model selection results indicate strong support for an effect of toe clipping on survival of Green Treefrogs ( Hyla cinerea ) and only limited support for an effect of toe clipping on capture probability. We estimate there was a mean absolute decrease in survival of 5.02% and 11.16% for Green Treefrogs with three and four toes removed, respectively, compared to individuals with just two toes removed. Results for Squirrel Treefrogs ( Hyla squirella ) indicate little support for an effect of toe clipping on survival but may indicate some support for a negative effect on capture probability. We believe that the return rate alone should not be used to examine survival of marked animals because constant capture probability must be assumed, and our examples demonstrate how capture probability may vary over time and among groups. Mark-recapture models provide a method for estimating the effect of toe clipping on anuran survival in situations where unique marks are applied.
Journal of Herpetology↗
Applying a Bayesian weighted surveillance approach to detect chronic wasting disease in white‐tailed deer
Surveillance is critical for early detection of emerging and re‐emerging infectious diseases. Weighted surveillance leverages heterogeneity in infection risk to increase sampling efficiency. Here, we apply a Bayesian approach to estimate weights for 16 surveillance classes of white‐tailed deer in Wisconsin, USA, relative to hunter‐harvested yearling males. We used these weights to conduct a surveillance programme for detecting chronic wasting disease (CWD) in white‐tailed deer at Shenandoah National Park (SHEN) in Virginia, USA. Generally, for surveillance, risk of infection increased with age and was greater in males. Clinical suspect deer had the highest risk, with weight estimates of 33.33 and 9.09 for community‐reported and hunter‐reported suspect deer, respectively. Fawns had the lowest risk with an estimated weight of 0.001. We used surveillance weights for Wisconsin deer to determine sampling effort required to detect a CWD‐positive case in SHEN if prevalence in yearling males ≥0.025. The sampling required to detect CWD was 37–91 adult deer, depending on the adult male:female ratio in the surveillance stream. We collected rectal biopsies from 49 female and 21 male adult deer, and 10 additional samples from vehicle‐killed deer. CWD was not detected and we concluded with 95% probability that prevalence in the reference population (yearling males) was between 0.0% and 3.6%. Synthesis and applications . Our approach allows managers to estimate relative surveillance weights for different host classes and quantify limits of disease detection in real time when only a sample of animals from a population can be tested, resulting in considerable cost savings for agencies performing wildlife disease detection surveillance. Additionally, it provides a rigorous means of estimating prevalence limits when a disease/pathogen is not detected in a sample set. It is therefore applicable to other wildlife, domestic animal and human disease systems, which can be characterized by surveillance classes with heterogeneous probability of infection. This methodology is also extendable to other disciplines such as invasive species, environmental toxicology, and generally, any ecological question seeking to efficiently use scarce financial and human resources to maximize the detection probability of a rare event.
Journal of Applied Ecology↗
Phosphorous digestibility and activity of intestinal phytase in hybrid tilapia, Oreochromis niloticus X O. aureus
Experiments were conducted to determine the degree to which phytate-bound phosphorus from plant protein sources could be used by hybrid tilapia (Oreochromis niloticus X O. aureus). Utilizing an inert marker technique with chromic oxide, hybrid tilapia in our study were effective at utilizing both inorganic and phytate phosphorus as evidenced by average apparent digestibility values of 93.2% and 90.0% for total and phytate phosphorus, respectively. Analysis of the intestinal brush border membrane of the tilapia revealed enzyme activity that was capable of hydrolyzing phytic acid. The presence of phytic acid hydrolyzing enzyme activity in the intestinal brush border provides a probable mechanism by which these hybrid tilapia are able to utilize phytate phosphorus effectively. ?? 2003 by The Haworth Press, Inc. All rights reserved.
Journal of Applied Aquaculture↗
Mark-resighting analysis of a California gull population
California gulls ( Larus californicus ) of known age and sex were censused on their breeding colony in 1979, 1980 and 1984 through 1993. Ages of 235 males and 196 females ranged from 4 to 27 years. Age classes used in the analysis were limited to 17, 4 through 19, and 20 or more as a final age category because data on gulls over 20 were sparse. Survival declined with age in a way that was parsimoniously modelled with a quadratic function. Other factors, sex and time, did not explain any variation in survival. Resighting depended on age, sex and time. Younger adults skipped breeding more frequently than did older adults, and females skipped breeding more frequently than did males. There was also good evidence for time dependence in resighting probability, but its inclusion in the model occurred at the expense of interpretability and precision. In a data set such as this, resighting probability may assume more importance than a mere 'nuisance parameter'. In this study, resighting history measured attendance at the breeding ground. In turn, attendance rates may be a manifestation of reproductive strategy, which can also have consequences for survival. In this situation, there may be heterogeneity in both survival and resighting probability that is unexplained by the model. While such complexity may well be a nuisance to deal with, it can also point to important biological questions.
Wyoming↗
Analysis of population change and movement using robust design removal data
In capture-mark-reencounter studies, Pollock’s robust design combines methods for open populations with methods for closed populations. Open population features of the robust design allow for estimation of rates of death or permanent emigration, and closed population features enhance estimation of population sizes. We describe a similar design, but for use with removal data. Data collection occurs on secondary sampling occasions clustered within primary sampling periods. Primary sampling periods are intervals of brief enough duration that it can be safely assumed that the population is unchanged by births, deaths, immigration or emigration during them; all population change and movement occurs between primary sampling periods. Our model provides a basis for inference about population size, changes in population size, and movement rates among sample locations between primary sampling periods. Movement rates are modeled as functions of distance and time. Capture probabilities are modeled as a function of effort. We apply the model to data obtained in attempting to eradicate an introduced population of veiled chameleons ( Chamaeleo calyptratus ) on the island of Maui in Hawaii.
Journal of Agricultural, Biological, and Environme↗
Concentrations, distribution, and sources of selenium from irrigated lands in western United States
Concentrations, distribution, and sources of selenium from irrigated lands were studied between 1986 and 1990 at 20 reconnaissance project areas in 17 western states under the Department of Interior's National Irrigation Water Quality Program. Samples of water, bottom sediment, whole‐body fish, and bird livers for analysis of selenium concentrations were collected before, during, and after irrigation season from streams, canals, lakes, and ground water in each project area. Selenium concentrations in water ranged from less than the detection limit of 1 μg/L in 42% of the 586 samples collected to 4,800 μg/L from a well in the Pine River Area, in southern Colorado. Selenium concentrations in 223 samples of bottom sediment ranged from less than the detection limit of 0.1 μg/g to 85 μg/g in a sample from the Middle Green River Basin, in Utah. Selenium concentrations in whole‐body fish (all species) ranged from 0.1 μg to 50 μg per gram dry weight, with the maximum concentration observed in a carp from the Gunnison River Basin, in western Colorado. Selenium concentrations in bird livers (all species) ranged from less than 0.32 μg to 170 μg per gram dry weight with the maximum concentration observed in the liver of an avocet from the Kendrick Reclamation Project, in Wyoming. Cretaceous‐age marine shales probably are the original sources for selenium in 16 of the 20 areas studied. In several areas, evaporative concentration of applied irrigation water and drainage of this water to wetlands, canals, streams, and lakes appears to be responsible for elevated concentrations of selenium.
Colorado, Utah, Wyoming↗